[ARVADOS] created: 4a466cd2caf121678a1d46d049c5b1e5477b6d50
Git user
git at public.curoverse.com
Sun Aug 21 22:10:37 EDT 2016
at 4a466cd2caf121678a1d46d049c5b1e5477b6d50 (commit)
commit 4a466cd2caf121678a1d46d049c5b1e5477b6d50
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Sun Aug 21 22:09:38 2016 -0400
8232: Remove outdated/misleading Docker install
diff --git a/build/run-build-docker-jobs-image.sh b/build/run-build-docker-jobs-image.sh
index 15f7881..933d488 100755
--- a/build/run-build-docker-jobs-image.sh
+++ b/build/run-build-docker-jobs-image.sh
@@ -118,18 +118,8 @@ timer_reset
# clean up the docker build environment
cd "$WORKSPACE"
-cd docker
-rm -f jobs-image
-rm -f config.yml
-
-# Get test config.yml file
-cp $HOME/docker/config.yml .
-
-if [[ ! -z "$tags" ]]; then
- COMMIT=${tags/,*/} ./build.sh jobs-image
-else
- ./build.sh jobs-image
-fi
+cd docker/jobs
+docker build -t arvados/jobs .
ECODE=$?
@@ -147,8 +137,8 @@ timer_reset
if [[ "$ECODE" != "0" ]]; then
title "upload arvados images SKIPPED because build failed"
else
- if [[ $upload == true ]]; then
- ## 20150526 nico -- *sometimes* dockerhub needs re-login
+ if [[ $upload == true ]]; then
+ ## 20150526 nico -- *sometimes* dockerhub needs re-login
## even though credentials are already in .dockercfg
docker login -u arvados
diff --git a/docker/.gitignore b/docker/.gitignore
deleted file mode 100644
index ff626a3..0000000
--- a/docker/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-*-image
-build/
diff --git a/docker/README.md b/docker/README.md
deleted file mode 100644
index 9c03e1b..0000000
--- a/docker/README.md
+++ /dev/null
@@ -1,81 +0,0 @@
-Deploying Arvados in Docker Containers
-======================================
-
-This file explains how to build and deploy Arvados servers in Docker
-containers, so that they can be run easily in different environments
-(a dedicated server, a developer's laptop, a virtual machine,
-etc).
-
-Prerequisites
--------------
-
-* Docker
-
- Docker is a Linux container management system. It is a very young system but
- is being developed rapidly.
- [Installation packages](http://www.docker.io/gettingstarted/)
- are available for several platforms.
-
- If a prebuilt docker package is not available for your platform, the
- short instructions for installing it are:
-
- 1. Create a `docker` group and add yourself to it.
-
- <pre>
- $ sudo addgroup docker
- $ sudo adduser `whoami` docker
- </pre>
-
- Log out and back in.
-
- 2. Add a `cgroup` filesystem and mount it:
-
- <pre>
- $ mkdir -p /cgroup
- $ grep cgroup /etc/fstab
- none /cgroup cgroup defaults 0 0
- $ sudo mount /cgroup
- </pre>
-
- 3. [Download and run a docker binary from docker.io.](http://docs.docker.io/en/latest/installation/binaries/)
-
-* Ruby (version 1.9.3 or greater)
-
-* sudo privileges to run `debootstrap`
-
-Building
---------
-
-Type `./build.sh` to configure and build the following Docker images:
-
- * arvados/api - the Arvados API server
- * arvados/compute - Arvados compute node image
- * arvados/doc - Arvados documentation
- * arvados/keep - Keep, the Arvados content-addressable filesystem
- * arvados/keepproxy - Keep proxy
- * arvados/shell - Arvados shell node image
- * arvados/sso - the Arvados single-signon authentication server
- * arvados/workbench - the Arvados console
-
-`build.sh` will generate reasonable defaults for all configuration
-settings. If you want more control over the way Arvados is
-configured, first copy `config.yml.example` to `config.yml` and edit
-it with appropriate configuration settings, and then run `./build.sh`.
-
-Running
--------
-
-The `arvdock` script in this directory is used to start, stop and
-restart Arvados servers on your machine. The simplest and easiest way
-to use it is `./arvdock start` to start the full complement of Arvados
-servers, and `./arvdock stop` and `./arvdock restart` to stop and
-restart all servers, respectively.
-
-Developers who are working on individual servers can start, stop or
-restart just those containers, e.g.:
-
-* `./arvdock start --api --sso` to start just the API and SSO services.
-* `./arvdock stop --keep` to stop just the Keep services.
-* `./arvdock restart --workbench=8000` restarts just the Workbench service on port 8000.
-
-For a full set of arguments, use `./arvdock --help`.
diff --git a/docker/api/.gitolite.rc b/docker/api/.gitolite.rc
deleted file mode 100644
index 855e103..0000000
--- a/docker/api/.gitolite.rc
+++ /dev/null
@@ -1,191 +0,0 @@
-# configuration variables for gitolite
-
-# This file is in perl syntax. But you do NOT need to know perl to edit it --
-# just mind the commas, use single quotes unless you know what you're doing,
-# and make sure the brackets and braces stay matched up!
-
-# (Tip: perl allows a comma after the last item in a list also!)
-
-# HELP for commands can be had by running the command with "-h".
-
-# HELP for all the other FEATURES can be found in the documentation (look for
-# "list of non-core programs shipped with gitolite" in the master index) or
-# directly in the corresponding source file.
-
-my $repo_aliases;
-my $aliases_src = "$ENV{HOME}/.gitolite/arvadosaliases.pl";
-if ($ENV{HOME} && (-e $aliases_src)) {
- $repo_aliases = do $aliases_src;
-}
-$repo_aliases ||= {};
-
-%RC = (
-
- # ------------------------------------------------------------------
-
- # default umask gives you perms of '0700'; see the rc file docs for
- # how/why you might change this
- UMASK => 0022,
-
- # look for "git-config" in the documentation
- GIT_CONFIG_KEYS => '',
-
- # comment out if you don't need all the extra detail in the logfile
- LOG_EXTRA => 1,
-
- # roles. add more roles (like MANAGER, TESTER, ...) here.
- # WARNING: if you make changes to this hash, you MUST run 'gitolite
- # compile' afterward, and possibly also 'gitolite trigger POST_COMPILE'
- ROLES => {
- READERS => 1,
- WRITERS => 1,
- },
-
- REPO_ALIASES => $repo_aliases,
-
- # ------------------------------------------------------------------
-
- # rc variables used by various features
-
- # the 'info' command prints this as additional info, if it is set
- # SITE_INFO => 'Please see http://blahblah/gitolite for more help',
-
- # the 'desc' command uses this
- # WRITER_CAN_UPDATE_DESC => 1,
- # the 'readme' command uses this
- # WRITER_CAN_UPDATE_README => 1,
-
- # the CpuTime feature uses these
- # display user, system, and elapsed times to user after each git operation
- # DISPLAY_CPU_TIME => 1,
- # display a warning if total CPU times (u, s, cu, cs) crosses this limit
- # CPU_TIME_WARN_LIMIT => 0.1,
-
- # the Mirroring feature needs this
- # HOSTNAME => "foo",
-
- # if you enabled 'Shell', you need this
- # SHELL_USERS_LIST => "$ENV{HOME}/.gitolite.shell-users",
-
- # ------------------------------------------------------------------
-
- # suggested locations for site-local gitolite code (see cust.html)
-
- # this one is managed directly on the server
- # LOCAL_CODE => "$ENV{HOME}/local",
-
- # or you can use this, which lets you put everything in a subdirectory
- # called "local" in your gitolite-admin repo. For a SECURITY WARNING
- # on this, see http://gitolite.com/gitolite/cust.html#pushcode
- # LOCAL_CODE => "$rc{GL_ADMIN_BASE}/local",
-
- # ------------------------------------------------------------------
-
- # List of commands and features to enable
-
- ENABLE => [
-
- # COMMANDS
-
- # These are the commands enabled by default
- 'help',
- 'desc',
- 'info',
- 'perms',
- 'writable',
-
- # Uncomment or add new commands here.
- # 'create',
- # 'fork',
- # 'mirror',
- # 'readme',
- # 'sskm',
- # 'D',
-
- # These FEATURES are enabled by default.
-
- # essential (unless you're using smart-http mode)
- 'ssh-authkeys',
-
- # creates git-config enties from gitolite.conf file entries like 'config foo.bar = baz'
- 'git-config',
-
- # creates git-daemon-export-ok files; if you don't use git-daemon, comment this out
- 'daemon',
-
- # creates projects.list file; if you don't use gitweb, comment this out
- 'gitweb',
-
- # These FEATURES are disabled by default; uncomment to enable. If you
- # need to add new ones, ask on the mailing list :-)
-
- # user-visible behaviour
-
- # prevent wild repos auto-create on fetch/clone
- # 'no-create-on-read',
- # no auto-create at all (don't forget to enable the 'create' command!)
- # 'no-auto-create',
-
- # access a repo by another (possibly legacy) name
- 'Alias',
-
- # give some users direct shell access
- # 'Shell',
-
- # set default roles from lines like 'option default.roles-1 = ...', etc.
- # 'set-default-roles',
-
- # show more detailed messages on deny
- # 'expand-deny-messages',
-
- # system admin stuff
-
- # enable mirroring (don't forget to set the HOSTNAME too!)
- # 'Mirroring',
-
- # allow people to submit pub files with more than one key in them
- # 'ssh-authkeys-split',
-
- # selective read control hack
- # 'partial-copy',
-
- # manage local, gitolite-controlled, copies of read-only upstream repos
- # 'upstream',
-
- # updates 'description' file instead of 'gitweb.description' config item
- # 'cgit',
-
- # allow repo-specific hooks to be added
- # 'repo-specific-hooks',
-
- # performance, logging, monitoring...
-
- # be nice
- # 'renice 10',
-
- # log CPU times (user, system, cumulative user, cumulative system)
- # 'CpuTime',
-
- # syntactic_sugar for gitolite.conf and included files
-
- # allow backslash-escaped continuation lines in gitolite.conf
- # 'continuation-lines',
-
- # create implicit user groups from directory names in keydir/
- # 'keysubdirs-as-groups',
-
- # allow simple line-oriented macros
- # 'macros',
-
- ],
-
-);
-
-# ------------------------------------------------------------------------------
-# per perl rules, this should be the last line in such a file:
-1;
-
-# Local variables:
-# mode: perl
-# End:
-# vim: set syn=perl:
diff --git a/docker/api/Dockerfile b/docker/api/Dockerfile
deleted file mode 100644
index 6a3428c..0000000
--- a/docker/api/Dockerfile
+++ /dev/null
@@ -1,75 +0,0 @@
-# Arvados API server Docker container.
-
-FROM arvados/passenger
-MAINTAINER Ward Vandewege <ward at curoverse.com>
-
-# Install postgres and apache.
-RUN apt-get update -q
-RUN apt-get install -qy \
- procps postgresql postgresql-server-dev-9.1 slurm-llnl munge \
- supervisor sudo libwww-perl libio-socket-ssl-perl libcrypt-ssleay-perl \
- libjson-perl cron openssh-server
-
-ADD munge.key /etc/munge/
-RUN chown munge:munge /etc/munge/munge.key && chmod 600 /etc/munge/munge.key
-ADD generated/slurm.conf /etc/slurm-llnl/
-
-RUN /usr/local/rvm/bin/rvm-exec default gem install arvados-cli arvados
-# /for crunch-dispatch
-
-RUN /bin/mkdir -p /usr/src/arvados/services
-ADD generated/api.tar.gz /usr/src/arvados/services/
-
-# Install generated config files
-ADD generated/database.yml /usr/src/arvados/services/api/config/database.yml
-ADD generated/omniauth.rb /usr/src/arvados/services/api/config/initializers/omniauth.rb
-RUN /bin/cp /usr/src/arvados/services/api/config/environments/production.rb.example /usr/src/arvados/services/api/config/environments/production.rb
-ADD generated/application.yml /usr/src/arvados/services/api/config/application.yml
-
-# Configure Rails databases.
-ENV RAILS_ENV production
-ADD generated/config_databases.sh /tmp/config_databases.sh
-ADD generated/superuser_token /tmp/superuser_token
-RUN /usr/local/rvm/bin/rvm-exec default bundle install --gemfile=/usr/src/arvados/services/api/Gemfile && \
- sh /tmp/config_databases.sh && \
- rm /tmp/config_databases.sh && \
- /etc/init.d/postgresql start && \
- cd /usr/src/arvados/services/api && \
- /usr/local/rvm/bin/rvm-exec default bundle exec rake db:structure:load && \
- /usr/local/rvm/bin/rvm-exec default bundle exec rake db:seed && \
- /usr/local/rvm/bin/rvm-exec default bundle exec rake assets:precompile && \
- /usr/local/rvm/bin/rvm-exec default ./script/create_superuser_token.rb $(cat /tmp/superuser_token) && \
- chown www-data:www-data config.ru && \
- chown www-data:www-data log -R && \
- mkdir -p tmp && \
- chown www-data:www-data tmp -R
-
-# Install a token for root
-RUN mkdir -p /root/.config/arvados; echo "ARVADOS_API_HOST=api" >> /root/.config/arvados/settings.conf && echo "ARVADOS_API_HOST_INSECURE=yes" >> /root/.config/arvados/settings.conf && echo "ARVADOS_API_TOKEN=$(cat /tmp/superuser_token)" >> /root/.config/arvados/settings.conf && chmod 600 /root/.config/arvados/settings.conf
-
-# Set up directory for job commit repo
-RUN mkdir -p /var/lib/arvados
-# Add crunch user
-RUN addgroup --gid 4005 crunch && mkdir /home/crunch && useradd --uid 4005 --gid 4005 crunch && chown crunch:crunch /home/crunch
-
-# Create keep and compute node objects
-ADD generated/keep_server_0.json /root/
-ADD generated/keep_server_1.json /root/
-ADD keep_proxy.json /root/
-
-# Set up update-gitolite.rb
-RUN mkdir /usr/local/arvados/config -p
-ADD generated/arvados-clients.yml /usr/src/arvados/services/api/config/
-ADD .gitolite.rc /usr/local/arvados/config/
-RUN ln /usr/src/arvados/services/api/script/arvados-git-sync.rb /usr/local/bin/
-
-# Supervisor.
-ADD supervisor.conf /etc/supervisor/conf.d/arvados.conf
-ADD generated/setup.sh /usr/local/bin/setup.sh
-ADD generated/setup-gitolite.sh /usr/local/bin/setup-gitolite.sh
-ADD crunch-dispatch-run.sh /usr/local/bin/crunch-dispatch-run.sh
-ADD munge.sh /usr/local/bin/munge.sh
-ADD passenger.sh /usr/local/bin/passenger.sh
-
-# Start the supervisor.
-CMD ["/usr/bin/supervisord", "-n"]
diff --git a/docker/api/apache2_foreground.sh b/docker/api/apache2_foreground.sh
deleted file mode 100755
index fc6028e..0000000
--- a/docker/api/apache2_foreground.sh
+++ /dev/null
@@ -1,7 +0,0 @@
-#! /bin/bash
-
-read pid cmd state ppid pgrp session tty_nr tpgid rest < /proc/self/stat
-trap "kill -TERM -$pgrp; exit" EXIT TERM KILL SIGKILL SIGTERM SIGQUIT
-
-source /etc/apache2/envvars
-/usr/sbin/apache2 -D FOREGROUND
diff --git a/docker/api/apache2_vhost.in b/docker/api/apache2_vhost.in
deleted file mode 100644
index 344e36d..0000000
--- a/docker/api/apache2_vhost.in
+++ /dev/null
@@ -1,50 +0,0 @@
-# VirtualHost definition for the Arvados API server
-
-<VirtualHost *:80>
- ServerName @@API_HOSTNAME@@.@@ARVADOS_DOMAIN@@
- ServerAdmin sysadmin at curoverse.com
-
- RedirectPermanent / https://@@API_HOSTNAME@@.@@ARVADOS_DOMAIN@@/
-
- LogLevel warn
- ErrorLog ${APACHE_LOG_DIR}/error.log
- CustomLog ${APACHE_LOG_DIR}/access.log combined
-
-</VirtualHost>
-
-<VirtualHost *:443>
- ServerName @@API_HOSTNAME@@.@@ARVADOS_DOMAIN@@
- ServerAdmin sysadmin at curoverse.com
-
- RailsEnv production
- RackBaseURI /
- RailsAppSpawnerIdleTime 1200
-
- # Enable streaming
- PassengerBufferResponse off
-
- # Index file and Document Root (where the public files are located)
- DirectoryIndex index.html
- DocumentRoot /usr/src/arvados/services/api/public
-
- LogLevel warn
- ErrorLog ${APACHE_LOG_DIR}/ssl_error.log
- CustomLog ${APACHE_LOG_DIR}/ssl_access.log combined
-
- <Directory /usr/src/arvados/services/api/public>
- Options Indexes FollowSymLinks MultiViews IncludesNoExec
- AllowOverride None
- Order allow,deny
- allow from all
- </Directory>
-
- <IfModule mod_ssl.c>
- SSLEngine on
- # SSLCertificateChainFile /etc/ssl/certs/startcom.sub.class1.server.ca.pem
- # SSLCACertificateFile /etc/ssl/certs/startcom.ca.pem
- SSLCertificateFile /etc/ssl/certs/ssl-cert-snakeoil.pem
- SSLCertificateKeyFile /etc/ssl/private/ssl-cert-snakeoil.key
- SetEnvIf User-Agent ".*MSIE.*" nokeepalive ssl-unclean-shutdown
- </IfModule>
-
-</VirtualHost>
diff --git a/docker/api/application.yml.in b/docker/api/application.yml.in
deleted file mode 100644
index 97eb66f..0000000
--- a/docker/api/application.yml.in
+++ /dev/null
@@ -1,67 +0,0 @@
-# Copy this file to application.yml and edit to suit.
-#
-# Consult application.default.yml for the full list of configuration
-# settings.
-#
-# The order of precedence is:
-# 1. config/environments/{RAILS_ENV}.rb (deprecated)
-# 2. Section in application.yml corresponding to RAILS_ENV (e.g., development)
-# 3. Section in application.yml called "common"
-# 4. Section in application.default.yml corresponding to RAILS_ENV
-# 5. Section in application.default.yml called "common"
-
-development:
- # The blob_signing_key is a string of alphanumeric characters used
- # to sign permission hints for Keep locators. It must be identical
- # to the permission key given to Keep. If you run both apiserver
- # and Keep in development, change this to a hardcoded string and
- # make sure both systems use the same value.
- blob_signing_key: ~
-
-production:
- host: api.@@ARVADOS_DOMAIN@@
-
- git_repo_ssh_base: "git at api.@@ARVADOS_DOMAIN@@:"
-
- # Docker setup doesn't include arv-git-httpd yet.
