[ARVADOS-DEV] updated: 97424aa89b3f279986621ec5f574670dacb5a836
Git user
git at public.curoverse.com
Wed Mar 2 10:24:44 EST 2016
Summary of changes:
arvbox/README.md | 121 -------
arvbox/bin/arvbox | 402 ---------------------
arvbox/lib/arvbox/docker/Dockerfile.base | 42 ---
arvbox/lib/arvbox/docker/Dockerfile.demo | 17 -
arvbox/lib/arvbox/docker/Dockerfile.dev | 16 -
.../lib/arvbox/docker/application_yml_override.py | 24 --
arvbox/lib/arvbox/docker/common.sh | 62 ----
arvbox/lib/arvbox/docker/createusers.sh | 34 --
arvbox/lib/arvbox/docker/crunch-setup.sh | 28 --
arvbox/lib/arvbox/docker/fuse.conf | 1 -
arvbox/lib/arvbox/docker/gitolite.rc | 213 -----------
arvbox/lib/arvbox/docker/keep-setup.sh | 51 ---
arvbox/lib/arvbox/docker/logger | 2 -
arvbox/lib/arvbox/docker/runit-docker/.gitignore | 32 --
arvbox/lib/arvbox/docker/runit-docker/LICENSE | 28 --
arvbox/lib/arvbox/docker/runit-docker/Makefile | 18 -
arvbox/lib/arvbox/docker/runit-docker/README.md | 24 --
.../arvbox/docker/runit-docker/debian/changelog | 12 -
.../lib/arvbox/docker/runit-docker/debian/compat | 1 -
.../lib/arvbox/docker/runit-docker/debian/control | 14 -
.../arvbox/docker/runit-docker/debian/copyright | 31 --
arvbox/lib/arvbox/docker/runit-docker/debian/docs | 1 -
arvbox/lib/arvbox/docker/runit-docker/debian/rules | 32 --
.../docker/runit-docker/debian/source/format | 1 -
arvbox/lib/arvbox/docker/runit-docker/runit-docker | 4 -
.../lib/arvbox/docker/runit-docker/runit-docker.c | 32 --
arvbox/lib/arvbox/docker/runsu.sh | 14 -
.../arvbox/docker/service/api/log/main/.gitstub | 0
arvbox/lib/arvbox/docker/service/api/log/run | 1 -
arvbox/lib/arvbox/docker/service/api/run | 1 -
arvbox/lib/arvbox/docker/service/api/run-service | 102 ------
.../docker/service/arv-git-httpd/log/main/.gitstub | 0
.../arvbox/docker/service/arv-git-httpd/log/run | 1 -
arvbox/lib/arvbox/docker/service/arv-git-httpd/run | 1 -
.../docker/service/arv-git-httpd/run-service | 27 --
.../crunch-dispatch-local/log/main/.gitstub | 0
.../docker/service/crunch-dispatch-local/log/run | 1 -
.../docker/service/crunch-dispatch-local/run | 1 -
.../service/crunch-dispatch-local/run-service | 22 --
.../service/crunch-dispatch0/log/main/.gitstub | 0
.../arvbox/docker/service/crunch-dispatch0/log/run | 1 -
.../lib/arvbox/docker/service/crunch-dispatch0/run | 1 -
.../docker/service/crunch-dispatch0/run-service | 2 -
.../service/crunch-dispatch1/log/main/.gitstub | 0
.../arvbox/docker/service/crunch-dispatch1/log/run | 1 -
.../lib/arvbox/docker/service/crunch-dispatch1/run | 1 -
.../docker/service/crunch-dispatch1/run-service | 3 -
.../arvbox/docker/service/doc/log/main/.gitstub | 0
arvbox/lib/arvbox/docker/service/doc/log/run | 1 -
arvbox/lib/arvbox/docker/service/doc/run | 1 -
arvbox/lib/arvbox/docker/service/doc/run-service | 41 ---
.../arvbox/docker/service/docker/log/main/.gitstub | 0
arvbox/lib/arvbox/docker/service/docker/log/run | 1 -
arvbox/lib/arvbox/docker/service/docker/run | 102 ------
.../docker/service/gitolite/log/main/.gitstub | 0
arvbox/lib/arvbox/docker/service/gitolite/log/run | 1 -
arvbox/lib/arvbox/docker/service/gitolite/run | 1 -
.../lib/arvbox/docker/service/gitolite/run-service | 116 ------
.../docker/service/keep-web/log/main/.gitstub | 0
arvbox/lib/arvbox/docker/service/keep-web/log/run | 1 -
arvbox/lib/arvbox/docker/service/keep-web/run | 1 -
.../lib/arvbox/docker/service/keep-web/run-service | 21 --
.../docker/service/keepproxy/log/main/.gitstub | 0
arvbox/lib/arvbox/docker/service/keepproxy/log/run | 1 -
arvbox/lib/arvbox/docker/service/keepproxy/run | 1 -
.../arvbox/docker/service/keepproxy/run-service | 41 ---
.../docker/service/keepstore0/log/main/.gitstub | 0