- git_repo_https_base: false
-
- # At minimum, you need a nice long randomly generated secret_token here.
- # Use a long string of alphanumeric characters (at least 36).
- secret_token: @@API_SECRET@@
-
- # blob_signing_key is required and must be identical to the
- # permission secret provisioned to Keep.
- # Use a long string of alphanumeric characters (at least 36).
- blob_signing_key: @@KEEP_SIGNING_SECRET@@
-
- uuid_prefix: @@API_HOSTNAME@@
-
- # compute_node_domain: example.org
- # compute_node_nameservers:
- # - 127.0.0.1
- # - 192.168.1.1
- #
- permit_create_collection_with_unsigned_manifest: true
- git_repositories_dir: /home/git/repositories
- crunch_job_wrapper: :slurm_immediate
- action_mailer.raise_delivery_errors: false
- action_mailer.perform_deliveries: false
-
- workbench_address: @@API_WORKBENCH_ADDRESS@@
-
- auto_setup_new_users: true
-
- auto_admin_first_user: true
-
- auto_setup_new_users_with_repository: true
-
- auto_setup_new_users_with_vm_uuid: @@API_HOSTNAME@@-2x53u-csbtkecoa669vkz
-
-test:
- uuid_prefix: zzzzz
- secret_token: <%= rand(2**512).to_s(36) %>
-
-common:
- #git_repositories_dir: /var/cache/git
- #git_internal_dir: /var/cache/arvados/internal.git
diff --git a/docker/api/apt.arvados.org.list b/docker/api/apt.arvados.org.list
deleted file mode 100644
index 7eb8716..0000000
--- a/docker/api/apt.arvados.org.list
+++ /dev/null
@@ -1,2 +0,0 @@
-# apt.arvados.org
-deb http://apt.arvados.org/ wheezy main
diff --git a/docker/api/arvados-clients.yml.in b/docker/api/arvados-clients.yml.in
deleted file mode 100644
index 6741328..0000000
--- a/docker/api/arvados-clients.yml.in
+++ /dev/null
@@ -1,6 +0,0 @@
-production:
- gitolite_url: 'git at api.@@ARVADOS_DOMAIN@@:gitolite-admin.git'
- gitolite_tmp: 'gitolite-tmp'
- arvados_api_host: 'api'
- arvados_api_token: '@@API_SUPERUSER_SECRET@@'
- arvados_api_host_insecure: true
diff --git a/docker/api/config_databases.sh.in b/docker/api/config_databases.sh.in
deleted file mode 100755
index b548c21..0000000
--- a/docker/api/config_databases.sh.in
+++ /dev/null
@@ -1,15 +0,0 @@
-#! /bin/sh
-
-# Configure postgresql in a docker instance.
-
-/bin/su postgres -c '/usr/lib/postgresql/9.1/bin/postgres --single -D /var/lib/postgresql/9.1/main -c config_file=/etc/postgresql/9.1/main/postgresql.conf' <<EOF
-alter role postgres with encrypted password '@@POSTGRES_ROOT_PW@@';
-
-create user @@ARVADOS_DEV_USER@@ with encrypted password '@@ARVADOS_DEV_PW@@';
-create database @@ARVADOS_DEV_DB@@ with owner @@ARVADOS_DEV_USER@@;
-
-create user @@ARVADOS_TEST_USER@@ with createdb encrypted password '@@ARVADOS_TEST_PW@@';
-
-create user @@ARVADOS_PROD_USER@@ with encrypted password '@@ARVADOS_PROD_PW@@';
-create database @@ARVADOS_PROD_DB@@ with owner @@ARVADOS_PROD_USER@@;
-EOF
diff --git a/docker/api/crunch-dispatch-run.sh b/docker/api/crunch-dispatch-run.sh
deleted file mode 100755
index 5103b1d..0000000
--- a/docker/api/crunch-dispatch-run.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/bin/bash
-set -e
-export PATH="$PATH":/usr/src/arvados/services/crunch
-export PERLLIB=/usr/src/arvados/sdk/perl/lib
-export ARVADOS_API_HOST=api
-export ARVADOS_API_HOST_INSECURE=yes
-export CRUNCH_DISPATCH_LOCKFILE=/var/lock/crunch-dispatch
-
-if [[ ! -e $CRUNCH_DISPATCH_LOCKFILE ]]; then
- touch $CRUNCH_DISPATCH_LOCKFILE
-fi
-
-export CRUNCH_JOB_BIN=/usr/src/arvados/services/crunch/crunch-job
-export HOME=`pwd`
-fuser -TERM -k $CRUNCH_DISPATCH_LOCKFILE || true
-
-# Give the compute nodes some time to start up
-sleep 5
-
-cd /usr/src/arvados/services/api
-export RAILS_ENV=production
-/usr/local/rvm/bin/rvm-exec default bundle install
-exec /usr/local/rvm/bin/rvm-exec default bundle exec ./script/crunch-dispatch.rb 2>&1
-
diff --git a/docker/api/database.yml.in b/docker/api/database.yml.in
deleted file mode 100644
index 5990319..0000000
--- a/docker/api/database.yml.in
+++ /dev/null
@@ -1,25 +0,0 @@
-development:
- adapter: postgresql
- encoding: utf8
- database: @@ARVADOS_DEV_DB@@
- username: @@ARVADOS_DEV_USER@@
- password: @@ARVADOS_DEV_PW@@
- host: localhost
-
-test:
- adapter: postgresql
- encoding: utf8
- template: template0
- database: @@ARVADOS_TEST_DB@@
- username: @@ARVADOS_TEST_USER@@
- password: @@ARVADOS_TEST_PW@@
- host: localhost
-
-production:
- adapter: postgresql
- encoding: utf8
- database: @@ARVADOS_PROD_DB@@
- username: @@ARVADOS_PROD_USER@@
- password: @@ARVADOS_PROD_PW@@
- host: localhost
-
diff --git a/docker/api/keep_proxy.json b/docker/api/keep_proxy.json
deleted file mode 100644
index 117e590..0000000
--- a/docker/api/keep_proxy.json
+++ /dev/null
@@ -1,6 +0,0 @@
-{
- "service_host": "localhost",
- "service_port": 9902,
- "service_ssl_flag": "false",
- "service_type": "proxy"
-}
diff --git a/docker/api/keep_server_0.json.in b/docker/api/keep_server_0.json.in
deleted file mode 100644
index d63c590..0000000
--- a/docker/api/keep_server_0.json.in
+++ /dev/null
@@ -1,6 +0,0 @@
-{
- "service_host": "keep_server_0.keep.@@ARVADOS_DOMAIN@@",
- "service_port": 25107,
- "service_ssl_flag": "false",
- "service_type": "disk"
-}
diff --git a/docker/api/keep_server_1.json.in b/docker/api/keep_server_1.json.in
deleted file mode 100644
index 53d5c64..0000000
--- a/docker/api/keep_server_1.json.in
+++ /dev/null
@@ -1,6 +0,0 @@
-{
- "service_host": "keep_server_1.keep.@@ARVADOS_DOMAIN@@",
- "service_port": 25107,
- "service_ssl_flag": "false",
- "service_type": "disk"
-}
diff --git a/docker/api/munge.key b/docker/api/munge.key
deleted file mode 100644
index 34036a0..0000000
Binary files a/docker/api/munge.key and /dev/null differ
diff --git a/docker/api/munge.sh b/docker/api/munge.sh
deleted file mode 100755
index ef10d01..0000000
--- a/docker/api/munge.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/sh
-rm -rf /var/run/munge
-exec /etc/init.d/munge start
diff --git a/docker/api/omniauth.rb.in b/docker/api/omniauth.rb.in
deleted file mode 100644
index 8daa300..0000000
--- a/docker/api/omniauth.rb.in
+++ /dev/null
@@ -1,18 +0,0 @@
-# Change this omniauth configuration to point to your registered provider
-# Since this is a registered application, add the app id and secret here
-APP_ID = '@@SSO_CLIENT_APP_ID@@'
-APP_SECRET = '@@SSO_CLIENT_SECRET@@'
-
-# Update your custom Omniauth provider URL here
-if '@@OMNIAUTH_URL@@' != ''
- CUSTOM_PROVIDER_URL = '@@OMNIAUTH_URL@@'
-else
- CUSTOM_PROVIDER_URL = 'https://@@SSO_HOSTNAME@@.@@ARVADOS_DOMAIN@@'
-end
-
-# This is a development sandbox, we use self-signed certificates
-OpenSSL::SSL::VERIFY_PEER = OpenSSL::SSL::VERIFY_NONE
-
-Rails.application.config.middleware.use OmniAuth::Builder do
- provider :josh_id, APP_ID, APP_SECRET, CUSTOM_PROVIDER_URL
-end
diff --git a/docker/api/passenger.sh b/docker/api/passenger.sh
deleted file mode 100755
index a62d9d5..0000000
--- a/docker/api/passenger.sh
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/bin/sh
-
-cd /usr/src/arvados/services/api
-export ARVADOS_WEBSOCKETS=1
-export RAILS_ENV=production
-/usr/local/rvm/bin/rvm-exec default bundle exec rake db:migrate
-exec /usr/local/rvm/bin/rvm-exec default bundle exec passenger start -p443 --ssl --ssl-certificate=/etc/ssl/certs/ssl-cert-snakeoil.pem --ssl-certificate-key=/etc/ssl/private/ssl-cert-snakeoil.key
diff --git a/docker/api/setup-gitolite.sh.in b/docker/api/setup-gitolite.sh.in
deleted file mode 100755
index 023ca5d..0000000
--- a/docker/api/setup-gitolite.sh.in
+++ /dev/null
@@ -1,73 +0,0 @@
-#!/bin/bash
-
-ssh-keygen -q -N '' -t rsa -f /root/.ssh/id_rsa
-
-useradd git
-mkdir /home/git
-
-# Set up gitolite repository
-cp ~root/.ssh/id_rsa.pub ~git/root-authorized_keys.pub
-chown git:git /home/git -R
-su - git -c "mkdir -p ~/bin"
-
-su - git -c "git clone git://github.com/sitaramc/gitolite"
-su - git -c "gitolite/install -ln ~/bin"
-su - git -c "PATH=/home/git/bin:$PATH gitolite setup -pk ~git/root-authorized_keys.pub"
-install -o git -g git -m 600 /usr/local/arvados/config/.gitolite.rc /home/git/
-
-# And make sure that the existing repos are equally readable, or the API server commit model will freak out...
-chmod 755 /home/git/repositories
-chmod +rx /home/git/repositories/*git -R
-
-# Now set up the gitolite repo(s) we use
-mkdir -p /usr/local/arvados/gitolite-tmp/
-# Make ssh store the host key
-ssh -o "StrictHostKeyChecking no" git at api.@@ARVADOS_DOMAIN@@ info
-# Now check out the tree
-git clone git at api.@@ARVADOS_DOMAIN@@:gitolite-admin.git /usr/local/arvados/gitolite-tmp/gitolite-admin/
-cd /usr/local/arvados/gitolite-tmp/gitolite-admin
-mkdir keydir/arvados
-mkdir conf/admin
-mkdir conf/auto
-echo "
-
- at arvados_git_user = arvados_git_user
-
-repo @all
- RW+ = @arvados_git_user
-
-" > conf/admin/arvados.conf
-echo '
-include "auto/*.conf"
-include "admin/*.conf"
-' >> conf/gitolite.conf
-
-#su - git -c "ssh-keygen -t rsa"
-cp /root/.ssh/id_rsa.pub keydir/arvados/arvados_git_user.pub
-# Replace the 'root' key with the user key, just in case
-cp /root/.ssh/authorized_keys keydir/root-authorized_keys.pub
-# But also make sure we have the root key installed so it can access all keys
-git add keydir/root-authorized_keys.pub
-git add keydir/arvados/arvados_git_user.pub
-git add conf/admin/arvados.conf
-git add keydir/arvados/
-git add conf/gitolite.conf
-git commit -a -m 'git server setup'
-git push
-
-# Prepopulate the arvados.git repo with our source. Silly, but until we can check out from remote trees,
-# we need this to make the tutorials work.
-su - git -c "git clone --bare git://github.com/curoverse/arvados.git /home/git/repositories/arvados.git"
-
-echo "ARVADOS_API_HOST_INSECURE=yes" > /etc/cron.d/gitolite-update
-echo "*/2 * * * * root /bin/bash -c 'source /etc/profile.d/rvm.sh && /usr/src/arvados/services/api/script/arvados-git-sync.rb production'" >> /etc/cron.d/gitolite-update
-
-# Create/update the repos now
-. /etc/profile.d/rvm.sh
-export ARVADOS_API_HOST=api
-export ARVADOS_API_HOST_INSECURE=yes
-export ARVADOS_API_TOKEN=@@API_SUPERUSER_SECRET@@
-/usr/local/arvados/update-gitolite.rb production
-
-echo "PATH=/usr/bin:/bin:/sbin" > /etc/cron.d/arvados-repo-update
-echo "*/5 * * * * git cd ~git/repositories/arvados.git; git fetch https://github.com/curoverse/arvados.git master:master" >> /etc/cron.d/arvados-repo-update
diff --git a/docker/api/setup.sh.in b/docker/api/setup.sh.in
deleted file mode 100755
index 2c7da92..0000000
--- a/docker/api/setup.sh.in
+++ /dev/null
@@ -1,82 +0,0 @@
-#!/bin/bash
-
-set -x
-
-if test -f /root/finished_arvados_setup ; then
- exit
-fi
-
-. /etc/profile.d/rvm.sh
-
-export ARVADOS_API_HOST=api
-export ARVADOS_API_HOST_INSECURE=yes
-export ARVADOS_API_TOKEN=@@API_SUPERUSER_SECRET@@
-export HOME=/root
-
-# Wait for API server to come up.
-while ! arv user current ; do sleep 1 ; done
-
-# Arvados repository object
-all_users_group_uuid="@@API_HOSTNAME@@-j7d0g-fffffffffffffff"
-
-arv user update --uuid @@API_HOSTNAME@@-tpzed-000000000000000 --user '{"username":"root"}'
-repo_uuid=`arv --format=uuid repository create --repository '{"owner_uuid":"@@API_HOSTNAME@@-tpzed-000000000000000", "name":"arvados"}'`
-echo "Arvados repository uuid is $repo_uuid"
-
-read -rd $'\000' newlink <<EOF; arv link create --link "$newlink"
-{
- "tail_uuid":"$all_users_group_uuid",
- "head_uuid":"$repo_uuid",
- "link_class":"permission",
- "name":"can_read"
-}
-EOF
-
-# Make sure the necessary keep_service objects exist
-arv keep_service list > /tmp/keep_service.list
-
-grep -q keep_server_0 /tmp/keep_service.list
-if [[ "$?" != "0" ]]; then
- arv keep_service create --keep-service "$(cat /root/keep_server_0.json)"
-fi
-
-grep -q keep_server_1 /tmp/keep_service.list
-if [[ "$?" != "0" ]]; then
- arv keep_service create --keep-service "$(cat /root/keep_server_1.json)"
-fi
-
-grep -q keep_proxy /tmp/keep_service.list
-if [[ "$?" != "0" ]]; then
- arv keep_service create --keep-service "$(cat /root/keep_proxy.json)"
-fi
-
-# User repository object
-# user_uuid=`arv --format=uuid user current`
-# repo_uuid=`arv --format=uuid repository create --repository '{"name":"@@ARVADOS_USER_NAME@@","fetch_url":"git at api.dev.arvados:@@ARVADOS_USER_NAME@@.git","push_url":"git at api.dev.arvados:@@ARVADOS_USER_NAME@@.git"}'`
-
-# echo "User repository uuid is $repo_uuid"
-
-# read -rd $'\000' newlink <<EOF; arv link create --link "$newlink"
-# {
-# "tail_uuid":"$user_uuid",
-# "head_uuid":"$repo_uuid",
-# "link_class":"permission",
-# "name":"can_write"
-# }
-# EOF
-
-# # Shell machine object
-shell_uuid=`arv --format=uuid virtual_machine create --virtual-machine '{"hostname":"shell"}'`
-arv virtual_machine create --virtual-machine '{"hostname":"shell.dev", "uuid": "@@API_HOSTNAME@@-2x53u-csbtkecoa669vkz"}'
-
-# read -rd $'\000' newlink <<EOF; arv link create --link "$newlink"
-# {
-# "tail_uuid":"$user_uuid",
-# "head_uuid":"$shell_uuid",
-# "link_class":"permission",
-# "name":"can_login",
-# "properties": {"username": "@@ARVADOS_USER_NAME@@"}
-# }
-# EOF
-
-touch /root/finished_arvados_setup
diff --git a/docker/api/slurm.conf.in b/docker/api/slurm.conf.in
deleted file mode 100644
index 7312a0e..0000000
--- a/docker/api/slurm.conf.in
+++ /dev/null
@@ -1,60 +0,0 @@
-
-ControlMachine=api
-#SlurmUser=slurmd
-SlurmctldPort=6817
-SlurmdPort=6818
-AuthType=auth/munge
-#JobCredentialPrivateKey=/etc/slurm-llnl/slurm-key.pem
-#JobCredentialPublicCertificate=/etc/slurm-llnl/slurm-cert.pem
-StateSaveLocation=/tmp
-SlurmdSpoolDir=/tmp/slurmd
-SwitchType=switch/none
-MpiDefault=none
-SlurmctldPidFile=/var/run/slurmctld.pid
-SlurmdPidFile=/var/run/slurmd.pid
-ProctrackType=proctrack/pgid
-CacheGroups=0
-ReturnToService=2
-TaskPlugin=task/affinity
-#
-# TIMERS
-SlurmctldTimeout=300
-SlurmdTimeout=300
-InactiveLimit=0
-MinJobAge=300
-KillWait=30
-Waittime=0
-#
-# SCHEDULING
-SchedulerType=sched/backfill
-#SchedulerType=sched/builtin
-SchedulerPort=7321
-#SchedulerRootFilter=
-#SelectType=select/linear
-SelectType=select/cons_res
-SelectTypeParameters=CR_CPU_Memory
-FastSchedule=1
-#
-# LOGGING
-SlurmctldDebug=3
-#SlurmctldLogFile=
-SlurmdDebug=3
-#SlurmdLogFile=
-JobCompType=jobcomp/none
-#JobCompLoc=
-JobAcctGatherType=jobacct_gather/none
-#JobAcctLogfile=
-#JobAcctFrequency=
-#
-# COMPUTE NODES
-NodeName=DEFAULT
-# CPUs=8 State=UNKNOWN RealMemory=6967 Weight=6967
-PartitionName=DEFAULT MaxTime=INFINITE State=UP
-PartitionName=compute Default=YES Shared=yes
-#PartitionName=sysadmin Hidden=YES Shared=yes
-
-NodeName=compute[0-1]
-#NodeName=compute0 RealMemory=6967 Weight=6967
-
-PartitionName=compute Nodes=compute[0-1]
-PartitionName=crypto Nodes=compute[0-1]
diff --git a/docker/api/superuser_token.in b/docker/api/superuser_token.in
deleted file mode 100644
index 49bb34e..0000000
--- a/docker/api/superuser_token.in
+++ /dev/null
@@ -1 +0,0 @@
-@@API_SUPERUSER_SECRET@@
diff --git a/docker/api/supervisor.conf b/docker/api/supervisor.conf
deleted file mode 100644
index b24e552..0000000
--- a/docker/api/supervisor.conf
+++ /dev/null
@@ -1,43 +0,0 @@
-[program:ssh]
-user=root
-command=/etc/init.d/ssh start
-startsecs=0
-
-[program:postgres]
-user=postgres
-command=/usr/lib/postgresql/9.1/bin/postgres -D /var/lib/postgresql/9.1/main -c config_file=/etc/postgresql/9.1/main/postgresql.conf
-autorestart=true
-
-[program:passenger]
-command=/usr/local/bin/passenger.sh
-autorestart=true
-
-[program:munge]
-user=root
-command=/usr/local/bin/munge.sh
-startsecs=0
-
-[program:slurm]
-user=root
-command=/etc/init.d/slurm-llnl start
-startsecs=0
-
-[program:cron]
-user=root
-command=/etc/init.d/cron start
-startsecs=0
-
-[program:setup]
-user=root
-command=/usr/local/bin/setup.sh
-startsecs=0
-
-[program:setup-gitolite]
-user=root
-command=/usr/local/bin/setup-gitolite.sh
-startsecs=0
-
-[program:crunch-dispatch]
-user=root
-command=/usr/local/bin/crunch-dispatch-run.sh
-autorestart=true
diff --git a/docker/arv-web/Dockerfile b/docker/arv-web/Dockerfile
deleted file mode 100644
index 11a9c17..0000000
--- a/docker/arv-web/Dockerfile
+++ /dev/null
@@ -1,15 +0,0 @@
-FROM arvados/passenger
-MAINTAINER Peter Amstutz <peter.amstutz at curoverse.com>
-
-ADD apache2_foreground.sh /etc/apache2/foreground.sh
-
-ADD apache2_vhost /etc/apache2/sites-available/arv-web
-RUN \
- mkdir /var/run/apache2 && \
- a2dissite default && \
- a2ensite arv-web && \
- a2enmod rewrite
-
-EXPOSE 80
-
-CMD ["/etc/apache2/foreground.sh"]
\ No newline at end of file
diff --git a/docker/arv-web/apache2_foreground.sh b/docker/arv-web/apache2_foreground.sh
deleted file mode 100755
index 76766a6..0000000
--- a/docker/arv-web/apache2_foreground.sh
+++ /dev/null
@@ -1,8 +0,0 @@
-#! /bin/bash
-
-read pid cmd state ppid pgrp session tty_nr tpgid rest < /proc/self/stat
-trap "kill -HUP -$pgrp" HUP
-trap "kill -TERM -$pgrp; exit" EXIT TERM QUIT
-
-source /etc/apache2/envvars
-/usr/sbin/apache2 -D FOREGROUND
diff --git a/docker/arv-web/apache2_vhost b/docker/arv-web/apache2_vhost
deleted file mode 100644
index 5268201..0000000
--- a/docker/arv-web/apache2_vhost
+++ /dev/null
@@ -1,19 +0,0 @@
-<VirtualHost *:80>
- # Index file and Document Root (where the public files are located)
- DirectoryIndex index.html
- DocumentRoot /mnt/public
- RackBaseURI /
-
- LogLevel warn
- ErrorLog ${APACHE_LOG_DIR}/error.log
- CustomLog ${APACHE_LOG_DIR}/access.log combined
-
- <Directory /mnt/public>
- Options Indexes IncludesNoExec
- Options -MultiViews
- AllowOverride All
- Order allow,deny
- Allow from all
- </Directory>
-
-</VirtualHost>
diff --git a/docker/arvdock b/docker/arvdock
deleted file mode 100755
index 43a384e..0000000
--- a/docker/arvdock
+++ /dev/null
@@ -1,559 +0,0 @@
-#!/bin/bash
-
-DOCKER=`which docker.io`
-
-if [[ "$DOCKER" == "" ]]; then
- DOCKER=`which docker`
-fi
-
-CURL=`which curl`
-
-COMPUTE_COUNTER=0
-
-ARVADOS_DOMAIN=dev.arvados
-
-function usage {
- echo >&2
- echo >&2 "usage: $0 (start|stop|restart|reset|test) [options]"
- echo >&2
- echo >&2 "start run new or restart stopped arvados containers"
- echo >&2 "stop stop arvados containers"
- echo >&2 "restart stop and then start arvados containers"
- echo >&2 "reset stop and delete containers WARNING: this will delete the data inside Arvados!"
- echo >&2 "test run tests"
- echo >&2
- echo >&2 "$0 options:"
- echo >&2 " -b[bridge], --bridge[=bridge] Docker bridge (default bridge docker0)"
- echo >&2 " -d[port], --doc[=port] Documentation server (default port 9898)"
- echo >&2 " -w[port], --workbench[=port] Workbench server (default port 9899)"
- echo >&2 " -s[port], --sso[=port] SSO server (default port 9901)"
- echo >&2 " -a[port], --api[=port] API server (default port 9900)"
- echo >&2 " -c, --compute Compute nodes (starts 2)"
- echo >&2 " -v, --vm Shell server"
- echo >&2 " -n, --nameserver Nameserver"
- echo >&2 " -k, --keep Keep servers"
- echo >&2 " -p, --keepproxy Keepproxy server"
- echo >&2 " -h, --help Display this help and exit"
- echo >&2 " --domain=dns.domain DNS domain used by containers (default dev.arvados)"
- echo >&2
- echo >&2 " If no options are given, the action is applied to all servers."
- echo >&2
- echo >&2 "$0 test [testname] [testname] ..."
- echo >&2 " By default, all tests are run."
-}
-
-function ip_address {
- local container=$1
- echo `$DOCKER inspect $container |grep IPAddress |cut -f4 -d\"`
-}
-
-function bridge_ip_address {
- local bridge_name=$1
- # FIXME: add a more robust check here.
- # because ip command could be mising, multiple docker bridges could be there.. etc.
- echo $(ip --oneline --family inet addr show dev "$bridge_name" | awk '{ print $4 }'| cut -d/ -f1 )
-}
-
-function start_container {
- bridge_ip=$(bridge_ip_address "$bridge")
-
- local args="-d -i -t"
- if [[ "$1" != '' ]]; then
- local port="$1"
- args="$args -p $port"
- fi
- if [[ "$2" != '' ]]; then
- local name="$2"
- if [[ "$name" == "api_server" ]]; then
- args="$args --dns=$bridge_ip --dns-search=compute.$ARVADOS_DOMAIN --hostname api -P --name $name"
- elif [[ "$name" == "compute" ]]; then
- name=$name$COMPUTE_COUNTER
- # We need --privileged because we run docker-inside-docker on the compute nodes
- args="$args --dns=$bridge_ip --dns-search=compute.$ARVADOS_DOMAIN --hostname compute$COMPUTE_COUNTER -P --privileged --name $name"
- let COMPUTE_COUNTER=$(($COMPUTE_COUNTER + 1))
- else
- args="$args --dns=$bridge_ip --dns-search=$ARVADOS_DOMAIN --hostname ${name#_server} --name $name"
- fi
- fi
- if [[ "$3" != '' ]]; then
- local volume="$3"
- args="$args --volumes-from $volume"
- fi
- if [[ "$4" != '' ]]; then
- local link="$4"
- args="$args --link $link"
- fi
- local image=$5
-
- `$DOCKER ps |grep -E "\b$name\b" -q`
- if [[ "$?" == "0" ]]; then
- echo "You have a running container with name $name -- skipping."
- return
- fi
-
- echo "Starting container: $name"
- `$DOCKER ps --all |grep -E "\b$name\b" -q`
- if [[ "$?" == "0" ]]; then
- echo " $DOCKER start $name"
- container=`$DOCKER start $name`
- else
- echo " $DOCKER run $args $image"
- container=`$DOCKER run $args $image`
- fi
-
- if [ "$?" != "0" -o "$container" = "" ]; then
- echo "Unable to start container"
- exit 1
- else
- echo "Started container: $container"
- fi
-
-}
-
-# Create a Docker data volume
-function make_keep_volumes () {
- `$DOCKER ps --all |grep -E "\bkeep_data\b" -q`
- if [[ "$?" == "0" ]]; then
- return
- fi
- docker create -v /keep-data --name keep_data arvados/keep
-}
-
-function do_start {
- local start_doc=false
- local start_sso=false
- local start_api=false
- local start_compute=false
- local start_workbench=false
- local start_vm=false
- local start_nameserver=false
- local start_keep=false
- local start_keepproxy=false
- local bridge="docker0"
- local
-
- # NOTE: This requires GNU getopt (part of the util-linux package on Debian-based distros).
- local TEMP=`getopt -o d::s::b:a::cw::nkpvh \
- --long doc::,sso::,api::,bridge:,compute,workbench::,nameserver,keep,keepproxy,vm,help,domain:: \
- -n "$0" -- "$@"`
-
- if [ $? != 0 ] ; then echo "Use -h for help"; exit 1 ; fi
-
- # Note the quotes around `$TEMP': they are essential!
- eval set -- "$TEMP"
-
- while [ $# -ge 1 ]
- do
- case $1 in
- -b | --bridge)
- case "$2" in
- *) start_bridge=$2; shift 2 ;;
- esac
- ;;
- -d | --doc)
- case "$2" in
- "") start_doc=9898; shift 2 ;;
- *) start_doc=$2; shift 2 ;;
- esac
- ;;
- -s | --sso)
- case "$2" in
- "") start_sso=9901; shift 2 ;;
- *) start_sso=$2; shift 2 ;;
- esac
- ;;
- -a | --api)
- case "$2" in
- "") start_api=9900; shift 2 ;;
- *) start_api=$2; shift 2 ;;
- esac
- ;;
- -c | --compute)
- start_compute=2
- shift
- ;;
- -w | --workbench)
- case "$2" in
- "") start_workbench=9899; shift 2 ;;
- *) start_workbench=$2; shift 2 ;;
- esac
- ;;
- -v | --vm)
- start_vm=true
- shift
- ;;
- -n | --nameserver)
- start_nameserver=true
- shift
- ;;
- -k | --keep)
- start_keep=true
- shift
- ;;
- -p | --keepproxy)
- start_keepproxy=true
- shift
- ;;
- --domain)
- case "$2" in
- *) ARVADOS_DOMAIN="$2"; shift 2 ;;
- esac
- ;;
- --)
- shift
- break
- ;;
- *)
- usage
- exit 1
- ;;
- esac
- done
-
- # If no options were selected, then start all servers.
- if [[ $start_doc == false &&
- $start_sso == false &&
- $start_api == false &&
- $start_compute == false &&
- $start_workbench == false &&
- $start_vm == false &&
- $start_nameserver == false &&
- $start_keep == false &&
- $start_keepproxy == false ]]
- then
- start_doc=9898
- start_sso=9901
- start_api=9900
- start_compute=2
- start_workbench=9899
- #start_vm=true
- start_nameserver=true
- start_keep=true
- start_keepproxy=true
- fi
-
- if [[ $start_nameserver != false ]]
- then
- $DOCKER ps | grep skydns >/dev/null
- need_skydns="$?"
-
- $DOCKER ps | grep skydock >/dev/null
- need_skydock="$?"
-
- if [[ "$need_skydns" != 0 || "$need_skydock" != 0 ]]
- then
- # skydns and skydock need to both be running before everything else.
- # If they are not running we need to shut everything down and start
- # over, otherwise DNS will be broken and the containers won't find each other.
- do_stop
- need_skydns=1
- need_skydock=1
- fi
-
- # We rely on skydock and skydns for dns discovery between the slurm controller and compute nodes,
- # so make sure they are running
- $DOCKER ps | grep skydns >/dev/null
- if [[ $need_skydns != "0" ]]; then
- echo "Detecting bridge '$bridge' IP for crosbymichael/skydns"
- bridge_ip=$(bridge_ip_address "$bridge")
-
- echo "Starting crosbymichael/skydns container..."
- $DOCKER rm "skydns" 2>/dev/null
- echo $DOCKER run -d -p $bridge_ip:53:53/udp --name skydns crosbymichael/skydns -nameserver 8.8.8.8:53 -domain arvados
- $DOCKER run -d -p $bridge_ip:53:53/udp --name skydns crosbymichael/skydns -nameserver 8.8.8.8:53 -domain arvados
- fi
- $DOCKER ps | grep skydock >/dev/null
- if [[ "$need_skydock" != "0" ]]; then
- echo "Starting crosbymichael/skydock container..."
- $DOCKER rm "skydock" 2>/dev/null
- echo $DOCKER run -d -v /var/run/docker.sock:/docker.sock --name skydock crosbymichael/skydock -ttl 30 -environment dev -s /docker.sock -domain arvados -name skydns
- $DOCKER run -d -v /var/run/docker.sock:/docker.sock --name skydock crosbymichael/skydock -ttl 30 -environment dev -s /docker.sock -domain arvados -name skydns
- fi
- fi
-
- if [[ $start_sso != false ]]
- then
- start_container "$start_sso:443" "sso_server" '' '' "arvados/sso"
- fi
-
- if [[ $start_api != false ]]
- then
- if [[ $start_sso != false ]]; then
- start_container "$start_api:443" "api_server" '' "sso_server:sso" "arvados/api"
- else
- start_container "$start_api:443" "api_server" '' '' "arvados/api"
- fi
- fi
-
- if [[ $start_compute != false ]]
- then
- for i in `seq 0 $(($start_compute - 1))`; do
- start_container "" "compute" '' "api_server:api" "arvados/compute"
- done
- fi
-
- if [[ $start_keep != false ]]
- then
- # create `keep_volumes' array with a list of keep mount points
- # remove any stale metadata from those volumes before starting them
- make_keep_volumes
- start_container "25107:25107" "keep_server_0" \
- "keep_data" \
- "api_server:api" \
- "arvados/keep"
- start_container "25108:25107" "keep_server_1" \
- "keep_data" \
- "api_server:api" \
- "arvados/keep"
- fi
-
- if [[ $start_keepproxy != false ]]
- then
- start_container "9902:9100" "keepproxy_server" '' \
- "api_server:api" \
- "arvados/keepproxy"
- fi
-
- if [[ $start_doc != false ]]
- then
- start_container "$start_doc:80" "doc_server" '' '' "arvados/doc"
- fi
-
- if [[ $start_vm != false ]]
- then
- start_container "" "shell" '' "api_server:api" "arvados/shell"
- fi
-
- if [[ $start_workbench != false ]]
- then
- start_container "" "workbench_server" '' "" "arvados/workbench"
- fi
-
- if [[ $start_api != false ]]
- then
- if [[ -f "api/generated/superuser_token" ]]
- then
- if [ -d $HOME/.config/arvados ] || mkdir -p $HOME/.config/arvados
- then
- cat >$HOME/.config/arvados/settings.conf <<EOF
-ARVADOS_API_HOST=$(ip_address "api_server")
-ARVADOS_API_HOST_INSECURE=yes
-ARVADOS_API_TOKEN=$(cat api/generated/superuser_token)
-EOF
- fi
- fi
- fi
-
- if [ "$(awk '($1 == "nameserver"){print $2; exit}' </etc/resolv.conf)" != "$bridge_ip" ]; then
- echo
- echo "******************************************************************"
- echo "To access Arvados you must add the Arvados nameserver to the top"
- echo "of your DNS configuration in /etc/resolv.conf:"
- echo "nameserver $bridge_ip"
- echo
- echo "Then run '$0 start' again"
- echo "******************************************************************"
- echo
- else
- while ! $CURL -k -L -f http://workbench.$ARVADOS_DOMAIN >/dev/null 2>/dev/null ; do
- echo "Waiting for Arvados to be ready."
- sleep 1
- done
-
- `$DOCKER ps |grep -E "\bdoc_server\b" -q`
- if [[ "$?" == "0" ]]; then
- echo
- echo "******************************************************************"
- echo "You can access the Arvados documentation at http://doc.$ARVADOS_DOMAIN"
- echo "******************************************************************"
- echo
- fi
-
- `$DOCKER ps |grep -E "\bworkbench_server\b" -q`
- if [[ "$?" == "0" ]]; then
- echo
- echo "********************************************************************"
- echo "You can access the Arvados workbench at http://workbench.$ARVADOS_DOMAIN"
- echo "********************************************************************"
- echo
- fi
- fi
-
-}
-
-function do_stop {
- local stop_doc=""
- local stop_sso=""
- local stop_api=""
- local stop_compute=""
- local stop_workbench=""
- local stop_nameserver=""
- local stop_vm=""
- local stop_keep=""
- local stop_keepproxy=""
-
- # NOTE: This requires GNU getopt (part of the util-linux package on Debian-based distros).
- local TEMP=`getopt -o dsacwnkpvh \
- --long doc,sso,api,compute,workbench,nameserver,keep,keepproxy,vm,help,domain:: \
- -n "$0" -- "$@"`
-
- if [ $? != 0 ] ; then echo "Use -h for help"; exit 1 ; fi
-
- # Note the quotes around `$TEMP': they are essential!
- eval set -- "$TEMP"
-
- while [ $# -ge 1 ]
- do
- case $1 in
- -d | --doc)
- stop_doc=doc_server ; shift ;;
- -s | --sso)
- stop_sso=sso_server ; shift ;;
- -a | --api)
- stop_api=api_server ; shift ;;
- -c | --compute)
- stop_compute=`$DOCKER ps |grep -E "\bcompute[0-9]+\b" |grep -v api_server |cut -f1 -d ' '` ; shift ;;
- -w | --workbench)
- stop_workbench=workbench_server ; shift ;;
- -n | --nameserver )
- stop_nameserver="skydock skydns" ; shift ;;
- -v | --vm )
- stop_vm="shell" ; shift ;;
- -k | --keep )
- stop_keep="keep_server_0 keep_server_1" ; shift ;;
- -p | --keepproxy )
- stop_keep="keepproxy_server" ; shift ;;
- --domain)
- case "$2" in
- *) ARVADOS_DOMAIN="$2"; shift 2 ;;
- esac
- ;;
- --)
- shift
- break
- ;;
- *)
- usage
- exit 1
- ;;
- esac
- done
-
- # If no options were selected, then stop all servers.