.../lib/arvbox/docker/service/keepstore0/log/run | 1 -
arvbox/lib/arvbox/docker/service/keepstore0/run | 1 -
.../arvbox/docker/service/keepstore0/run-service | 3 -
.../docker/service/keepstore1/log/main/.gitstub | 0
.../lib/arvbox/docker/service/keepstore1/log/run | 1 -
arvbox/lib/arvbox/docker/service/keepstore1/run | 1 -
.../arvbox/docker/service/keepstore1/run-service | 3 -
.../docker/service/postgres/log/main/.gitstub | 0
arvbox/lib/arvbox/docker/service/postgres/log/run | 1 -
arvbox/lib/arvbox/docker/service/postgres/run | 12 -
.../lib/arvbox/docker/service/postgres/run-service | 14 -
arvbox/lib/arvbox/docker/service/ready/run | 1 -
arvbox/lib/arvbox/docker/service/ready/run-service | 96 -----
.../arvbox/docker/service/sdk/log/main/.gitstub | 0
arvbox/lib/arvbox/docker/service/sdk/log/run | 1 -
arvbox/lib/arvbox/docker/service/sdk/run | 5 -
arvbox/lib/arvbox/docker/service/sdk/run-service | 24 --
.../docker/service/slurmctld/log/main/.gitstub | 0
arvbox/lib/arvbox/docker/service/slurmctld/log/run | 1 -
arvbox/lib/arvbox/docker/service/slurmctld/run | 31 --
.../arvbox/docker/service/slurmd/log/main/.gitstub | 0
arvbox/lib/arvbox/docker/service/slurmd/log/run | 1 -
arvbox/lib/arvbox/docker/service/slurmd/run | 6 -
.../arvbox/docker/service/ssh/log/main/.gitstub | 0
arvbox/lib/arvbox/docker/service/ssh/log/run | 1 -
arvbox/lib/arvbox/docker/service/ssh/run | 10 -
.../arvbox/docker/service/sso/log/main/.gitstub | 0
arvbox/lib/arvbox/docker/service/sso/log/run | 1 -
arvbox/lib/arvbox/docker/service/sso/run | 1 -
arvbox/lib/arvbox/docker/service/sso/run-service | 87 -----
.../lib/arvbox/docker/service/vm/log/main/.gitstub | 0
arvbox/lib/arvbox/docker/service/vm/log/run | 1 -
arvbox/lib/arvbox/docker/service/vm/run | 21 --
arvbox/lib/arvbox/docker/service/vm/run-service | 36 --
.../docker/service/workbench/log/main/.gitstub | 0
arvbox/lib/arvbox/docker/service/workbench/log/run | 1 -
arvbox/lib/arvbox/docker/service/workbench/run | 15 -
.../arvbox/docker/service/workbench/run-service | 40 --
arvbox/lib/arvbox/docker/waitforpostgres.sh | 4 -
106 files changed, 2174 deletions(-)
delete mode 100644 arvbox/README.md
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delete mode 100644 arvbox/lib/arvbox/docker/Dockerfile.base
delete mode 100644 arvbox/lib/arvbox/docker/Dockerfile.demo
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delete mode 100755 arvbox/lib/arvbox/docker/application_yml_override.py
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delete mode 100755 arvbox/lib/arvbox/docker/waitforpostgres.sh
via 97424aa89b3f279986621ec5f574670dacb5a836 (commit)
from 623af8e46e921f59abeeee9e7ae8ec4aef890b5b (commit)
Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit 97424aa89b3f279986621ec5f574670dacb5a836
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Wed Mar 2 10:24:08 2016 -0500
Remove arvbox from arvados-dev (now in arvados/tools) refs #8231
diff --git a/arvbox/README.md b/arvbox/README.md
deleted file mode 100644
index 8098686..0000000
--- a/arvbox/README.md
+++ /dev/null
@@ -1,121 +0,0 @@
-# Arvados-in-a-box
-
-Self-contained development, demonstration and testing environment for Arvados.
-
-## Quick start
-
-```
-$ bin/arvbox reboot localdemo
-```
-
-## Usage
-
-```
-Arvados-in-a-box
-
-arvbox (build|start|run|open|shell|ip|stop|reboot|reset|destroy|log|svrestart)
-
-build <config> build arvbox Docker image
-start|run <config> start arvbox container
-open open arvbox workbench in a web browser
-shell enter arvbox shell
-ip print arvbox ip address
-stop stop arvbox container
-restart <config> stop, then run again
-reboot <config> stop, build arvbox Docker image, run
-reset delete arvbox arvados data (be careful!)