- if [[ $stop_doc == "" &&
- $stop_sso == "" &&
- $stop_api == "" &&
- $stop_compute == "" &&
- $stop_workbench == "" &&
- $stop_vm == "" &&
- $stop_nameserver == "" &&
- $stop_keep == "" &&
- $stop_keepproxy == "" ]]
- then
- stop_doc=doc_server
- stop_sso=sso_server
- stop_api=api_server
- stop_compute=`$DOCKER ps |grep -E "\bcompute[0-9]+\b" |grep -v api_server |cut -f1 -d ' '`
- stop_workbench=workbench_server
- stop_vm=shell
- stop_nameserver="skydock skydns"
- stop_keep="keep_server_0 keep_server_1"
- stop_keepproxy="keepproxy_server"
- fi
-
- $DOCKER stop $stop_doc $stop_sso $stop_api $stop_compute $stop_workbench $stop_nameserver $stop_keep $stop_keepproxy $stop_vm \
- 2>/dev/null
-}
-
-function do_test {
- local alltests
- if [ $# -lt 1 ]
- then
- alltests="python-sdk api"
- else
- alltests="$@"
- fi
-
- for testname in $alltests
- do
- echo "testing $testname..."
- case $testname in
- python-sdk)
- do_start --api --keep --sso
- export ARVADOS_API_HOST=$(ip_address "api_server")
- export ARVADOS_API_HOST_INSECURE=yes
- export ARVADOS_API_TOKEN=$(cat api/generated/superuser_token)
- python -m unittest discover ../sdk/python
- ;;
- api)
- $DOCKER run -t -i arvados/api \
- /usr/src/arvados/services/api/script/rake_test.sh
- ;;
- *)
- echo >&2 "unknown test $testname"
- ;;
- esac
- done
-}
-
-function do_reset {
- for name in skydock skydns workbench_server shell doc_server keepproxy_server keep_server_0 keep_server_1 compute0 compute1 api_server keepproxy keep_data sso_server
- do
- `$DOCKER ps |grep -E "\b$name\b" -q`
- if [[ "$?" == "0" ]]; then
- echo " $DOCKER stop $name"
- $DOCKER stop $name
- fi
- `$DOCKER ps --all |grep -E "\b$name\b" -q`
- if [[ "$?" == "0" ]]; then
- echo " $DOCKER rm $name"
- $DOCKER rm $name
- fi
- done
-}
-
-if [ "$DOCKER" == '' ]
-then
- echo "Docker not found. Please install it first."
- exit 2
-fi
-
-if [ "$CURL" == '' ]
-then
- echo "Curl not found. Please install it first."
- exit 3
-fi
-
-if [ $# -lt 1 ]
-then
- usage
- exit 1
-fi
-
-case $1 in
- start)
- shift
- do_start $@
- ;;
- stop)
- shift
- do_stop $@
- ;;
- restart)
- shift
- do_stop $@
- do_start $@
- ;;
- test)
- shift
- do_test $@
- ;;
- reset)
- shift
- do_reset $@
- ;;
- *)
- usage
- exit 1
- ;;
-esac
diff --git a/docker/base/Dockerfile b/docker/base/Dockerfile
deleted file mode 100644
index 5eeabc8..0000000
--- a/docker/base/Dockerfile
+++ /dev/null
@@ -1,43 +0,0 @@
-# Arvados base image (wheezy+rvm+Arvados source) in Docker
-
-# Based on Debian Wheezy
-FROM arvados/debian:wheezy
-MAINTAINER Ward Vandewege <ward at curoverse.com>
-
-ENV DEBIAN_FRONTEND noninteractive
-
-# Install prerequisite packages for Arvados
-# * git, curl, rvm
-# * Arvados source code in /usr/src/arvados, for preseeding gem installation
-
-ADD apt.arvados.org.list /etc/apt/sources.list.d/
-RUN apt-key adv --keyserver pool.sks-keyservers.net --recv 1078ECD7
-RUN apt-get update -q
-
-## 2015-06-29 nico
-## KNOWN BUG: python-oauth2client needs specific versions
-## python-pyasn1=0.1.7 python-pyasn1-modules=0.0.5
-## but apt-get doesn't resolv them correctly. we have to
-## do it by hand here (or add apt_preferences if it gets too hairy)
-RUN apt-get install -qy apt-utils git curl \
- libcurl3 libcurl3-gnutls libcurl4-openssl-dev locales \
- postgresql-server-dev-9.1 python-arvados-python-client \
- python-google-api-python-client python-oauth2client python-pyasn1=0.1.7 python-pyasn1-modules=0.0.5
-
-RUN gpg --keyserver pool.sks-keyservers.net --recv-keys D39DC0E3 && \
- /bin/sed -ri 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && \
- /usr/sbin/locale-gen && \
- curl -L https://get.rvm.io | bash -s stable && \
- /usr/local/rvm/bin/rvm install 2.1 && \
- /usr/local/rvm/bin/rvm alias create default ruby-2.1 && \
- /bin/mkdir -p /usr/src/arvados
-
-ADD generated/arvados.tar.gz /usr/src/arvados/
-
-# Update gem. This (hopefully) fixes
-# https://github.com/rubygems/rubygems.org/issues/613.
-RUN /usr/local/rvm/bin/rvm-exec default gem update --system && \
- /usr/local/rvm/bin/rvm-exec default gem install bundler -v 1.9.9 && \
- /usr/local/rvm/bin/rvm-exec default bundle install --gemfile=/usr/src/arvados/apps/workbench/Gemfile && \
- /usr/local/rvm/bin/rvm-exec default bundle install --gemfile=/usr/src/arvados/services/api/Gemfile && \
- /usr/local/rvm/bin/rvm-exec default bundle install --gemfile=/usr/src/arvados/doc/Gemfile
diff --git a/docker/base/apt.arvados.org.list b/docker/base/apt.arvados.org.list
deleted file mode 100644
index 7eb8716..0000000
--- a/docker/base/apt.arvados.org.list
+++ /dev/null
@@ -1,2 +0,0 @@
-# apt.arvados.org
-deb http://apt.arvados.org/ wheezy main
diff --git a/docker/bcbio-nextgen/Dockerfile b/docker/bcbio-nextgen/Dockerfile
deleted file mode 100644
index 8f6e774..0000000
--- a/docker/bcbio-nextgen/Dockerfile
+++ /dev/null
@@ -1,47 +0,0 @@
-# Install Arvados SDK into bcbio-nextgen Docker image.
-#
-# To build bcbio-nextgen:
-#
-# $ git clone https://github.com/chapmanb/bcbio-nextgen.git
-# $ cd bcbio-nextgen
-# $ docker build
-# $ docker tag <image> bcbio-nextgen
-#
-
-FROM bcbio-nextgen
-MAINTAINER Peter Amstutz <peter.amstutz at curoverse.com>
-
-USER root
-
-# Install Ruby 2.1.0
-RUN apt-get remove --quiet --assume-yes ruby && \
- curl -L https://get.rvm.io | bash -s stable && \
- /usr/local/rvm/bin/rvm install 2.1.0 && \
- /bin/mkdir -p /usr/src/arvados
-
-ADD generated/arvados.tar.gz /usr/src/arvados/
-ENV GEM_HOME /usr/local/rvm/gems/ruby-2.1.0
-ENV GEM_PATH /usr/local/rvm/gems/ruby-2.1.0:/usr/local/rvm/gems/ruby-2.1.0 at global
-ENV PATH /usr/local/rvm/gems/ruby-2.1.0/bin:/usr/local/rvm/gems/ruby-2.1.0 at global/bin:/usr/local/rvm/rubies/ruby-2.1.0/bin:/usr/local/rvm/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
-
-# Install dependencies and set up system.
-# The FUSE packages help ensure that we can install the Python SDK (arv-mount).
-RUN /usr/bin/apt-get update && \
- /usr/bin/apt-get install --quiet --assume-yes python-dev python-llfuse python-pip \
- libio-socket-ssl-perl libjson-perl liburi-perl libwww-perl \
- fuse libattr1-dev libfuse-dev && \
- /usr/sbin/adduser --disabled-password \
- --gecos 'Crunch execution user' crunch && \
- /usr/bin/install --directory --owner=crunch --group=crunch --mode=0700 /keep /tmp/crunch-src /tmp/crunch-job && \
- /bin/ln -s /usr/src/arvados /usr/local/src/arvados
-
-# Install Arvados packages.
-RUN gem update --system && \
- find /usr/src/arvados/sdk -name '*.gem' -print0 | \
- xargs -0rn 1 gem install && \
- cd /usr/src/arvados/services/fuse && \
- python setup.py install && \
- cd /usr/src/arvados/sdk/python && \
- python setup.py install
-
-USER crunch
diff --git a/docker/build.sh b/docker/build.sh
deleted file mode 100755
index 77aeb1f..0000000
--- a/docker/build.sh
+++ /dev/null
@@ -1,41 +0,0 @@
-#! /bin/bash
-
-# make sure a Ruby version greater than or equal to 1.9.3 is installed before proceeding
-if ! ruby -e 'exit RUBY_VERSION >= "1.9.3"' 2>/dev/null
-then
- echo "Building the Arvados docker containers requires at least Ruby 1.9.3."
- echo "Please install ruby 1.9.3 or higher before executing this script."
- exit 1
-fi
-
-function usage {
- echo >&2
- echo >&2 "usage: $0 [options]"
- echo >&2
- echo >&2 "Calling $0 without arguments will build all Arvados docker images"
- echo >&2
- echo >&2 "$0 options:"
- echo >&2 " -h, --help Print this help text"
- echo >&2 " clean Clear all build information"
- echo >&2 " realclean clean and remove all Arvados Docker images except arvados/debian"
- echo >&2 " deepclean realclean and remove arvados/debian, crosbymichael/skydns and "
- echo >&2 " crosbymichael/skydns Docker images"
- echo >&2
-}
-
-if [ "$1" = '-h' ] || [ "$1" = '--help' ]; then
- usage
- exit 1
-fi
-
-build_tools/build.rb
-
-if [[ "$?" == "0" ]]; then
- DOCKER=`which docker.io`
-
- if [[ "$DOCKER" == "" ]]; then
- DOCKER=`which docker`
- fi
-
- DOCKER=$DOCKER /usr/bin/make -f build_tools/Makefile $*
-fi
diff --git a/docker/build_tools/Makefile b/docker/build_tools/Makefile
deleted file mode 100644
index 8a757d0..0000000
--- a/docker/build_tools/Makefile
+++ /dev/null
@@ -1,281 +0,0 @@
-# This is the 'shell hack'. Call make with DUMP=1 to see the effect.
-ifdef DUMP
-OLD_SHELL := $(SHELL)
-SHELL = $(warning [$@])$(OLD_SHELL) -x
-endif
-
-all: skydns-image skydock-image api-image compute-image doc-image workbench-image keep-image keep-proxy-image sso-image shell-image
-
-IMAGE_FILES := $(shell ls *-image 2>/dev/null |grep -v -E 'debian-arvados-image|skydns-image|skydock-image')
-GENERATED_DIRS := $(shell ls */generated 2>/dev/null)
-
-# `make clean' removes the files generated in the build directory
-# but does not remove any docker images generated in previous builds
-clean:
- @echo "make clean"
- - at rm -rf build
- +@[ "$(IMAGE_FILES)" = "" ] || rm -f $(IMAGE_FILES) 2>/dev/null
- +@[ "$(GENERATED_DIRS)" = "" ] || rm -rf */generated 2>/dev/null
-
-DEBIAN_IMAGE := $(shell $(DOCKER) images -q arvados/debian |head -n1)
-
-REALCLEAN_CONTAINERS := $(shell $(DOCKER) ps -a |grep -e arvados -e api_server -e keep_server -e keep_proxy_server -e doc_server -e workbench_server |cut -f 1 -d' ')
-# Generate a list of docker images tagged as arvados/*
-# but exclude those tagged as arvados/build
-ADI_TEMPFILE := $(shell mktemp)
-ARVADOS_DOCKER_IMAGES := $(shell $(DOCKER) images -q arvados/* |sort > $(ADI_TEMPFILE))
-ABDI_TEMPFILE := $(shell mktemp)
-ARVADOS_BUILD_DOCKER_IMAGES := $(shell $(DOCKER) images -q arvados/build |sort > $(ABDI_TEMPFILE))
-REALCLEAN_IMAGES := $(shell comm -3 $(ADI_TEMPFILE) $(ABDI_TEMPFILE) |grep -v $(DEBIAN_IMAGE) 2>/dev/null)
-DEEPCLEAN_IMAGES := $(shell comm -3 $(ADI_TEMPFILE) $(ABDI_TEMPFILE))
-SKYDNS_CONTAINERS := $(shell $(DOCKER) ps -a |grep -e crosbymichael/skydns -e crosbymichael/skydock |cut -f 1 -d' ')
-SKYDNS_IMAGES := $(shell $(DOCKER) images -q crosbymichael/skyd*)
-
-# `make realclean' will also remove the Arvados docker images (but not the
-# arvados/debian image) and force subsequent makes to build the entire chain
-# from the ground up
-realclean: clean
- @echo "make realclean"
- +@[ "`$(DOCKER) ps -q`" = '' ] || $(DOCKER) stop `$(DOCKER) ps -q`
- +@[ "$(REALCLEAN_CONTAINERS)" = '' ] || $(DOCKER) rm $(REALCLEAN_CONTAINERS)
- +@[ "$(REALCLEAN_IMAGES)" = '' ] || $(DOCKER) rmi $(REALCLEAN_IMAGES)
-
-# `make deepclean' will remove all Arvados docker images and the skydns/skydock
-# images and force subsequent makes to build the entire chain from the ground up
-deepclean: clean
- @echo "make deepclean"
- - at rm -f debian-arvados-image 2>/dev/null
- - at rm -f skydns-image skydock-image 2>/dev/null
- +@[ "`$(DOCKER) ps -q`" = '' ] || $(DOCKER) stop `$(DOCKER) ps -q`
- +@[ "$(REALCLEAN_CONTAINERS)" = '' ] || $(DOCKER) rm $(REALCLEAN_CONTAINERS)
- +@[ "$(DEEPCLEAN_IMAGES)" = '' ] || $(DOCKER) rmi $(DEEPCLEAN_IMAGES)
- +@[ "$(SKYDNS_CONTAINERS)" = '' ] || $(DOCKER) rm $(SKYDNS_CONTAINERS)
- +@[ "$(SKYDNS_IMAGES)" = '' ] || $(DOCKER) rmi $(SKYDNS_IMAGES)
-
-# ============================================================
-# Dependencies for */generated files which are prerequisites
-# for building docker images.
-
-CONFIG_RB = build_tools/config.rb
-
-BUILD = build/.buildstamp
-
-BASE_DEPS = base/Dockerfile config.yml $(BASE_GENERATED)
-
-SLURM_DEPS = slurm/Dockerfile config.yml $(SLURM_GENERATED)
-
-JOBS_DEPS = jobs/Dockerfile
-
-ARV_WEB_DEPS = arv-web/Dockerfile arv-web/apache2_foreground.sh arv-web/apache2_vhost
-
-JAVA_BWA_SAMTOOLS_DEPS = java-bwa-samtools/Dockerfile
-
-API_DEPS = api/* config.yml $(API_GENERATED)
-
-SHELL_DEPS = shell/* config.yml $(SHELL_GENERATED)
-
-COMPUTE_DEPS = compute/* config.yml $(COMPUTE_GENERATED)
-
-DOC_DEPS = doc/Dockerfile $(DOC_GENERATED)
-
-WORKBENCH_DEPS = workbench/Dockerfile \
- config.yml \
- $(WORKBENCH_GENERATED)
-
-KEEP_DEPS = keep/Dockerfile config.yml $(KEEP_GENERATED)
-
-KEEP_PROXY_DEPS = keepproxy/Dockerfile config.yml $(KEEP_PROXY_GENERATED)
-
-SSO_DEPS = config.yml $(SSO_GENERATED)
-
-BCBIO_NEXTGEN_DEPS = bcbio-nextgen/Dockerfile
-
-BASE_GENERATED = base/generated/arvados.tar.gz
-
-COMPUTE_GENERATED_IN = compute/*.in
-COMPUTE_GENERATED = compute/generated/*
-
-KEEP_GENERATED_IN = keep/*.in
-KEEP_GENERATED = keep/generated/*
-
-KEEP_PROXY_GENERATED_IN = keepproxy/*.in
-KEEP_PROXY_GENERATED = keepproxy/generated/*
-
-API_GENERATED_IN = api/*.in
-API_GENERATED = api/generated/*
-
-SHELL_GENERATED_IN = shell/*.in
-SHELL_GENERATED = shell/generated/*
-
-SLURM_GENERATED_IN = slurm/*.in
-SLURM_GENERATED = slurm/generated/*
-
-WORKBENCH_GENERATED_IN = workbench/*.in
-WORKBENCH_GENERATED = workbench/generated/*
-
-SSO_GENERATED_IN = sso/*.in
-SSO_GENERATED = sso/generated/*
-
-DOC_GENERATED_IN = doc/*.in
-DOC_GENERATED = doc/generated/*
-
-KEEP_DEPS += keep/generated/bin/keepproxy
-KEEP_DEPS += keep/generated/bin/keepstore
-keep/generated/bin/%: $(wildcard build/services/%/*.go)
- mkdir -p keep/generated/src/git.curoverse.com
- ln -sfn ../../../../.. keep/generated/src/git.curoverse.com/arvados.git
- GOPATH=$(shell pwd)/keep/generated go get $(@:keep/generated/bin/%=git.curoverse.com/arvados.git/services/%)
-
-KEEP_PROXY_DEPS += keepproxy/generated/bin/keepproxy
-keepproxy/generated/bin/%: $(wildcard build/services/%/*.go)
- mkdir -p keepproxy/generated/src/git.curoverse.com
- ln -sfn ../../../../.. keepproxy/generated/src/git.curoverse.com/arvados.git
- GOPATH=$(shell pwd)/keepproxy/generated go get $(@:keepproxy/generated/bin/%=git.curoverse.com/arvados.git/services/%)
-
-$(BUILD):
- mkdir -p build
- rsync -rlp --exclude=docker/ --exclude='**/log/*' --exclude='**/tmp/*' \
- --chmod=Da+rx,Fa+rX ../ build/
- find build/ -name \*.gem -delete
- cd build/services/fuse/ && python setup.py build
- cd build/sdk/python/ && python setup.py build
- cd build/sdk/cli && gem build arvados-cli.gemspec
- cd build/sdk/ruby && gem build arvados.gemspec
- touch build/.buildstamp
-
-$(SLURM_GENERATED): $(BUILD)
- $(CONFIG_RB) slurm
- mkdir -p slurm/generated
-
-$(BASE_GENERATED): $(BUILD)
- $(CONFIG_RB) base
- mkdir -p base/generated
- tar -czf base/generated/arvados.tar.gz -C build .
-
-$(API_GENERATED): $(API_GENERATED_IN)
- $(CONFIG_RB) api
-
-$(SHELL_GENERATED): $(SHELL_GENERATED_IN)
- $(CONFIG_RB) shell
-
-$(WORKBENCH_GENERATED): $(WORKBENCH_GENERATED_IN)
- $(CONFIG_RB) workbench
-
-$(COMPUTE_GENERATED): $(COMPUTE_GENERATED_IN)
- $(CONFIG_RB) compute
-
-$(SSO_GENERATED): $(SSO_GENERATED_IN)
- $(CONFIG_RB) sso
-
-$(DOC_GENERATED): $(DOC_GENERATED_IN)
- $(CONFIG_RB) doc
-
-$(KEEP_GENERATED): $(KEEP_GENERATED_IN)
- $(CONFIG_RB) keep
-
-$(KEEP_PROXY_GENERATED): $(KEEP_PROXY_GENERATED_IN)
- $(CONFIG_RB) keepproxy
-
-DOCKER_BUILD = $(DOCKER) build --rm=true
-
-# ============================================================
-# The main Arvados servers: api, doc, workbench, compute
-
-api-image: passenger-image $(BUILD) $(API_DEPS)
- @echo "Building api-image"
- mkdir -p api/generated
- tar -czf api/generated/api.tar.gz -C build/services api
- $(DOCKER_BUILD) -t arvados/api api
- date >api-image
-
-shell-image: base-image $(BUILD) $(SHELL_DEPS)
- @echo "Building shell-image"
- mkdir -p shell/generated
- $(DOCKER_BUILD) -t arvados/shell shell
- date >shell-image
-
-compute-image: slurm-image $(BUILD) $(COMPUTE_DEPS)
- @echo "Building compute-image"
- $(DOCKER_BUILD) -t arvados/compute compute
- date >compute-image
-
-doc-image: base-image $(BUILD) $(DOC_DEPS)
- @echo "Building doc-image"
- mkdir -p doc/generated
- tar -czf doc/generated/doc.tar.gz -C build doc
- $(DOCKER_BUILD) -t arvados/doc doc
- date >doc-image
-
-keep-image: debian-arvados-image $(BUILD) $(KEEP_DEPS)
- @echo "Building keep-image"
- $(DOCKER_BUILD) -t arvados/keep keep
- date >keep-image
-
-keep-proxy-image: debian-arvados-image $(BUILD) $(KEEP_PROXY_DEPS)
- @echo "Building keep-proxy-image"
- $(DOCKER_BUILD) -t arvados/keepproxy keepproxy
- date >keep-proxy-image
-
-jobs-image: debian-arvados-image $(BUILD) $(JOBS_DEPS)
- $(DOCKER_BUILD) --build-arg COMMIT=$(COMMIT) -t arvados/jobs jobs
- date >jobs-image
-
-java-bwa-samtools-image: jobs-image $(BUILD) $(JAVA_BWA_SAMTOOLS_DEPS)
- $(DOCKER_BUILD) -t arvados/jobs-java-bwa-samtools java-bwa-samtools
- date >java-bwa-samtools-image
-
-bcbio-nextgen-image: $(BUILD) $(BASE_GENERATED) $(BCBIO_NEXTGEN_DEPS)
- rm -rf bcbio-nextgen/generated
- cp -r base/generated bcbio-nextgen
- $(DOCKER_BUILD) -t arvados/bcbio-nextgen bcbio-nextgen
- date >bcbio-nextgen-image
-
-workbench-image: passenger-image $(BUILD) $(WORKBENCH_DEPS)
- @echo "Building workbench-image"
- mkdir -p workbench/generated
- tar -czf workbench/generated/workbench.tar.gz -C build/apps workbench
- $(DOCKER_BUILD) -t arvados/workbench workbench
- date >workbench-image
-
-sso-image: passenger-image $(SSO_DEPS)
- @echo "Building sso-image"
- $(DOCKER_BUILD) -t arvados/sso sso
- date >sso-image
-
-arv-web-image: passenger-image $(ARV_WEB_DEPS)
- $(DOCKER_BUILD) -t arvados/arv-web arv-web
- date >arv-web-image
-
-# ============================================================
-# The arvados/base image is the base Debian image plus packages
-# that are dependencies for every Arvados service.
-
-passenger-image: base-image
- @echo "Building passenger-image"
- $(DOCKER_BUILD) -t arvados/passenger passenger
- date >passenger-image
-
-slurm-image: base-image $(SLURM_DEPS)
- @echo "Building slurm-image"
- $(DOCKER_BUILD) -t arvados/slurm slurm
- date >slurm-image
-
-base-image: debian-arvados-image $(BASE_DEPS)
- @echo "Building base-image"
- $(DOCKER_BUILD) -t arvados/base base
- date >base-image
-
-debian-arvados-image:
- @echo "Building debian-arvados-image"
- ./mkimage-debootstrap.sh arvados/debian wheezy http://ftp.us.debian.org/debian/
- date >debian-arvados-image
-
-skydns-image:
- @echo "Downloading skydns-image"
- $(DOCKER) pull crosbymichael/skydns
- date >skydns-image
-
-skydock-image:
- @echo "Downloading skydock-image"
- $(DOCKER) pull crosbymichael/skydock
- date >skydock-image
diff --git a/docker/build_tools/build.rb b/docker/build_tools/build.rb
deleted file mode 100755
index e3309a9..0000000
--- a/docker/build_tools/build.rb
+++ /dev/null
@@ -1,232 +0,0 @@
-#! /usr/bin/env ruby
-
-require 'optparse'
-require 'tempfile'
-require 'yaml'
-
-def main options
- if not ip_forwarding_enabled?
- warn "NOTE: IP forwarding must be enabled in the kernel."
- warn "Turning IP forwarding on now."
- sudo %w(/sbin/sysctl net.ipv4.ip_forward=1)
- end
-
- # Check that:
- # * Docker is installed and can be found in the user's path
- # * Docker can be run as a non-root user
- # - TODO: put the user in the docker group if necessary
- # - TODO: mount cgroup automatically
- # - TODO: start the docker service if not started
-
- docker_path = %x(which docker.io).chomp
-
- if docker_path.empty?
- docker_path = %x(which docker).chomp
- end
-
- if docker_path.empty?
- warn "Docker not found."
- warn ""
- warn "Please make sure that Docker has been installed and"
- warn "can be found in your PATH."
- warn ""
- warn "Installation instructions for a variety of platforms can be found at"
- warn "http://docs.docker.io/en/latest/installation/"
- exit 1
- elsif not docker_ok? docker_path
- warn "WARNING: docker could not be run."
- warn "Please make sure that:"
- warn " * You have permission to read and write /var/run/docker.sock"
- warn " * a 'cgroup' volume is mounted on your machine"
- warn " * the docker daemon is running"
- exit 2
- end
-
- # Check that debootstrap is installed.
- if not debootstrap_ok?
- warn "Installing debootstrap."
- sudo '/usr/bin/apt-get', 'install', 'debootstrap'
- end
-
- # Generate a config.yml if it does not exist or is empty
- if not File.size? 'config.yml'
- print "Generating config.yml.\n"
- # print "Arvados needs to know the email address of the administrative user,\n"
- # print "so that when that user logs in they are automatically made an admin.\n"
- # print "This should be an email address associated with a Google account.\n"
- # print "\n"
- # admin_email_address = ""
- # until is_valid_email? admin_email_address
- # print "Enter your Google ID email address here: "
- # admin_email_address = gets.strip
- # if not is_valid_email? admin_email_address
- # print "That doesn't look like a valid email address. Please try again.\n"
- # end
- # end
-
- # print "Arvados needs to know the shell login name for the administrative user.\n"
- # print "This will also be used as the name for your git repository.\n"
- # print "\n"
- # user_name = ""
- # until is_valid_user_name? user_name
- # print "Enter a shell login name here: "
- # user_name = gets.strip
- # if not is_valid_user_name? user_name
- # print "That doesn't look like a valid shell login name. Please try again.\n"
- # end
- # end
-
- File.open 'config.yml', 'w' do |config_out|
- config_out.write "# If a _PW or _SECRET variable is set to an empty string, a password\n"
- config_out.write "# will be chosen randomly at build time. This is the\n"
- config_out.write "# recommended setting.\n\n"
- config = YAML.load_file 'config.yml.example'
- #config['API_AUTO_ADMIN_USER'] = admin_email_address
- #config['ARVADOS_USER_NAME'] = user_name
- config['API_HOSTNAME'] = generate_api_hostname
- config['API_WORKBENCH_ADDRESS'] = 'false'
- config.each_key do |var|
- config_out.write "#{var}: #{config[var]}\n"
- end
- end
- end
-
- # If all prerequisites are met, go ahead and build.
- if ip_forwarding_enabled? and
- docker_ok? docker_path and
- debootstrap_ok? and
- File.exists? 'config.yml'
- exit 0
- else
- exit 6
- end
-end
-
-# sudo
-# Execute the arg list 'cmd' under sudo.
-# cmd can be passed either as a series of arguments or as a
-# single argument consisting of a list, e.g.:
-# sudo 'apt-get', 'update'
-# sudo(['/usr/bin/gpasswd', '-a', ENV['USER'], 'docker'])
-# sudo %w(/usr/bin/apt-get install lxc-docker)
-#
-def sudo(*cmd)
- # user can pass a single list in as an argument
- # to allow usage like: sudo %w(apt-get install foo)
- warn "You may need to enter your password here."
- if cmd.length == 1 and cmd[0].class == Array
- cmd = cmd[0]
- end
- system '/usr/bin/sudo', *cmd
-end
-
-# is_valid_email?
-# Returns true if its arg looks like a valid email address.
-# This is a very very loose sanity check.
-#
-def is_valid_email? str
- str.match /^\S+@\S+\.\S+$/
-end
-
-# is_valid_user_name?
-# Returns true if its arg looks like a valid unix username.
-# This is a very very loose sanity check.
-#
-def is_valid_user_name? str
- # borrowed from Debian's adduser (version 3.110)
- str.match /^[_.A-Za-z0-9][-\@_.A-Za-z0-9]*\$?$/
-end
-
-# generate_api_hostname
-# Generates a 5-character randomly chosen API hostname.
-#
-def generate_api_hostname
- rand(2**256).to_s(36)[0...5]
-end
-
-# ip_forwarding_enabled?
-# Returns 'true' if IP forwarding is enabled in the kernel
-#
-def ip_forwarding_enabled?
- %x(/sbin/sysctl -n net.ipv4.ip_forward) == "1\n"
-end
-
-# debootstrap_ok?
-# Returns 'true' if debootstrap is installed and working.
-#
-def debootstrap_ok?
- return system '/usr/sbin/debootstrap --version > /dev/null 2>&1'
-end
-
-# docker_ok?
-# Returns 'true' if docker can be run as the current user.
-#
-def docker_ok?(docker_path)
- return system "#{docker_path} images > /dev/null 2>&1"
-end
-
-# install_docker
-# Determines which Docker package is suitable for this Linux distro
-# and installs it, resolving any dependencies.
-# NOTE: not in use yet.
-
-def install_docker
- linux_distro = %x(lsb_release --id).split.last
- linux_release = %x(lsb_release --release).split.last
- linux_version = linux_distro + " " + linux_release
- kernel_release = `uname -r`
-
- case linux_distro
- when 'Ubuntu'
- if not linux_release.match '^1[234]\.'
- warn "Arvados requires at least Ubuntu 12.04 (Precise Pangolin)."
- warn "Your system is Ubuntu #{linux_release}."
- exit 3
- end
- if linux_release.match '^12' and kernel_release.start_with? '3.2'
- # Ubuntu Precise ships with a 3.2 kernel and must be upgraded.
- warn "Your kernel #{kernel_release} must be upgraded to run Docker."
- warn "To do this:"
- warn " sudo apt-get update"
- warn " sudo apt-get install linux-image-generic-lts-raring linux-headers-generic-lts-raring"
- warn " sudo reboot"
- exit 4
- else
- # install AUFS
- sudo 'apt-get', 'update'
- sudo 'apt-get', 'install', "linux-image-extra-#{kernel_release}"
- end
-
- # add Docker repository
- sudo %w(/usr/bin/apt-key adv
- --keyserver keyserver.ubuntu.com
- --recv-keys 36A1D7869245C8950F966E92D8576A8BA88D21E9)
- source_file = Tempfile.new('arv')
- source_file.write("deb http://get.docker.io/ubuntu docker main\n")
- source_file.close
- sudo '/bin/mv', source_file.path, '/etc/apt/sources.list.d/docker.list'
- sudo %w(/usr/bin/apt-get update)
- sudo %w(/usr/bin/apt-get install lxc-docker)
-
- # Set up for non-root access
- sudo %w(/usr/sbin/groupadd docker)
- sudo '/usr/bin/gpasswd', '-a', ENV['USER'], 'docker'
- sudo %w(/usr/sbin/service docker restart)
- when 'Debian'
- else
- warn "Must be running a Debian or Ubuntu release in order to run Docker."
- exit 5
- end
-end
-
-
-if __FILE__ == $PROGRAM_NAME
- options = { :makefile => File.join(File.dirname(__FILE__), 'Makefile') }
- OptionParser.new do |opts|
- opts.on('-m', '--makefile MAKEFILE-PATH',
- 'Path to the Makefile used to build Arvados Docker images') do |mk|
- options[:makefile] = mk
- end
- end
- main options
-end
diff --git a/docker/build_tools/config.rb b/docker/build_tools/config.rb
deleted file mode 100755
index 296bc20..0000000
--- a/docker/build_tools/config.rb
+++ /dev/null
@@ -1,74 +0,0 @@
-#! /usr/bin/env ruby
-
-require 'yaml'
-require 'fileutils'
-require 'digest'
-
-abort 'Error: Ruby >= 1.9.3 required.' if RUBY_VERSION < '1.9.3'
-
-# Initialize config settings from config.yml
-config = YAML.load_file('config.yml')
-
-# ============================================================
-# Add dynamically chosen config settings. These settings should
-# be suitable for any installation.
-
-# Any _PW/_SECRET config settings represent passwords/secrets. If they
-# are blank, choose a password. Make sure the generated password
-# doesn't change if config.yml doesn't change. Otherwise, keys won't
-# match any more if (say) keep's files get regenerated but apiserver's
-# don't.
-config.sort.map do |var,val|
- if (var.end_with?('_PW') || var.end_with?('_SECRET')) && (config[var].nil? || config[var].empty?)
- config[var] = Digest::SHA1.hexdigest(`hostname` + var + config.to_yaml)
- end
-end
-
-# ============================================================
-# For each *.in file in the docker directories, substitute any
-# @@variables@@ found in the file with the appropriate config
-# variable. Support up to 10 levels of nesting.
-#
-# TODO(twp): add the *.in files directory to the source tree, and
-# when expanding them, add them to the "generated" directory with
-# the same tree structure as in the original source. Then all
-# the files can be added to the docker container with a single ADD.
-
-if ARGV[0] and ARGV[0].length > 0
- globdir = ARGV[0]
-else
- globdir = '*'
-end
-
-FileUtils.rm_r Dir.glob(globdir + '/generated/*')
-
-File.umask(022)
-Dir.glob(globdir + '/*.in') do |template_file|
- generated_dir = File.join(File.dirname(template_file), 'generated')
- Dir.mkdir(generated_dir) unless Dir.exists? generated_dir
- output_path = File.join(generated_dir, File.basename(template_file, '.in'))
- output_mode = (File.stat(template_file).mode & 0100) ? 0755 : 0644
- File.open(output_path, "w", output_mode) do |output|
- File.open(template_file) do |input|
- input.each_line do |line|
-
- # This count is used to short-circuit potential
- # infinite loops of variable substitution.
- @count = 0
- while @count < 10
- @out = line.gsub!(/@@(.*?)@@/) do |var|
- if config.key?(Regexp.last_match[1])
- config[Regexp.last_match[1]]
- else
- var.gsub!(/@@/, '@_NOT_FOUND_@')
- end
- end
- break if @out.nil?
- @count += 1
- end
-
- output.write(line)
- end
- end
- end
-end
diff --git a/docker/compute/Dockerfile b/docker/compute/Dockerfile
deleted file mode 100644
index 60b5fa4..0000000
--- a/docker/compute/Dockerfile
+++ /dev/null
@@ -1,29 +0,0 @@
-# Arvados compute node Docker container.
-
-FROM arvados/slurm
-MAINTAINER Ward Vandewege <ward at curoverse.com>
-
-RUN apt-get update -q
-## 20150915 nico -- fuse.postint has sporatic failures, spliting this up to see if it helps
-RUN apt-get install -qy fuse
-RUN apt-get install -qy supervisor python-pip python-gflags python-google-api-python-client python-virtualenv libattr1-dev libfuse-dev python-dev python-llfuse crunchstat python-arvados-fuse cron dnsmasq
-
-ADD fuse.conf /etc/fuse.conf
-RUN chmod 644 /etc/fuse.conf
-
-RUN /usr/local/rvm/bin/rvm-exec default gem install arvados-cli arvados
-
-# Install Docker from the Arvados package repository (cf. arvados/base)
-RUN apt-get install -qy iptables ca-certificates lxc apt-transport-https docker.io
-
-RUN addgroup --gid 4005 crunch && mkdir /home/crunch && useradd --uid 4005 --gid 4005 crunch && usermod crunch -G fuse,docker && chown crunch:crunch /home/crunch
-
-# Supervisor.
-ADD supervisor.conf /etc/supervisor/conf.d/arvados.conf
-ADD generated/setup.sh /usr/local/bin/setup.sh
-ADD wrapdocker /usr/local/bin/wrapdocker.sh
-ADD munge.sh /usr/local/bin/munge.sh
-
-VOLUME /var/lib/docker
-# Start the supervisor.
-CMD ["/usr/bin/supervisord", "-n"]
diff --git a/docker/compute/fuse.conf b/docker/compute/fuse.conf
deleted file mode 100644
index 4ed21ba..0000000
--- a/docker/compute/fuse.conf
+++ /dev/null
@@ -1,10 +0,0 @@
-# Set the maximum number of FUSE mounts allowed to non-root users.
-# The default is 1000.
-#
-#mount_max = 1000
-
-# Allow non-root users to specify the 'allow_other' or 'allow_root'
-# mount options.
-#
-user_allow_other
-
diff --git a/docker/compute/munge.sh b/docker/compute/munge.sh
deleted file mode 100755
index ef10d01..0000000
--- a/docker/compute/munge.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/sh
-rm -rf /var/run/munge
-exec /etc/init.d/munge start
diff --git a/docker/compute/setup.sh.in b/docker/compute/setup.sh.in
deleted file mode 100755
index efb2c41..0000000
--- a/docker/compute/setup.sh.in
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/bin/bash
-
-. /etc/profile.d/rvm.sh
-
-export ARVADOS_API_HOST=api
-export ARVADOS_API_HOST_INSECURE=yes
-export ARVADOS_API_TOKEN=@@API_SUPERUSER_SECRET@@
-export HOME=/root
-
-# Wait for API server to come up.