-destroy delete all arvbox code and data (be careful!)
-log <service> tail log of specified service
-svrestart <service> restart specified service inside arvbox
-clone <from> <to> clone an arvbox
-```
-
-## Requirements
-
-* Linux 3.x+ and Docker 1.9+
-* Minimum of 3 GiB of RAM + additional memory to run jobs
-* Minimum of 3 GiB of disk + storage for actual data
-
-## Configs
-
-### dev
-Development configuration. Boots a complete Arvados environment inside the
-container. The "arvados", "arvado-dev" and "sso-devise-omniauth-provider" code
-directories along data directories "postgres", "var", "passenger" and "gems"
-are bind mounted from the host file system for easy access and persistence
-across container rebuilds. Services are bound to the Docker container's
-network IP address and can only be accessed on the local host.
-
-In "dev" mode, you can override the default autogenerated settings of Rails
-projects by adding "application.yml.override" to any Rails project (sso, api,
-workbench). This can be used to test out API server settings or point
-Workbench at an alternate API server.
-
-### localdemo
-Demo configuration. Boots a complete Arvados environment inside the container.
-Unlike the development configuration, code directories are included in the demo
-image, and data directories are stored in a separate data volume container.
-Services are bound to the Docker container's network IP address and can only be
-accessed on the local host.
-
-### test
-Run the test suite.
-
-### publicdev
-Publicly accessible development configuration. Similar to 'dev' except that
-service ports are published to the host's IP address and can accessed by anyone
-who can connect to the host system. WARNING! The public arvbox configuration
-is NOT SECURE and must not be placed on a public IP address or used for
-production work.
-
-### publicdemo
-Publicly accessible development configuration. Similar to 'localdemo' except
-that service ports are published to the host's IP address and can accessed by
-anyone who can connect to the host system. WARNING! The public arvbox configuration
-is NOT SECURE and must not be placed on a public IP address or used for
-production work.
-
-## Environment variables
-
-### ARVBOX_DOCKER
-The location of Dockerfile.base and associated files used by "arvbox build".
-default: result of $(readlink -f $(dirname $0)/../lib/arvbox/docker)
-
-### ARVBOX_CONTAINER
-The name of the Docker container to manipulate.
-default: arvbox
-
-### ARVBOX_BASE
-The base directory to store persistent data for arvbox containers.
-default: $HOME/.arvbox
-
-### ARVBOX_DATA
-The base directory to store persistent data for the current container.
-default: $ARVBOX_BASE/$ARVBOX_CONTAINER
-
-### ARVADOS_ROOT
-The root directory of the Arvados source tree
-default: $ARVBOX_DATA/arvados
-
-### ARVADOS_DEV_ROOT
-The root directory of the Arvados-dev source tree
-default: $ARVBOX_DATA/arvados-dev
-
-### SSO_ROOT
-The root directory of the SSO source tree
-default: $ARVBOX_DATA/sso-devise-omniauth-provider
-
-### ARVBOX_PUBLISH_IP
-The IP address on which to publish services when running in public
-configuration. Overrides default detection of the host's IP address.
-
-## Notes
-
-Services are designed to install and auto-configure on start or restart. For
-example, the service script for keepstore always compiles keepstore from source
-and registers the daemon with the API server.
-
-Services are run with process supervision, so a service which exits will be
-restarted. Dependencies between services are handled by repeatedly trying and
-failing the service script until dependencies are fulfilled (by other service
-scripts) enabling the service script to complete.
diff --git a/arvbox/bin/arvbox b/arvbox/bin/arvbox
deleted file mode 100755
index d790cb6..0000000
--- a/arvbox/bin/arvbox
+++ /dev/null
@@ -1,402 +0,0 @@
-#!/bin/sh
-
-set -e
-
-if ! test -d /sys/fs/cgroup ; then
- echo "Arvbox requires cgroups to be mounted at /sys/fs/cgroup in order to use"
- echo "Docker-in-Docker. Older operating systems that put cgroups in other"
- echo "places (such as /cgroup) are not supported."
- exit 1
-fi
-
-if ! which docker >/dev/null 2>/dev/null ; then
- echo "Arvbox requires Docker. To install, run the following command as root:"
- echo "curl -sSL https://get.docker.com/ | sh"
- exit 1
-fi
-
-if test -z "$ARVBOX_DOCKER" ; then
- if which greadlink >/dev/null 2>/dev/null ; then
- ARVBOX_DOCKER=$(greadlink -f $(dirname $0)/../lib/arvbox/docker)
- else
- ARVBOX_DOCKER=$(readlink -f $(dirname $0)/../lib/arvbox/docker)
- fi
-fi
-
-if test -z "$ARVBOX_CONTAINER" ; then
- ARVBOX_CONTAINER=arvbox
-fi
-
-if test -z "$ARVBOX_BASE" ; then
- ARVBOX_BASE="$HOME/.arvbox"
-fi
-
-if test -z "$ARVBOX_DATA" ; then
- ARVBOX_DATA="$ARVBOX_BASE/$ARVBOX_CONTAINER"
-fi
-
-if test -z "$ARVADOS_ROOT" ; then
- ARVADOS_ROOT="$ARVBOX_DATA/arvados"
-fi
-
-if test -z "$ARVADOS_DEV_ROOT" ; then
- ARVADOS_DEV_ROOT="$ARVBOX_DATA/arvados-dev"
-fi
-
-if test -z "$SSO_ROOT" ; then
- SSO_ROOT="$ARVBOX_DATA/sso-devise-omniauth-provider"
-fi
-
-PG_DATA="$ARVBOX_DATA/postgres"
-VAR_DATA="$ARVBOX_DATA/var"
-PASSENGER="$ARVBOX_DATA/passenger"
-GEMS="$ARVBOX_DATA/gems"
-
-getip() {
- docker inspect $ARVBOX_CONTAINER | grep \"IPAddress\" | head -n1 | tr -d ' ":,\n' | cut -c10-
-}
-
-updateconf() {
- if test -f ~/.config/arvados/$ARVBOX_CONTAINER.conf ; then
- sed "s/ARVADOS_API_HOST=.*/ARVADOS_API_HOST=$(getip):8000/" <$HOME/.config/arvados/$ARVBOX_CONTAINER.conf >$HOME/.config/arvados/$ARVBOX_CONTAINER.conf.tmp
- mv ~/.config/arvados/$ARVBOX_CONTAINER.conf.tmp ~/.config/arvados/$ARVBOX_CONTAINER.conf
- else
- mkdir -p $HOME/.config/arvados
- cat >$HOME/.config/arvados/$ARVBOX_CONTAINER.conf <<EOF
-ARVADOS_API_HOST=$(getip):8000
-ARVADOS_API_TOKEN=
-ARVADOS_API_HOST_INSECURE=true
-EOF
- fi
-}
-
-wait_for_arvbox() {
- FF=/tmp/arvbox-fifo-$$
- mkfifo $FF
- docker logs -f $ARVBOX_CONTAINER > $FF &
- LOGPID=$!
- while read line ; do
- echo $line
- if echo $line | grep "Workbench is running at" >/dev/null ; then
- kill $LOGPID
- fi
- done < $FF
- rm $FF
- echo
- if test -n "$localip" ; then
- echo "export ARVADOS_API_HOST=$localip:8000"
- else
- echo "export ARVADOS_API_HOST=$(getip):8000"
- fi
-}
-
-run() {
- if docker ps -a | grep -E "$ARVBOX_CONTAINER$" -q ; then
- echo "Container $ARVBOX_CONTAINER is already running, use stop, restart or reboot"
- exit 0
- fi
-
- if echo "$1" | grep '^public' ; then
- if test -n "$ARVBOX_PUBLISH_IP" ; then
- localip=$ARVBOX_PUBLISH_IP
- else
- defaultdev=$(/sbin/ip route|awk '/default/ { print $5 }')
- localip=$(ip addr show $defaultdev | grep 'inet ' | sed 's/ *inet \(.*\)\/.*/\1/')
- fi
- iptemp=$(tempfile)
- echo $localip > $iptemp
- chmod og+r $iptemp
- PUBLIC="--volume=$iptemp:/var/run/localip_override
- --publish=80:80
- --publish=8000:8000
- --publish=8900:8900
- --publish=9001:9001
- --publish=9002:9002
- --publish=25100:25100
- --publish=25107:25107
- --publish=25108:25108
- --publish=8001:8001"
- else
- PUBLIC=""
- fi
-
- if echo "$1" | grep 'demo$' ; then
- if test -d "$ARVBOX_DATA" ; then
- echo "It looks like you already have a development container named $ARVBOX_CONTAINER."