-while ! arv user current ; do sleep 1 ; done
-
-if ! test -f /root/node.json ; then
- arv node create --node "{\"hostname\": \"$(hostname)\"}" > /root/node.json
-
- # Make sure /dev/fuse permissions are correct (the device appears after fuse is loaded)
- chmod 1660 /dev/fuse && chgrp fuse /dev/fuse
-fi
-
-UUID=`grep \"uuid\" /root/node.json |cut -f4 -d\"`
-PING_SECRET=`grep \"ping_secret\" /root/node.json |cut -f4 -d\"`
-
-if ! test -f /etc/cron.d/node_ping ; then
- echo "*/5 * * * * root /usr/bin/curl -k -d ping_secret=$PING_SECRET https://api/arvados/v1/nodes/$UUID/ping" > /etc/cron.d/node_ping
-fi
-
-/usr/bin/curl -k -d ping_secret=$PING_SECRET https://api/arvados/v1/nodes/$UUID/ping?ping_secret=$PING_SECRET
diff --git a/docker/compute/supervisor.conf b/docker/compute/supervisor.conf
deleted file mode 100644
index b3c715b..0000000
--- a/docker/compute/supervisor.conf
+++ /dev/null
@@ -1,28 +0,0 @@
-[program:munge]
-user=root
-command=/usr/local/bin/munge.sh
-startsecs=0
-
-[program:slurm]
-user=root
-command=/etc/init.d/slurm-llnl start
-startsecs=0
-
-[program:cron]
-user=root
-command=/etc/init.d/cron start
-startsecs=0
-
-[program:setup]
-user=root
-command=/usr/local/bin/setup.sh
-startsecs=0
-
-[program:docker]
-user=root
-command=/usr/local/bin/wrapdocker.sh
-
-[program:dnsmasq]
-user=root
-command=/etc/init.d/dnsmasq start
-startsecs=0
diff --git a/docker/compute/wrapdocker b/docker/compute/wrapdocker
deleted file mode 100755
index cee1302..0000000
--- a/docker/compute/wrapdocker
+++ /dev/null
@@ -1,90 +0,0 @@
-#!/bin/bash
-
-# Borrowed from https://github.com/jpetazzo/dind under Apache2
-# and slightly modified.
-
-# First, make sure that cgroups are mounted correctly.
-CGROUP=/sys/fs/cgroup
-: {LOG:=stdio}
-
-[ -d $CGROUP ] ||
- mkdir $CGROUP
-
-mountpoint -q $CGROUP ||
- mount -n -t tmpfs -o uid=0,gid=0,mode=0755 cgroup $CGROUP || {
- echo "Could not make a tmpfs mount. Did you use -privileged?"
- exit 1
- }
-
-if [ -d /sys/kernel/security ] && ! mountpoint -q /sys/kernel/security
-then
- mount -t securityfs none /sys/kernel/security || {
- echo "Could not mount /sys/kernel/security."
- echo "AppArmor detection and -privileged mode might break."
- }
-fi
-
-# Mount the cgroup hierarchies exactly as they are in the parent system.
-for SUBSYS in $(cut -d: -f2 /proc/1/cgroup)
-do
- [ -d $CGROUP/$SUBSYS ] || mkdir $CGROUP/$SUBSYS
- mountpoint -q $CGROUP/$SUBSYS ||
- mount -n -t cgroup -o $SUBSYS cgroup $CGROUP/$SUBSYS
-
- # The two following sections address a bug which manifests itself
- # by a cryptic "lxc-start: no ns_cgroup option specified" when
- # trying to start containers withina container.
- # The bug seems to appear when the cgroup hierarchies are not
- # mounted on the exact same directories in the host, and in the
- # container.
-
- # Named, control-less cgroups are mounted with "-o name=foo"
- # (and appear as such under /proc/<pid>/cgroup) but are usually
- # mounted on a directory named "foo" (without the "name=" prefix).
- # Systemd and OpenRC (and possibly others) both create such a
- # cgroup. To avoid the aforementioned bug, we symlink "foo" to
- # "name=foo". This shouldn't have any adverse effect.
- echo $SUBSYS | grep -q ^name= && {
- NAME=$(echo $SUBSYS | sed s/^name=//)
- ln -s $SUBSYS $CGROUP/$NAME
- }
-
- # Likewise, on at least one system, it has been reported that
- # systemd would mount the CPU and CPU accounting controllers
- # (respectively "cpu" and "cpuacct") with "-o cpuacct,cpu"
- # but on a directory called "cpu,cpuacct" (note the inversion
- # in the order of the groups). This tries to work around it.
- [ $SUBSYS = cpuacct,cpu ] && ln -s $SUBSYS $CGROUP/cpu,cpuacct
-done
-
-# Note: as I write those lines, the LXC userland tools cannot setup
-# a "sub-container" properly if the "devices" cgroup is not in its
-# own hierarchy. Let's detect this and issue a warning.
-grep -q :devices: /proc/1/cgroup ||
- echo "WARNING: the 'devices' cgroup should be in its own hierarchy."
-grep -qw devices /proc/1/cgroup ||
- echo "WARNING: it looks like the 'devices' cgroup is not mounted."
-
-# Now, close extraneous file descriptors.
-pushd /proc/self/fd >/dev/null
-for FD in *
-do
- case "$FD" in
- # Keep stdin/stdout/stderr
- [012])
- ;;
- # Nuke everything else
- *)
- eval exec "$FD>&-"
- ;;
- esac
-done
-popd >/dev/null
-
-
-# If a pidfile is still around (for example after a container restart),
-# delete it so that docker can start.
-rm -rf /var/run/docker.pid
-
-exec docker -d
-
diff --git a/docker/config.yml.example b/docker/config.yml.example
deleted file mode 100644
index f40c0fe..0000000
--- a/docker/config.yml.example
+++ /dev/null
@@ -1,91 +0,0 @@
-# Configuration for the Rails databases (database names,
-# usernames and passwords).
-
-# Username for your Arvados user. This will be used as your shell login name
-# as well as the name for your git repository.
-ARVADOS_USER_NAME:
-
-# ARVADOS_DOMAIN: the Internet domain of this installation.
-# ARVADOS_DNS_SERVER: the authoritative nameserver for ARVADOS_DOMAIN.
-ARVADOS_DOMAIN: dev.arvados
-ARVADOS_DNS_SERVER: # e.g. 192.168.0.1
-
-# ==============================
-# API server settings
-# ==============================
-
-# The API server hostname. Must be a 5-character
-# string unique within this installation. This string
-# will also be used as config.uuid_prefix.
-API_HOSTNAME: # e.g. qr1hi
-
-# The e-mail address of the user you would like to become marked as an admin
-# user on their first login.
-# In the default configuration, authentication happens through the Arvados SSO
-# server, which uses openid against Google's servers, so in that case this
-# should be an address associated with a Google account.
-API_AUTO_ADMIN_USER:
-
-# The location of the Workbench application where users should be
-# redirected if they point their browsers at the API server, e.g.,
-# https://localhost:9899
-API_WORKBENCH_ADDRESS:
-
-# If a _PW variable is set to an empty string, a password
-# will be chosen randomly at build time. This is the
-# recommended setting.
-ARVADOS_DEV_DB: arvados_development
-ARVADOS_DEV_USER: arvados_dev
-ARVADOS_DEV_PW:
-ARVADOS_TEST_DB: arvados_test
-ARVADOS_TEST_USER: arvados_test
-ARVADOS_TEST_PW:
-ARVADOS_PROD_DB: arvados_production
-ARVADOS_PROD_USER: arvados_prod
-ARVADOS_PROD_PW:
-
-# If a _SECRET variable is set to an empty string, a password
-# will be chosen randomly at build time. This is the
-# recommended setting.
-
-# The signing key shared by Keep at the API server to verify
-# blob permission signatures.
-KEEP_SIGNING_SECRET:
-
-# The value for the Rails config.secret_token setting.
-API_SECRET:
-
-# A "superuser" token with which servers can authenticate to
-# the API server, before an administrative user has been created.
-# Leave this blank to generate a secret randomly at build time (recommended).
-API_SUPERUSER_SECRET:
-
-# More than anything this should be auto-generated, but
-# we don't presently have a good place to store it. So just
-# change it and don't be dumb.
-POSTGRES_ROOT_PW: dummy_pw
-
-# The URL of the SSO server that you want your API server to use. If
-# blank, use the sso docker container.
-OMNIAUTH_URL:
-
-# ==============================
-# Workbench settings
-# ==============================
-WORKBENCH_RAILS_MODE: production
-WORKBENCH_DATA_IMPORT_DIR: /data/arvados-workbench-upload/data
-WORKBENCH_DATA_EXPORT_DIR: /data/arvados-workbench-download/data
-WORKBENCH_VCF_PIPELINE_UUID:
-WORKBENCH_SITE_NAME: Arvados Workbench
-WORKBENCH_INSECURE_HTTPS: true
-WORKBENCH_ACTIVATION_CONTACT_LINK: mailto:arvados at curoverse.com
-WORKBENCH_SECRET:
-
-# ==============================
-# SSO settings
-# ==============================
-SSO_HOSTNAME: sso
-SSO_SECRET:
-SSO_CLIENT_NAME: devsandbox
-SSO_CLIENT_APP_ID: local_docker_installation
-SSO_CLIENT_SECRET:
diff --git a/docker/doc/Dockerfile b/docker/doc/Dockerfile
deleted file mode 100644
index 1492675..0000000
--- a/docker/doc/Dockerfile
+++ /dev/null
@@ -1,29 +0,0 @@
-# Arvados Documentation Docker container.
-
-FROM arvados/base
-maintainer Ward Vandewege <ward at curoverse.com>
-
-# Install packages
-RUN /bin/mkdir -p /usr/src/arvados && \
- apt-get update -q && \
- apt-get install -qy curl procps apache2-mpm-worker
-
-ADD generated/doc.tar.gz /usr/src/arvados/
-
-# Build static site
-RUN /usr/local/rvm/bin/rvm-exec default bundle install --gemfile=/usr/src/arvados/doc/Gemfile && \
- /bin/sed -ri 's/^baseurl: .*$/baseurl: /' /usr/src/arvados/doc/_config.yml && \
- cd /usr/src/arvados/doc && \
- LANG="en_US.UTF-8" LC_ALL="en_US.UTF-8" /usr/local/rvm/bin/rvm-exec default bundle exec rake generate arvados_api_host=api.dev.arvados arvados_workbench_host=workbench.dev.arvados
-
-
-# Configure Apache
-ADD generated/apache2_vhost /etc/apache2/sites-available/doc
-RUN \
- a2dissite default && \
- a2ensite doc
-
-ADD apache2_foreground.sh /etc/apache2/foreground.sh
-
-# Start Apache
-CMD ["/etc/apache2/foreground.sh"]
diff --git a/docker/doc/apache2_foreground.sh b/docker/doc/apache2_foreground.sh
deleted file mode 100755
index fc6028e..0000000
--- a/docker/doc/apache2_foreground.sh
+++ /dev/null
@@ -1,7 +0,0 @@
-#! /bin/bash
-
-read pid cmd state ppid pgrp session tty_nr tpgid rest < /proc/self/stat
-trap "kill -TERM -$pgrp; exit" EXIT TERM KILL SIGKILL SIGTERM SIGQUIT
-
-source /etc/apache2/envvars
-/usr/sbin/apache2 -D FOREGROUND
diff --git a/docker/doc/apache2_vhost.in b/docker/doc/apache2_vhost.in
deleted file mode 100644
index 76da6d0..0000000
--- a/docker/doc/apache2_vhost.in
+++ /dev/null
@@ -1,11 +0,0 @@
-
-ServerName doc.@@ARVADOS_DOMAIN@@
-
-<VirtualHost *:80>
- ServerAdmin sysadmin at curoverse.com
-
- ServerName doc.@@ARVADOS_DOMAIN@@
-
- DocumentRoot /usr/src/arvados/doc/.site/
-
-</VirtualHost>
diff --git a/docker/install_sdk.sh b/docker/install_sdk.sh
deleted file mode 100755
index 1c07c9d..0000000
--- a/docker/install_sdk.sh
+++ /dev/null
@@ -1,13 +0,0 @@
-#! /bin/sh
-
-# Install prerequisites.
-sudo apt-get install curl libcurl3 libcurl3-gnutls libcurl4-openssl-dev python-pip
-
-# Install RVM.
-curl -sSL https://get.rvm.io | bash -s stable
-source ~/.rvm/scripts/rvm
-rvm install 2.1.0
-
-# Install arvados-cli.
-gem install arvados-cli
-sudo pip install --upgrade httplib2
diff --git a/docker/java-bwa-samtools/Dockerfile b/docker/java-bwa-samtools/Dockerfile
deleted file mode 100644
index 2a73977..0000000
--- a/docker/java-bwa-samtools/Dockerfile
+++ /dev/null
@@ -1,23 +0,0 @@
-FROM arvados/jobs
-MAINTAINER Peter Amstutz <peter.amstutz at curoverse.com>
-
-USER root
-
-RUN apt-get update -q
-RUN apt-get install -qy openjdk-7-jre-headless && \
- cd /tmp && \
- curl --location http://cache.arvados.org/sourceforge.net/project/bio-bwa/bwa-0.7.9a.tar.bz2 -o bwa-0.7.9a.tar.bz2 && \
- tar xjf bwa-0.7.9a.tar.bz2 && \
- cd bwa-0.7.9a && \
- make && \
- (find . -executable -type f -print0 | xargs -0 -I {} mv {} /usr/local/bin) && \
- rm -r /tmp/bwa-0.7.9a* && \
- cd /tmp && \
- curl --location http://cache.arvados.org/sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2 -o samtools-0.1.19.tar.bz2 && \
- tar xjf samtools-0.1.19.tar.bz2 && \
- cd samtools-0.1.19 && \
- make && \
- (find . -executable -type f -print0 | xargs -0 -I {} mv {} /usr/local/bin) && \
- rm -r /tmp/samtools-0.1.19*
-
-USER crunch
diff --git a/docker/keep/Dockerfile b/docker/keep/Dockerfile
deleted file mode 100644
index 08e5175..0000000
--- a/docker/keep/Dockerfile
+++ /dev/null
@@ -1,14 +0,0 @@
-# Based on Debian Wheezy
-FROM arvados/debian:wheezy
-MAINTAINER Ward Vandewege <ward at curoverse.com>
-
-ADD generated/bin/keepstore /usr/local/bin/
-ADD generated/bin/keepproxy /usr/local/bin/
-ADD generated/run-keep /usr/local/bin/
-
-ADD generated/keep_signing_secret /etc/
-
-RUN mkdir /keep-data
-
-# Start keep
-CMD ["/usr/local/bin/run-keep"]
diff --git a/docker/keep/keep_signing_secret.in b/docker/keep/keep_signing_secret.in
deleted file mode 100644
index e5b39c8..0000000
--- a/docker/keep/keep_signing_secret.in
+++ /dev/null
@@ -1 +0,0 @@
-@@KEEP_SIGNING_SECRET@@
\ No newline at end of file
diff --git a/docker/keep/run-keep.in b/docker/keep/run-keep.in
deleted file mode 100755
index 385f0e6..0000000
--- a/docker/keep/run-keep.in
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/bin/sh
-
-pkf="/etc/keep_signing_secret"
-if [ -s "$pkf" ]
-then
- permission_args="-permission-key-file=$pkf -enforce-permissions"
-else
- permission_args=""
-fi
-
-exec keepstore $permission_args -listen=":25107" -volume="/keep-data"
diff --git a/docker/keepproxy/Dockerfile b/docker/keepproxy/Dockerfile
deleted file mode 100644
index e8df168..0000000
--- a/docker/keepproxy/Dockerfile
+++ /dev/null
@@ -1,12 +0,0 @@
-# Based on Debian Wheezy
-FROM arvados/debian:wheezy
-MAINTAINER Ward Vandewege <ward at curoverse.com>
-
-RUN apt-get update -q
-RUN apt-get install -qy ca-certificates
-
-ADD generated/bin/keepproxy /usr/local/bin/
-ADD generated/run-keepproxy /usr/local/bin/
-
-# Start keep
-CMD ["/usr/local/bin/run-keepproxy"]
diff --git a/docker/keepproxy/run-keepproxy.in b/docker/keepproxy/run-keepproxy.in
deleted file mode 100755
index 4bd934d..0000000
--- a/docker/keepproxy/run-keepproxy.in
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/bin/sh
-
-export ARVADOS_API_HOST=api
-export ARVADOS_API_HOST_INSECURE=yes
-# This should be an anonymous token, but we don't have a good way
-# to get one while building the images
-export ARVADOS_API_TOKEN=@@API_SUPERUSER_SECRET@@
-
-read pid cmd state ppid pgrp session tty_nr tpgid rest < /proc/self/stat
-trap "kill -TERM -$pgrp; exit" HUP EXIT TERM QUIT
-
-while /bin/true ; do
- keepproxy -listen=':9100'
- sleep 1
-done
diff --git a/docker/mkimage-debootstrap.sh b/docker/mkimage-debootstrap.sh
deleted file mode 100755
index 2ad79ef..0000000
--- a/docker/mkimage-debootstrap.sh
+++ /dev/null
@@ -1,240 +0,0 @@
-#!/bin/bash
-set -e
-
-variant='minbase'
-include='iproute,iputils-ping'
-arch='amd64' # intentionally undocumented for now
-skipDetection=
-strictDebootstrap=
-justTar=
-
-usage() {
- echo >&2
-
- echo >&2 "usage: $0 [options] repo suite [mirror]"
-
- echo >&2
- echo >&2 'options: (not recommended)'
- echo >&2 " -p set an http_proxy for debootstrap"
- echo >&2 " -v $variant # change default debootstrap variant"
- echo >&2 " -i $include # change default package includes"
- echo >&2 " -d # strict debootstrap (do not apply any docker-specific tweaks)"
- echo >&2 " -s # skip version detection and tagging (ie, precise also tagged as 12.04)"
- echo >&2 " # note that this will also skip adding universe and/or security/updates to sources.list"
- echo >&2 " -t # just create a tarball, especially for dockerbrew (uses repo as tarball name)"
-
- echo >&2
- echo >&2 " ie: $0 username/debian squeeze"
- echo >&2 " $0 username/debian squeeze http://ftp.uk.debian.org/debian/"
-
- echo >&2
- echo >&2 " ie: $0 username/ubuntu precise"
- echo >&2 " $0 username/ubuntu precise http://mirrors.melbourne.co.uk/ubuntu/"
-
- echo >&2
- echo >&2 " ie: $0 -t precise.tar.bz2 precise"
- echo >&2 " $0 -t wheezy.tgz wheezy"
- echo >&2 " $0 -t wheezy-uk.tar.xz wheezy http://ftp.uk.debian.org/debian/"
-
- echo >&2
-}
-
-# these should match the names found at http://www.debian.org/releases/
-debianStable=wheezy
-debianUnstable=sid
-# this should match the name found at http://releases.ubuntu.com/
-ubuntuLatestLTS=precise
-
-while getopts v:i:a:p:dst name; do
- case "$name" in
- p)
- http_proxy="$OPTARG"
- ;;
- v)
- variant="$OPTARG"
- ;;
- i)
- include="$OPTARG"
- ;;
- a)
- arch="$OPTARG"
- ;;
- d)
- strictDebootstrap=1
- ;;
- s)
- skipDetection=1
- ;;
- t)
- justTar=1
- ;;
- ?)