- echo "Set ARVBOX_CONTAINER to set a different name for your demo container"
- exit 1
- fi
-
- if ! (docker ps -a | grep -E "$ARVBOX_CONTAINER-data$" -q) ; then
- docker create -v /var/lib/postgresql -v /var/lib/arvados --name $ARVBOX_CONTAINER-data arvados/arvbox-demo /bin/true
- fi
-
- docker run \
- --detach \
- --name=$ARVBOX_CONTAINER \
- --privileged \
- --volumes-from $ARVBOX_CONTAINER-data \
- $PUBLIC \
- arvados/arvbox-demo
- updateconf
- wait_for_arvbox
- else
- mkdir -p "$PG_DATA" "$VAR_DATA" "$PASSENGER" "$GEMS"
-
- if ! test -d "$ARVADOS_ROOT" ; then
- git clone https://github.com/curoverse/arvados.git "$ARVADOS_ROOT"
- fi
- if ! test -d "$SSO_ROOT" ; then
- git clone https://github.com/curoverse/sso-devise-omniauth-provider.git "$SSO_ROOT"
- fi
-
- if test "$1" = test ; then
- shift
-
- if ! test -d "$ARVADOS_DEV_ROOT" ; then
- git clone https://github.com/curoverse/arvados-dev.git "$ARVADOS_DEV_ROOT"
- fi
-
- mkdir -p $VAR_DATA/test
-
- docker run \
- --detach \
- --name=$ARVBOX_CONTAINER \
- --privileged \
- "--volume=$ARVADOS_ROOT:/usr/src/arvados:rw" \
- "--volume=$ARVADOS_DEV_ROOT:/usr/src/arvados-dev:rw" \
- "--volume=$SSO_ROOT:/usr/src/sso:rw" \
- "--volume=$PG_DATA:/var/lib/postgresql:rw" \
- "--volume=$VAR_DATA:/var/lib/arvados:rw" \
- "--volume=$PASSENGER:/var/lib/passenger:rw" \
- "--volume=$GEMS:/var/lib/gems:rw" \
- arvados/arvbox-dev \
- /usr/local/bin/runsvinit -svdir=/etc/test-service
-
- docker exec -ti \
- $ARVBOX_CONTAINER \
- /usr/local/lib/arvbox/runsu.sh \
- /usr/local/lib/arvbox/waitforpostgres.sh
-
- docker exec -ti \
- $ARVBOX_CONTAINER \
- /usr/local/lib/arvbox/runsu.sh \
- /var/lib/arvbox/service/sso/run-service --only-setup
-
- docker exec -ti \
- $ARVBOX_CONTAINER \
- /usr/local/lib/arvbox/runsu.sh \
- /var/lib/arvbox/service/api/run-service --only-setup
-
- docker exec -ti \
- $ARVBOX_CONTAINER \
- /usr/local/lib/arvbox/runsu.sh \
- /usr/src/arvados-dev/jenkins/run-tests.sh \
- --temp /var/lib/arvados/test \
- WORKSPACE=/usr/src/arvados \
- GEM_HOME=/var/lib/gems \
- "$@"
- elif echo "$1" | grep 'dev$' ; then
- docker run \
- --detach \
- --name=$ARVBOX_CONTAINER \
- --privileged \
- "--volume=$ARVADOS_ROOT:/usr/src/arvados:rw" \
- "--volume=$SSO_ROOT:/usr/src/sso:rw" \
- "--volume=$PG_DATA:/var/lib/postgresql:rw" \
- "--volume=$VAR_DATA:/var/lib/arvados:rw" \
- "--volume=$PASSENGER:/var/lib/passenger:rw" \
- "--volume=$GEMS:/var/lib/gems:rw" \
- $PUBLIC \
- arvados/arvbox-dev
- updateconf
- wait_for_arvbox
- echo "The Arvados source code is checked out at: $ARVADOS_ROOT"
- else
- echo "Unknown configuration '$1'"
- fi
- fi
-}
-
-stop() {
- if docker ps -a --filter "status=running" | grep -E "$ARVBOX_CONTAINER$" -q ; then
- docker stop $ARVBOX_CONTAINER
- fi
-
- VOLUMES=--volumes=true
- if docker ps -a --filter "status=created" | grep -E "$ARVBOX_CONTAINER$" -q ; then
- docker rm $VOLUMES $ARVBOX_CONTAINER
- fi
- if docker ps -a --filter "status=exited" | grep -E "$ARVBOX_CONTAINER$" -q ; then
- docker rm $VOLUMES $ARVBOX_CONTAINER
- fi
-}
-
-build() {
- if ! test -f "$ARVBOX_DOCKER/Dockerfile.base" ; then
- echo "Could not find Dockerfile ($ARVBOX_DOCKER/Dockerfile.base)"
- exit 1
- fi
- docker build -t arvados/arvbox-base -f "$ARVBOX_DOCKER/Dockerfile.base" "$ARVBOX_DOCKER"
- if test "$1" = localdemo -o "$1" = publicdemo ; then
- docker build -t arvados/arvbox-demo -f "$ARVBOX_DOCKER/Dockerfile.demo" "$ARVBOX_DOCKER"
- else
- docker build -t arvados/arvbox-dev -f "$ARVBOX_DOCKER/Dockerfile.dev" "$ARVBOX_DOCKER"
- fi
-}
-
-check() {
- case "$1" in
- localdemo|publicdemo|dev|publicdev|test)
- true
- ;;
- *)
- echo "Argument to $subcmd must be one of localdemo, publicdemo, dev, publicdev, test"
- exit 1
- ;;
- esac
-}
-
-subcmd="$1"
-if test -n "$subcmd" ; then
- shift
-fi
-case "$subcmd" in
- build)
- check $@
- build $@
- ;;
-
- start|run)
- check $@
- run $@
- ;;
-
- sh*)
- docker exec -ti $ARVBOX_CONTAINER /usr/bin/env TERM=$TERM GEM_HOME=/var/lib/gems /bin/bash
- ;;
-
- stop)
- stop
- ;;
-
- restart)
- check $@
- stop
- run $@
- ;;
-
- reboot)
- check $@
- stop
- build $@
- run $@
- ;;
-
- ip|open)
- if test "$subcmd" = 'ip' ; then
- echo $(getip)
- else
- xdg-open http://$(getip)
- fi
- ;;
-
- status)
- echo "Selected: $ARVBOX_CONTAINER"
- if docker ps -a --filter "status=running" | grep -E "$ARVBOX_CONTAINER$" -q ; then
- echo "Status: running"
- echo "IP: $(getip)"
- else
- echo "Status: not running"
- fi
- if test -d "$ARVBOX_DATA" ; then
- echo "Data: $ARVBOX_DATA"
- elif docker ps -a | grep -E "$ARVBOX_CONTAINER-data$" -q ; then
- echo "Data: $ARVBOX_CONTAINER-data"
- else
- echo "Data: none"
- fi
- ;;
-
- reset|destroy)
- stop
- if test -d "$ARVBOX_DATA" ; then
- if test "$subcmd" = destroy ; then
- if test "$1" != -f ; then
- echo "WARNING! This will delete your entire arvbox ($ARVBOX_DATA)."
- echo "Use destroy -f if you really mean it."
- exit 1
- fi
- set -x
- rm -rf "$ARVBOX_DATA"
- else
- if test "$1" != -f ; then
- echo "WARNING! This will delete your arvbox data ($ARVBOX_DATA)."
- echo "Code and downloaded packages will be preserved."
- echo "Use reset -f if you really mean it."
- exit 1
- fi
- set -x
- rm -rf "$ARVBOX_DATA/postgres"
- rm -rf "$ARVBOX_DATA/var"
- fi
- else
- if test "$1" != -f ; then
- echo "WARNING! This will delete your data container $ARVBOX_CONTAINER-data. Use -f if you really mean it."
- exit 1
- fi
- set -x
- docker rm "$ARVBOX_CONTAINER-data"
- fi
- ;;
-
- log)
- if test -n "$1" ; then
- docker exec -ti $ARVBOX_CONTAINER /usr/bin/env TERM=$TERM less --follow-name +GF "/etc/service/$1/log/main/current"
- else
- docker exec -ti $ARVBOX_CONTAINER /usr/bin/env TERM=$TERM tail $(docker exec -ti $ARVBOX_CONTAINER find -L /etc -path '/etc/service/*/log/main/current' -printf " %p")
- fi
- ;;
-
- sv)
- if test -n "$1" ; then
- docker exec -ti $ARVBOX_CONTAINER sv "$1" "$2"
- else
- echo "Usage: $0 $subcmd <service>"
- echo "Available services:"
- docker exec -ti $ARVBOX_CONTAINER ls /etc/service
- fi
- ;;
-
- clone)
- if test -n "$2" ; then
- cp -r "$ARVBOX_BASE/$1" "$ARVBOX_BASE/$2"
- echo "Created new arvbox $2"
- echo "export ARVBOX_CONTAINER=$2"
- else
- echo "clone <from> <to> clone an arvbox"
- echo "available arvboxes: $(ls $ARVBOX_BASE)"
- fi
- ;;
-
- *)
- echo "Arvados-in-a-box"
- echo
- echo "$(basename $0) (build|start|run|open|shell|ip|stop|reboot|reset|destroy|log|svrestart)"
- echo
- echo "build <config> build arvbox Docker image"
- echo "start|run <config> start $ARVBOX_CONTAINER container"
- echo "open open arvbox workbench in a web browser"
- echo "shell enter arvbox shell"
- echo "ip print arvbox ip address"
- echo "status print some information about current arvbox"
- echo "stop stop arvbox container"
- echo "restart <config> stop, then run again"
- echo "reboot <config> stop, build arvbox Docker image, run"
- echo "reset delete arvbox arvados data (be careful!)"
- echo "destroy delete all arvbox code and data (be careful!)"