- usage
- exit 0
- ;;
- esac
-done
-shift $(($OPTIND - 1))
-
-repo="$1"
-suite="$2"
-mirror="${3:-}" # stick to the default debootstrap mirror if one is not provided
-
-if [ ! "$repo" ] || [ ! "$suite" ]; then
- usage
- exit 1
-fi
-
-# some rudimentary detection for whether we need to "sudo" our docker calls
-set +e
-docker=`which docker.io`
-if [[ "$docker" == "" ]]; then
- docker=`which docker`
-fi
-set -e
-
-if $docker version > /dev/null 2>&1; then
- docker="$docker"
-elif sudo $docker version > /dev/null 2>&1; then
- docker="sudo $docker"
-elif command -v $docker > /dev/null 2>&1; then
- docker="$docker"
-else
- echo >&2 "warning: either docker isn't installed, or your current user cannot run it;"
- echo >&2 " this script is not likely to work as expected"
- sleep 3
- docker='docker' # give us a command-not-found later
-fi
-
-# make sure we have an absolute path to our final tarball so we can still reference it properly after we change directory
-if [ "$justTar" ]; then
- if [ ! -d "$(dirname "$repo")" ]; then
- echo >&2 "error: $(dirname "$repo") does not exist"
- exit 1
- fi
- repo="$(cd "$(dirname "$repo")" && pwd -P)/$(basename "$repo")"
-fi
-
-# will be filled in later, if [ -z "$skipDetection" ]
-lsbDist=''
-
-target="${TMPDIR:-/tmp}/docker-rootfs-debootstrap-$suite-$$-$RANDOM"
-
-cd "$(dirname "$(readlink -f "$BASH_SOURCE")")"
-returnTo="$(pwd -P)"
-
-set -x
-
-# bootstrap
-mkdir -p "$target"
-sudo http_proxy=$http_proxy debootstrap --verbose --variant="$variant" --include="$include" --arch="$arch" "$suite" "$target" "$mirror"
-
-cd "$target"
-
-if [ -z "$strictDebootstrap" ]; then
- # prevent init scripts from running during install/update
- # policy-rc.d (for most scripts)
- echo $'#!/bin/sh\nexit 101' | sudo tee usr/sbin/policy-rc.d > /dev/null
- sudo chmod +x usr/sbin/policy-rc.d
- # initctl (for some pesky upstart scripts)
- sudo chroot . dpkg-divert --local --rename --add /sbin/initctl
- sudo ln -sf /bin/true sbin/initctl
- # see https://github.com/dotcloud/docker/issues/446#issuecomment-16953173
-
- # shrink the image, since apt makes us fat (wheezy: ~157.5MB vs ~120MB)
- sudo chroot . apt-get clean
-
- # while we're at it, apt is unnecessarily slow inside containers
- # this forces dpkg not to call sync() after package extraction and speeds up install
- # the benefit is huge on spinning disks, and the penalty is nonexistent on SSD or decent server virtualization
- echo 'force-unsafe-io' | sudo tee etc/dpkg/dpkg.cfg.d/02apt-speedup > /dev/null
- # we want to effectively run "apt-get clean" after every install to keep images small
- echo 'DPkg::Post-Invoke {"/bin/rm -f /var/cache/apt/archives/*.deb || true";};' | sudo tee etc/apt/apt.conf.d/no-cache > /dev/null
-
- # helpful undo lines for each the above tweaks (for lack of a better home to keep track of them):
- # rm /usr/sbin/policy-rc.d
- # rm /sbin/initctl; dpkg-divert --rename --remove /sbin/initctl
- # rm /etc/dpkg/dpkg.cfg.d/02apt-speedup
- # rm /etc/apt/apt.conf.d/no-cache
-
- if [ -z "$skipDetection" ]; then
- # see also rudimentary platform detection in hack/install.sh
- lsbDist=''
- if [ -r etc/lsb-release ]; then
- lsbDist="$(. etc/lsb-release && echo "$DISTRIB_ID")"
- fi
- if [ -z "$lsbDist" ] && [ -r etc/debian_version ]; then
- lsbDist='Debian'
- fi
-
- case "$lsbDist" in
- Debian)
- # add the updates and security repositories
- if [ "$suite" != "$debianUnstable" -a "$suite" != 'unstable' ]; then
- # ${suite}-updates only applies to non-unstable
- sudo sed -i "p; s/ $suite main$/ ${suite}-updates main/" etc/apt/sources.list
-
- # same for security updates
- echo "deb http://security.debian.org/ $suite/updates main" | sudo tee -a etc/apt/sources.list > /dev/null
- fi
- ;;
- Ubuntu)
- # add the universe, updates, and security repositories
- sudo sed -i "
- s/ $suite main$/ $suite main universe/; p;
- s/ $suite main/ ${suite}-updates main/; p;
- s/ $suite-updates main/ ${suite}-security main/
- " etc/apt/sources.list
- ;;
- esac
- fi
-fi
-
-if [ "$justTar" ]; then
- # create the tarball file so it has the right permissions (ie, not root)
- touch "$repo"
-
- # fill the tarball
- sudo tar --numeric-owner -caf "$repo" .
-else
- # create the image (and tag $repo:$suite)
- sudo tar --numeric-owner -c . | $docker import - $repo:$suite
-
- # test the image
- [[ "$(/usr/bin/tty || true)" != "not a tty" ]] && RUN_OPTS="-i -t"
- $docker run $RUN_OPS $repo:$suite echo success
-
- if [ -z "$skipDetection" ]; then
- case "$lsbDist" in
- Debian)
- if [ "$suite" = "$debianStable" -o "$suite" = 'stable' ] && [ -r etc/debian_version ]; then
- # tag latest
- $docker tag -f $repo:$suite $repo:latest
-
- if [ -r etc/debian_version ]; then
- # tag the specific debian release version (which is only reasonable to tag on debian stable)
- ver=$(cat etc/debian_version)
- $docker tag -f $repo:$suite $repo:$ver
- fi
- fi
- ;;
- Ubuntu)
- if [ "$suite" = "$ubuntuLatestLTS" ]; then
- # tag latest
- $docker tag -f $repo:$suite $repo:latest
- fi
- if [ -r etc/lsb-release ]; then
- lsbRelease="$(. etc/lsb-release && echo "$DISTRIB_RELEASE")"
- if [ "$lsbRelease" ]; then
- # tag specific Ubuntu version number, if available (12.04, etc.)
- $docker tag -f $repo:$suite $repo:$lsbRelease
- fi
- fi
- ;;
- esac
- fi
-fi
-
-# cleanup
-cd "$returnTo"
-sudo rm -rf "$target"
diff --git a/docker/passenger/Dockerfile b/docker/passenger/Dockerfile
deleted file mode 100644
index 77aeb66..0000000
--- a/docker/passenger/Dockerfile
+++ /dev/null
@@ -1,19 +0,0 @@
-# Arvados passenger image
-
-FROM arvados/base
-MAINTAINER Ward Vandewege <ward at curoverse.com>
-
-# Install packages and build the passenger apache module
-
-RUN apt-get update -q
-RUN apt-get install -qy \
- apt-utils git curl procps apache2-mpm-worker \
- libcurl4-openssl-dev apache2-threaded-dev \
- libapr1-dev libaprutil1-dev
-
-RUN cd /usr/src/arvados/services/api && \
- /usr/local/rvm/bin/rvm-exec default bundle exec passenger-install-apache2-module --auto --languages ruby
-
-RUN cd /usr/src/arvados/services/api && \
- /usr/local/rvm/bin/rvm-exec default bundle exec passenger-install-apache2-module --snippet > /etc/apache2/conf.d/passenger
-
diff --git a/docker/postgresql/Dockerfile b/docker/postgresql/Dockerfile
deleted file mode 100644
index a99a886..0000000
--- a/docker/postgresql/Dockerfile
+++ /dev/null
@@ -1,35 +0,0 @@
-# PostgreSQL Docker container for Arvados.
-
-FROM arvados/debian:wheezy
-MAINTAINER Ward Vandewege <ward at curoverse.com>
-
-# TODO(twp): parameterize variables via autoconf or similar.
-ENV POSTGRES_ROOT_PW dummy_pw
-
-ENV ARVADOS_DEV_DB arvados_development
-ENV ARVADOS_DEV_USER arvados
-ENV ARVADOS_DEV_PW dummy_pw
-
-ENV ARVADOS_TEST_DB arvados_test
-ENV ARVADOS_TEST_USER arvados
-ENV ARVADOS_TEST_PW dummy_pw
-
-ENV ARVADOS_PROD_DB arvados_production
-ENV ARVADOS_PROD_USER arvados
-ENV ARVADOS_PROD_PW dummy_pw
-
-# Install postgres and apache
-RUN apt-get install -qy procps postgresql postgresql-server-dev-9.1
-
-# Configure databases and users.
-ADD postgresql.conf /etc/postgresql/9.1/main/
-ADD pg_hba.conf /etc/postgresql/9.1/main/
-
-ADD postgresql_config.sh /tmp/postgresql_config.sh
-RUN /tmp/postgresql_config.sh
-RUN rm /tmp/postgresql_config.sh
-
-# Accept database connections on port 5432 from outside the container.
-EXPOSE 5432
-
-CMD ["/bin/su", "postgres", "-c", "/usr/lib/postgresql/9.1/bin/postgres -D /var/lib/postgresql/9.1/main -c config_file=/etc/postgresql/9.1/main/postgresql.conf"]
diff --git a/docker/postgresql/pg_hba.conf b/docker/postgresql/pg_hba.conf
deleted file mode 100644
index c5486ad..0000000
--- a/docker/postgresql/pg_hba.conf
+++ /dev/null
@@ -1,15 +0,0 @@
-# For full documentation see
-# http://www.postgresql.org/docs/9.1/static/auth-pg-hba-conf.html
-
-# Database administrative login by Unix domain socket
-local all postgres peer
-
-# TYPE DATABASE USER ADDRESS METHOD
-host all all 0.0.0.0/0 md5
-
-# "local" is for Unix domain socket connections only
-local all all peer
-# IPv4 local connections:
-host all all 127.0.0.1/32 md5
-# IPv6 local connections:
-host all all ::1/128 md5
diff --git a/docker/postgresql/postgresql.conf b/docker/postgresql/postgresql.conf
deleted file mode 100644
index 3da7c1b..0000000
--- a/docker/postgresql/postgresql.conf
+++ /dev/null
@@ -1,20 +0,0 @@
-# For full documentation on run-time settings see
-# http://www.postgresql.org/docs/9.2/static/runtime-config.html
-
-listen_addresses = '*'
-data_directory = '/var/lib/postgresql/9.1/main' # use data in another directory
-hba_file = '/etc/postgresql/9.1/main/pg_hba.conf' # host-based authentication file
-ident_file = '/etc/postgresql/9.1/main/pg_ident.conf' # ident configuration file
-external_pid_file = '/var/run/postgresql/9.1-main.pid' # write an extra PID file
-port = 5432 # (change requires restart)
-max_connections = 100 # (change requires restart)
-unix_socket_directory = '/var/run/postgresql' # (change requires restart)
-ssl = true # (change requires restart)
-shared_buffers = 24MB # min 128kB
-log_line_prefix = '%t ' # special values:
-datestyle = 'iso, mdy'
-lc_messages = 'C' # locale for system error message
-lc_monetary = 'C' # locale for monetary formatting
-lc_numeric = 'C' # locale for number formatting
-lc_time = 'C' # locale for time formatting
-default_text_search_config = 'pg_catalog.english'
diff --git a/docker/shell/Dockerfile b/docker/shell/Dockerfile
deleted file mode 100644
index 3e6e3e4..0000000
--- a/docker/shell/Dockerfile
+++ /dev/null
@@ -1,24 +0,0 @@
-# Slurm node Docker container.
-
-FROM arvados/base
-MAINTAINER Ward Vandewege <ward at curoverse.com>
-
-RUN apt-get update -q
-RUN apt-get install -qy \
- python-pip python-gflags python-google-api-python-client \
- python-virtualenv libattr1-dev libfuse-dev python-dev python-llfuse fuse \
- crunchstat python-arvados-fuse cron vim supervisor openssh-server
-
-ADD fuse.conf /etc/fuse.conf
-RUN chmod 644 /etc/fuse.conf
-
-ADD generated/superuser_token /tmp/superuser_token
-
-RUN /usr/local/rvm/bin/rvm-exec default gem install arvados-cli arvados
-
-# Supervisor.
-ADD supervisor.conf /etc/supervisor/conf.d/arvados.conf
-ADD generated/setup.sh /usr/local/bin/setup.sh
-
-# Start the supervisor.
-CMD ["/usr/bin/supervisord", "-n"]
diff --git a/docker/shell/fuse.conf b/docker/shell/fuse.conf
deleted file mode 100644
index 4ed21ba..0000000
--- a/docker/shell/fuse.conf
+++ /dev/null
@@ -1,10 +0,0 @@
-# Set the maximum number of FUSE mounts allowed to non-root users.
-# The default is 1000.
-#
-#mount_max = 1000
-
-# Allow non-root users to specify the 'allow_other' or 'allow_root'
-# mount options.
-#
-user_allow_other
-
diff --git a/docker/shell/setup.sh.in b/docker/shell/setup.sh.in
deleted file mode 100755
index 03beb4b..0000000
--- a/docker/shell/setup.sh.in
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/bin/bash
-
-USER_NAME="@@ARVADOS_USER_NAME@@"
-
-useradd $USER_NAME -s /bin/bash
-mkdir /home/$USER_NAME/.ssh -p
-
-# Install our token
-mkdir -p /home/$USER_NAME/.config/arvados;
-echo "ARVADOS_API_HOST=api" >> /home/$USER_NAME/.config/arvados/settings.conf
-echo "ARVADOS_API_HOST_INSECURE=yes" >> /home/$USER_NAME/.config/arvados/settings.conf
-echo "ARVADOS_API_TOKEN=$(cat /tmp/superuser_token)" >> /home/$USER_NAME/.config/arvados/settings.conf
-chmod 600 /home/$USER_NAME/.config/arvados/settings.conf
-
-chown $USER_NAME:$USER_NAME /home/$USER_NAME -R
-
-rm -f /tmp/superuser_token
-
-
diff --git a/docker/shell/superuser_token.in b/docker/shell/superuser_token.in
deleted file mode 100644
index 49bb34e..0000000
--- a/docker/shell/superuser_token.in
+++ /dev/null
@@ -1 +0,0 @@
-@@API_SUPERUSER_SECRET@@
diff --git a/docker/shell/supervisor.conf b/docker/shell/supervisor.conf
deleted file mode 100644
index 97ad540..0000000
--- a/docker/shell/supervisor.conf
+++ /dev/null
@@ -1,15 +0,0 @@
-[program:ssh]
-user=root
-command=/etc/init.d/ssh start
-startsecs=0
-
-[program:cron]
-user=root
-command=/etc/init.d/cron start
-startsecs=0
-
-[program:setup]
-user=root
-command=/usr/local/bin/setup.sh
-startsecs=0
-
diff --git a/docker/slurm/Dockerfile b/docker/slurm/Dockerfile
deleted file mode 100644
index 28a3c3b..0000000
--- a/docker/slurm/Dockerfile
+++ /dev/null
@@ -1,12 +0,0 @@
-# Slurm node Docker container.
-
-FROM arvados/base
-MAINTAINER Ward Vandewege <ward at curoverse.com>
-
-RUN apt-get update -q
-RUN apt-get install -qy slurm-llnl munge
-
-ADD munge.key /etc/munge/
-RUN chown munge:munge /etc/munge/munge.key && chmod 600 /etc/munge/munge.key
-ADD generated/slurm.conf /etc/slurm-llnl/
-
diff --git a/docker/slurm/munge.key b/docker/slurm/munge.key
deleted file mode 100644
index 34036a0..0000000
Binary files a/docker/slurm/munge.key and /dev/null differ
diff --git a/docker/slurm/slurm.conf.in b/docker/slurm/slurm.conf.in
deleted file mode 100644
index 7312a0e..0000000
--- a/docker/slurm/slurm.conf.in
+++ /dev/null
@@ -1,60 +0,0 @@
-
-ControlMachine=api
-#SlurmUser=slurmd
-SlurmctldPort=6817
-SlurmdPort=6818
-AuthType=auth/munge
-#JobCredentialPrivateKey=/etc/slurm-llnl/slurm-key.pem
-#JobCredentialPublicCertificate=/etc/slurm-llnl/slurm-cert.pem
-StateSaveLocation=/tmp
-SlurmdSpoolDir=/tmp/slurmd
-SwitchType=switch/none
-MpiDefault=none
-SlurmctldPidFile=/var/run/slurmctld.pid
-SlurmdPidFile=/var/run/slurmd.pid
-ProctrackType=proctrack/pgid
-CacheGroups=0
-ReturnToService=2
-TaskPlugin=task/affinity
-#
-# TIMERS
-SlurmctldTimeout=300
-SlurmdTimeout=300
-InactiveLimit=0
-MinJobAge=300
-KillWait=30
-Waittime=0
-#
-# SCHEDULING
-SchedulerType=sched/backfill
-#SchedulerType=sched/builtin
-SchedulerPort=7321
-#SchedulerRootFilter=
-#SelectType=select/linear
-SelectType=select/cons_res
-SelectTypeParameters=CR_CPU_Memory
-FastSchedule=1
-#
-# LOGGING
-SlurmctldDebug=3
-#SlurmctldLogFile=
-SlurmdDebug=3
-#SlurmdLogFile=
-JobCompType=jobcomp/none
-#JobCompLoc=
-JobAcctGatherType=jobacct_gather/none
-#JobAcctLogfile=
-#JobAcctFrequency=
-#
-# COMPUTE NODES
-NodeName=DEFAULT
-# CPUs=8 State=UNKNOWN RealMemory=6967 Weight=6967
-PartitionName=DEFAULT MaxTime=INFINITE State=UP
-PartitionName=compute Default=YES Shared=yes
-#PartitionName=sysadmin Hidden=YES Shared=yes
-
-NodeName=compute[0-1]
-#NodeName=compute0 RealMemory=6967 Weight=6967
-
-PartitionName=compute Nodes=compute[0-1]
-PartitionName=crypto Nodes=compute[0-1]
diff --git a/docker/slurm/supervisor.conf b/docker/slurm/supervisor.conf
deleted file mode 100644
index 64f86b1..0000000
--- a/docker/slurm/supervisor.conf
+++ /dev/null
@@ -1,7 +0,0 @@
-[program:munge]
-user=root
-command=/etc/init.d/munge start
-
-[program:slurm]
-user=root
-command=/etc/init.d/slurm-llnl start
diff --git a/docker/sso/Dockerfile b/docker/sso/Dockerfile
deleted file mode 100644
index 7d99ac6..0000000
--- a/docker/sso/Dockerfile
+++ /dev/null
@@ -1,32 +0,0 @@
-# Arvados API server Docker container.