- echo "log <service> tail log of specified service"
- echo "sv <start|stop|restart> <service> change state of service inside arvbox"
- echo "clone <from> <to> clone an arvbox"
- ;;
-esac
diff --git a/arvbox/lib/arvbox/docker/Dockerfile.base b/arvbox/lib/arvbox/docker/Dockerfile.base
deleted file mode 100644
index 280ac68..0000000
--- a/arvbox/lib/arvbox/docker/Dockerfile.base
+++ /dev/null
@@ -1,42 +0,0 @@
-FROM debian:8
-
-RUN apt-get update && \
- DEBIAN_FRONTEND=noninteractive apt-get -yq install \
- postgresql-9.4 git gcc golang-go runit \
- ruby rake bundler curl libpq-dev \
- libcurl4-openssl-dev libssl-dev zlib1g-dev libpcre3-dev \
- openssh-server python-setuptools netcat-traditional \
- libpython-dev fuse libfuse-dev python-pip python-yaml \
- pkg-config libattr1-dev python-llfuse python-pycurl \
- libwww-perl libio-socket-ssl-perl libcrypt-ssleay-perl \
- libjson-perl nginx gitolite3 lsof python-epydoc graphviz \
- apt-transport-https ca-certificates slurm-wlm
-
-VOLUME /var/lib/docker
-VOLUME /var/log/nginx
-VOLUME /etc/ssl/private
-
-RUN apt-key adv --keyserver hkp://pool.sks-keyservers.net:80 --recv-keys 58118E89F3A912897C070ADBF76221572C52609D || \
- apt-key adv --keyserver hkp://pgp.mit.edu:80 --recv-keys 58118E89F3A912897C070ADBF76221572C52609D
-
-RUN mkdir -p /etc/apt/sources.list.d && \
- echo deb https://apt.dockerproject.org/repo debian-jessie main > /etc/apt/sources.list.d/docker.list && \
- apt-get update && \
- DEBIAN_FRONTEND=noninteractive apt-get -yq install docker-engine=1.9.1-0~jessie
-
-RUN rm -rf /var/lib/postgresql && mkdir -p /var/lib/postgresql
-
-RUN cd /root && \
- GOPATH=$PWD go get github.com/curoverse/runsvinit && \
- install bin/runsvinit /usr/local/bin
-
-ADD fuse.conf /etc/
-
-ADD crunch-setup.sh gitolite.rc \
- keep-setup.sh common.sh createusers.sh \
- logger runsu.sh waitforpostgres.sh \
- application_yml_override.py \
- /usr/local/lib/arvbox/
-
-# Start the supervisor.
-CMD ["/usr/local/bin/runsvinit"]
diff --git a/arvbox/lib/arvbox/docker/Dockerfile.demo b/arvbox/lib/arvbox/docker/Dockerfile.demo
deleted file mode 100644
index 1f13415..0000000
--- a/arvbox/lib/arvbox/docker/Dockerfile.demo
+++ /dev/null
@@ -1,17 +0,0 @@
-FROM arvados/arvbox-base
-
-RUN cd /usr/src && \
- git clone https://github.com/curoverse/arvados.git && \
- git clone https://github.com/curoverse/sso-devise-omniauth-provider.git sso
-
-ADD service/ /var/lib/arvbox/service
-RUN rmdir /etc/service && ln -sf /var/lib/arvbox/service /etc
-
-RUN chown -R 1000:1000 /usr/src && /usr/local/lib/arvbox/createusers.sh
-
-RUN sudo -u arvbox /var/lib/arvbox/service/sso/run-service --only-deps
-RUN sudo -u arvbox /var/lib/arvbox/service/api/run-service --only-deps
-RUN sudo -u arvbox /var/lib/arvbox/service/workbench/run-service --only-deps
-RUN sudo -u arvbox /var/lib/arvbox/service/doc/run-service --only-deps
-RUN sudo -u arvbox /var/lib/arvbox/service/vm/run-service --only-deps
-RUN sudo -u arvbox /var/lib/arvbox/service/sdk/run-service
diff --git a/arvbox/lib/arvbox/docker/Dockerfile.dev b/arvbox/lib/arvbox/docker/Dockerfile.dev
deleted file mode 100644
index 051c274..0000000
--- a/arvbox/lib/arvbox/docker/Dockerfile.dev
+++ /dev/null
@@ -1,16 +0,0 @@
-FROM arvados/arvbox-base
-
-RUN apt-get update && \
- DEBIAN_FRONTEND=noninteractive apt-get -yq install \
- python-virtualenv python3-virtualenv linkchecker xvfb iceweasel
-
-RUN set -e && \
- PJS=phantomjs-1.9.7-linux-x86_64 && \