-
-FROM arvados/passenger
-MAINTAINER Ward Vandewege <ward at curoverse.com>
-
-RUN git clone git://github.com/curoverse/sso-devise-omniauth-provider.git /usr/src/sso-provider && \
- /usr/local/rvm/bin/rvm-exec default bundle install --gemfile=/usr/src/sso-provider/Gemfile
-
-# Install generated config files
-ADD generated/seeds.rb /usr/src/sso-provider/db/seeds.rb
-ADD generated/database.yml /usr/src/sso-provider/config/database.yml
-ADD generated/application.yml /usr/src/sso-provider/config/application.yml
-ADD generated/apache2_vhost /etc/apache2/sites-available/sso-provider
-ADD generated/apache2_vhost /etc/apache2/sites-available/sso-provider
-
-# Configure Apache and Passenger.
-RUN a2dissite default && \
- a2ensite sso-provider && \
- a2enmod rewrite && \
- a2enmod ssl && \
- cd /usr/src/sso-provider && \
- cp config/environments/production.rb.example config/environments/production.rb && \
- RAILS_ENV=production /usr/local/rvm/bin/rvm-exec default bundle exec rake db:setup && \
- /usr/local/rvm/bin/rvm-exec default bundle exec rake assets:precompile && \
- chown www-data:www-data log config.ru -R && \
- chown www-data:www-data db db/production.sqlite3 && \
- /bin/mkdir /var/run/apache2
-
-ADD apache2_foreground.sh /etc/apache2/foreground.sh
-
-# Start the supervisor.
-CMD ["/etc/apache2/foreground.sh"]
diff --git a/docker/sso/apache2_foreground.sh b/docker/sso/apache2_foreground.sh
deleted file mode 100755
index fc6028e..0000000
--- a/docker/sso/apache2_foreground.sh
+++ /dev/null
@@ -1,7 +0,0 @@
-#! /bin/bash
-
-read pid cmd state ppid pgrp session tty_nr tpgid rest < /proc/self/stat
-trap "kill -TERM -$pgrp; exit" EXIT TERM KILL SIGKILL SIGTERM SIGQUIT
-
-source /etc/apache2/envvars
-/usr/sbin/apache2 -D FOREGROUND
diff --git a/docker/sso/apache2_vhost.in b/docker/sso/apache2_vhost.in
deleted file mode 100644
index 465a1e6..0000000
--- a/docker/sso/apache2_vhost.in
+++ /dev/null
@@ -1,50 +0,0 @@
-# VirtualHost definition for the Arvados API server
-
-<VirtualHost *:80>
- ServerName @@SSO_HOSTNAME@@.@@ARVADOS_DOMAIN@@
- ServerAdmin sysadmin at curoverse.com
-
- RedirectPermanent / https://@@SSO_HOSTNAME@@.@@ARVADOS_DOMAIN@@/
-
- LogLevel warn
- ErrorLog ${APACHE_LOG_DIR}/error.log
- CustomLog ${APACHE_LOG_DIR}/access.log combined
-
-</VirtualHost>
-
-<VirtualHost *:443>
- ServerName @@SSO_HOSTNAME@@.@@ARVADOS_DOMAIN@@
- ServerAdmin sysadmin at curoverse.com
-
- RailsEnv production
- RackBaseURI /
- RailsAppSpawnerIdleTime 1200
-
- # Enable streaming
- PassengerBufferResponse off
-
- # Index file and Document Root (where the public files are located)
- DirectoryIndex index.html
- DocumentRoot /usr/src/sso-provider/public
-
- LogLevel warn
- ErrorLog ${APACHE_LOG_DIR}/ssl_error.log
- CustomLog ${APACHE_LOG_DIR}/ssl_access.log combined
-
- <Directory /usr/src/sso-provider/public>
- Options Indexes FollowSymLinks MultiViews IncludesNoExec
- AllowOverride None
- Order allow,deny
- allow from all
- </Directory>
-
- <IfModule mod_ssl.c>
- SSLEngine on
- # SSLCertificateChainFile /etc/ssl/certs/startcom.sub.class1.server.ca.pem
- # SSLCACertificateFile /etc/ssl/certs/startcom.ca.pem
- SSLCertificateFile /etc/ssl/certs/ssl-cert-snakeoil.pem
- SSLCertificateKeyFile /etc/ssl/private/ssl-cert-snakeoil.key
- SetEnvIf User-Agent ".*MSIE.*" nokeepalive ssl-unclean-shutdown
- </IfModule>
-
-</VirtualHost>
diff --git a/docker/sso/application.yml.in b/docker/sso/application.yml.in
deleted file mode 100644
index 6063851..0000000
--- a/docker/sso/application.yml.in
+++ /dev/null
@@ -1,30 +0,0 @@
-#
-# Consult application.default.yml for the full list of configuration
-# settings.
-#
-# The order of precedence is:
-# 1. config/environments/{RAILS_ENV}.rb (deprecated)
-# 2. Section in application.yml corresponding to RAILS_ENV (e.g., development)
-# 3. Section in application.yml called "common"
-# 4. Section in application.default.yml corresponding to RAILS_ENV
-# 5. Section in application.default.yml called "common"
-
-production:
- allow_account_registration: true
-
- secret_token: @@SSO_SECRET@@
- uuid_prefix: 'zzzzz'
-
- # If true, allow new creation of new accounts in the SSO server's internal
- # user database.
- allow_account_registration: true
-
-development:
- # No development settings
-
-test:
- # No test settings
-
-common:
- # No common settings
-
diff --git a/docker/sso/database.yml.in b/docker/sso/database.yml.in
deleted file mode 100644
index 025d62a..0000000
--- a/docker/sso/database.yml.in
+++ /dev/null
@@ -1,22 +0,0 @@
-# SQLite version 3.x
-# gem install sqlite3-ruby (not necessary on OS X Leopard)
-development:
- adapter: sqlite3
- database: db/development.sqlite3
- pool: 5
- timeout: 5000
-
-# Warning: The database defined as "test" will be erased and
-# re-generated from your development database when you run "rake".
-# Do not set this db to the same as development or production.
-test:
- adapter: sqlite3
- database: db/test.sqlite3
- pool: 5
- timeout: 5000
-
-production:
- adapter: sqlite3
- database: db/production.sqlite3
- pool: 5
- timeout: 5000
diff --git a/docker/sso/seeds.rb.in b/docker/sso/seeds.rb.in
deleted file mode 100644
index b35b939..0000000
--- a/docker/sso/seeds.rb.in
+++ /dev/null
@@ -1,9 +0,0 @@
-
-Client.delete_all
-
-c = Client.new()
-c.name = "@@SSO_CLIENT_NAME@@"
-c.app_id = "@@SSO_CLIENT_APP_ID@@"
-c.app_secret = "@@SSO_CLIENT_SECRET@@"
-c.save!
-
diff --git a/docker/workbench/.gitignore b/docker/workbench/.gitignore
deleted file mode 100644
index bf969c3..0000000
--- a/docker/workbench/.gitignore
+++ /dev/null
@@ -1,3 +0,0 @@
-apache2_vhost
-production.rb
-secret_token.rb
diff --git a/docker/workbench/Dockerfile b/docker/workbench/Dockerfile
deleted file mode 100644
index 148153a..0000000
--- a/docker/workbench/Dockerfile
+++ /dev/null
@@ -1,37 +0,0 @@
-# Arvados Workbench Docker container.
-
-FROM arvados/passenger
-MAINTAINER Ward Vandewege <ward at curoverse.com>
-
-# We need graphviz for the provenance graphs
-RUN apt-get update -q
-RUN apt-get install -qy graphviz
-
-# Update Arvados source
-RUN /bin/mkdir -p /usr/src/arvados/apps
-ADD generated/workbench.tar.gz /usr/src/arvados/apps/
-ADD generated/workbench_rails_env /etc/
-RUN /bin/cp /usr/src/arvados/apps/workbench/config/environments/$(cat /etc/workbench_rails_env).rb.example /usr/src/arvados/apps/workbench/config/environments/$(cat /etc/workbench_rails_env).rb
-ADD generated/application.yml /usr/src/arvados/apps/workbench/config/application.yml
-
-RUN RAILS_ENV=$(cat /etc/workbench_rails_env) && \
- /usr/local/rvm/bin/rvm-exec default bundle install --gemfile=/usr/src/arvados/apps/workbench/Gemfile && \
- touch /usr/src/arvados/apps/workbench/log/$RAILS_ENV.log && \
- chmod 666 /usr/src/arvados/apps/workbench/log/$RAILS_ENV.log && \
- touch /usr/src/arvados/apps/workbench/db/$RAILS_ENV.sqlite3 && \
- cd /usr/src/arvados/apps/workbench && \
- /usr/local/rvm/bin/rvm-exec default bundle exec rake assets:precompile && \
- chown -R www-data:www-data /usr/src/arvados/apps/workbench
-
-# Configure Apache
-ADD generated/apache2_vhost /etc/apache2/sites-available/workbench
-RUN \
- a2dissite default && \
- a2ensite workbench && \
- a2enmod rewrite && \
- /bin/mkdir /var/run/apache2
-
-ADD apache2_foreground.sh /etc/apache2/foreground.sh
-
-# Start Apache
-CMD ["/etc/apache2/foreground.sh"]
diff --git a/docker/workbench/apache2_foreground.sh b/docker/workbench/apache2_foreground.sh
deleted file mode 100755
index fc6028e..0000000
--- a/docker/workbench/apache2_foreground.sh
+++ /dev/null
@@ -1,7 +0,0 @@
-#! /bin/bash
-
-read pid cmd state ppid pgrp session tty_nr tpgid rest < /proc/self/stat
-trap "kill -TERM -$pgrp; exit" EXIT TERM KILL SIGKILL SIGTERM SIGQUIT
-
-source /etc/apache2/envvars
-/usr/sbin/apache2 -D FOREGROUND
diff --git a/docker/workbench/apache2_vhost.in b/docker/workbench/apache2_vhost.in
deleted file mode 100644
index ba9e7f8..0000000
--- a/docker/workbench/apache2_vhost.in
+++ /dev/null
@@ -1,35 +0,0 @@
-
-<VirtualHost *:80>
-
- ServerName workbench.@@ARVADOS_DOMAIN@@
- ServerAdmin sysadmin at curoverse.com
-
- RailsEnv @@WORKBENCH_RAILS_MODE@@
- RackBaseURI /
- RailsAppSpawnerIdleTime 1200
-
- # Index file and Document Root (where the public files are located)
- DirectoryIndex index.html
- DocumentRoot /usr/src/arvados/apps/workbench/public
-
- LogLevel warn
- ErrorLog ${APACHE_LOG_DIR}/error.log
- CustomLog ${APACHE_LOG_DIR}/access.log combined
-
- <Directory /usr/src/arvados/apps/workbench>
- Options Indexes FollowSymLinks MultiViews IncludesNoExec
- AllowOverride None
- Order allow,deny
- allow from all
- </Directory>
-
- <IfModule mod_ssl.c>
- SSLEngine off
- # SSLCertificateChainFile /etc/ssl/certs/startcom.sub.class1.server.ca.pem
- # SSLCACertificateFile /etc/ssl/certs/startcom.ca.pem
- SSLCertificateFile /etc/ssl/certs/ssl-cert-snakeoil.pem
- SSLCertificateKeyFile /etc/ssl/private/ssl-cert-snakeoil.key
- SetEnvIf User-Agent ".*MSIE.*" nokeepalive ssl-unclean-shutdown
- </IfModule>
-
-</VirtualHost>
diff --git a/docker/workbench/application.yml.in b/docker/workbench/application.yml.in
deleted file mode 100644
index 5e16928..0000000
--- a/docker/workbench/application.yml.in
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copy this file to application.yml and edit to suit.
-#
-# Consult application.default.yml for the full list of configuration
-# settings.
-#
-# The order of precedence is:
-# 1. config/environments/{RAILS_ENV}.rb (deprecated)
-# 2. Section in application.yml corresponding to RAILS_ENV (e.g., development)
-# 3. Section in application.yml called "common"
-# 4. Section in application.default.yml corresponding to RAILS_ENV
-# 5. Section in application.default.yml called "common"
-
-common:
- # At minimum, you need a nice long randomly generated secret_token here.
- secret_token: @@WORKBENCH_SECRET@@
-
- # You probably also want to point to your API server.
- arvados_login_base: 'https://api.@@ARVADOS_DOMAIN@@/login'
- arvados_v1_base: 'https://api.@@ARVADOS_DOMAIN@@/arvados/v1'
- arvados_insecure_https: @@WORKBENCH_INSECURE_HTTPS@@
-
- data_import_dir: @@WORKBENCH_DATA_IMPORT_DIR@@
- data_export_dir: @@WORKBENCH_DATA_EXPORT_DIR@@
-
- site_name: @@WORKBENCH_SITE_NAME@@
- activation_contact_link: @@WORKBENCH_ACTIVATION_CONTACT_LINK@@
-
- arvados_docsite: http://doc.@@ARVADOS_DOMAIN@@
- force_ssl: false
diff --git a/docker/workbench/production.rb.in b/docker/workbench/production.rb.in
deleted file mode 100644
index bc3bd33..0000000
--- a/docker/workbench/production.rb.in
+++ /dev/null
@@ -1,91 +0,0 @@
-ArvadosWorkbench::Application.configure do
- # Settings specified here will take precedence over those in config/application.rb
-
- # Code is not reloaded between requests
- config.cache_classes = true
-
- # Full error reports are disabled and caching is turned on
- config.consider_all_requests_local = false
- config.action_controller.perform_caching = true
-
- # Disable Rails's static asset server (Apache or nginx will already do this)
- config.serve_static_assets = false
-
- # Compress JavaScripts and CSS
- config.assets.compress = true
-
- # Don't fallback to assets pipeline if a precompiled asset is missed
- config.assets.compile = false
-
- # Generate digests for assets URLs
- config.assets.digest = true
-
- # Defaults to nil and saved in location specified by config.assets.prefix
- # config.assets.manifest = YOUR_PATH
-
- # Specifies the header that your server uses for sending files
- # config.action_dispatch.x_sendfile_header = "X-Sendfile" # for apache
- # config.action_dispatch.x_sendfile_header = 'X-Accel-Redirect' # for nginx
-
- # Force all access to the app over SSL, use Strict-Transport-Security, and use secure cookies.
- # config.force_ssl = true
-
- # See everything in the log (default is :info)
- # config.log_level = :debug
-
- # Prepend all log lines with the following tags
- # config.log_tags = [ :subdomain, :uuid ]
-
- # Use a different logger for distributed setups
- # config.logger = ActiveSupport::TaggedLogging.new(SyslogLogger.new)
-
- # Use a different cache store in production
- # config.cache_store = :mem_cache_store
-
- # Enable serving of images, stylesheets, and JavaScripts from an asset server
- # config.action_controller.asset_host = "http://assets.example.com"
-
- # Precompile additional assets (application.js, application.css, and all non-JS/CSS are already added)
- # config.assets.precompile += %w( search.js )
-
- # Disable delivery errors, bad email addresses will be ignored
- # config.action_mailer.raise_delivery_errors = false
-
- # Enable threaded mode
- # config.threadsafe!
-
- # Enable locale fallbacks for I18n (makes lookups for any locale fall back to
- # the I18n.default_locale when a translation can not be found)
- config.i18n.fallbacks = true
-
- # Send deprecation notices to registered listeners
- config.active_support.deprecation = :notify
-
- # Log the query plan for queries taking more than this (works
- # with SQLite, MySQL, and PostgreSQL)
- # config.active_record.auto_explain_threshold_in_seconds = 0.5
-
- # Log timing data for API transactions
- config.profiling_enabled = false
-
- config.arvados_login_base = 'https://' + ENV['API_PORT_443_TCP_ADDR'].to_s + '/login'
- config.arvados_v1_base = 'https://' + ENV['API_PORT_443_TCP_ADDR'].to_s + '/arvados/v1'
- config.arvados_insecure_https = @@WORKBENCH_INSECURE_HTTPS@@ # true = do not check server certificate
-
- config.data_import_dir = '@@WORKBENCH_DATA_IMPORT_DIR@@'
- config.data_export_dir = '@@WORKBENCH_DATA_EXPORT_DIR@@'
-
- # Authentication stub: hard code pre-approved API tokens.
- # config.accept_api_token = { rand(2**256).to_s(36) => true }
- config.accept_api_token = {}
-
- config.vcf_pipeline_uuid = '@@WORKBENCH_VCF_PIPELINE_UUID@@'
-
- config.site_name = '@@WORKBENCH_SITE_NAME@@'
- config.activation_contact_link = '@@WORKBENCH_ACTIVATION_CONTACT_LINK@@'
- config.arvados_docsite = 'http://doc.arvados.org'
-
- config.arvados_theme = 'default'
-
- config.show_user_agreement_inline = false
-end
diff --git a/docker/workbench/secret_token.rb.in b/docker/workbench/secret_token.rb.in
deleted file mode 100644
index 91c1a5c..0000000
--- a/docker/workbench/secret_token.rb.in
+++ /dev/null
@@ -1,7 +0,0 @@
-# Be sure to restart your server when you modify this file.
-
-# Your secret key for verifying the integrity of signed cookies.
-# If you change this key, all old signed cookies will become invalid!
-# Make sure the secret is at least 30 characters and all random,
-# no regular words or you'll be exposed to dictionary attacks.
-ArvadosWorkbench::Application.config.secret_token = '@@WORKBENCH_SECRET@@'
diff --git a/docker/workbench/workbench_rails_env.in b/docker/workbench/workbench_rails_env.in
deleted file mode 100644
index f4f7638..0000000
--- a/docker/workbench/workbench_rails_env.in
+++ /dev/null
@@ -1 +0,0 @@
-@@WORKBENCH_RAILS_MODE@@
\ No newline at end of file
-----------------------------------------------------------------------
hooks/post-receive
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