- curl -L -o/tmp/$PJS.tar.bz2 https://bitbucket.org/ariya/phantomjs/downloads/$PJS.tar.bz2 && \
- tar -C /usr/local -xjf /tmp/$PJS.tar.bz2 && \
- ln -s ../$PJS/bin/phantomjs /usr/local/bin/
-
-ADD service/ /var/lib/arvbox/service
-RUN rmdir /etc/service && ln -sf /var/lib/arvbox/service /etc
-
-RUN mkdir /etc/test-service && ln -sf /var/lib/arvbox/service/postgres /etc/test-service
diff --git a/arvbox/lib/arvbox/docker/application_yml_override.py b/arvbox/lib/arvbox/docker/application_yml_override.py
deleted file mode 100755
index 98a8e48..0000000
--- a/arvbox/lib/arvbox/docker/application_yml_override.py
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env python
-
-import yaml
-
-try:
- with open("application.yml.override") as f:
- b = yaml.load(f)
-except IOError:
- exit()
-
-with open("application.yml") as f:
- a = yaml.load(f)
-
-def recursiveMerge(a, b):
- if isinstance(a, dict) and isinstance(b, dict):
- for k in b:
- print k
- a[k] = recursiveMerge(a.get(k), b[k])
- return a
- else:
- return b
-
-with open("application.yml", "w") as f:
- yaml.dump(recursiveMerge(a, b), f)
diff --git a/arvbox/lib/arvbox/docker/common.sh b/arvbox/lib/arvbox/docker/common.sh
deleted file mode 100644
index 4c2de47..0000000
--- a/arvbox/lib/arvbox/docker/common.sh
+++ /dev/null
@@ -1,62 +0,0 @@
-
-if test -s /var/run/localip_override ; then
- localip=$(cat /var/run/localip_override)
-else
- defaultdev=$(/sbin/ip route|awk '/default/ { print $5 }')
- localip=$(ip addr show $defaultdev | grep 'inet ' | sed 's/ *inet \(.*\)\/.*/\1/')
-fi
-
-export GEM_HOME=/var/lib/gems
-export GEM_PATH=/var/lib/gems
-
-declare -A services
-services=(
- [workbench]=80
- [api]=8000
- [sso]=8900
- [arv-git-httpd]=9001
- [keep-web]=9002
- [keepproxy]=25100
- [keepstore0]=25107
- [keepstore1]=25108
- [ssh]=22
- [doc]=8001
-)
-
-if test "$(id arvbox -u 2>/dev/null)" = 0 ; then
- PGUSER=postgres
- PGGROUP=postgres
-else
- PGUSER=arvbox
- PGGROUP=arvbox
-fi
-
-run_bundler() {
- if test -f Gemfile.lock ; then
- frozen=--frozen
- else
- frozen=""
- fi
- if ! flock /var/lib/arvados/gems.lock bundle install --path $GEM_HOME --local --no-deployment $frozen "$@" ; then
- flock /var/lib/arvados/gems.lock bundle install --path $GEM_HOME --no-deployment $frozen "$@"
- fi
-}
-
-pip_install() {
- pushd /var/lib/arvados/pip
- for p in $(ls http*.tar.gz) ; do
- if test -f $p ; then
- ln -sf $p $(echo $p | sed 's/.*%2F\(.*\)/\1/')
- fi
- done
- for p in $(ls http*.whl) ; do
- if test -f $p ; then
- ln -sf $p $(echo $p | sed 's/.*%2F\(.*\)/\1/')
- fi
- done
- popd
-
- if ! pip install --no-index --find-links /var/lib/arvados/pip $1 ; then
- pip install $1
- fi
-}
diff --git a/arvbox/lib/arvbox/docker/createusers.sh b/arvbox/lib/arvbox/docker/createusers.sh
deleted file mode 100755
index b77c9c2..0000000
--- a/arvbox/lib/arvbox/docker/createusers.sh
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/bin/bash
-
-set -e -o pipefail
-
-if ! grep "^arvbox:" /etc/passwd >/dev/null 2>/dev/null ; then
- HOSTUID=$(ls -nd /usr/src/arvados | sed 's/ */ /' | cut -d' ' -f4)
- HOSTGID=$(ls -nd /usr/src/arvados | sed 's/ */ /' | cut -d' ' -f5)
- FUSEGID=$(ls -nd /dev/fuse | sed 's/ */ /' | cut -d' ' -f5)
-
- mkdir -p /var/lib/arvados/git /var/lib/gems /var/lib/passenger
-
- groupadd --gid $HOSTGID --non-unique arvbox
- groupadd --gid $FUSEGID --non-unique fuse
- groupadd --gid $HOSTGID --non-unique git
- useradd --home-dir /var/lib/arvados \
- --uid $HOSTUID --gid $HOSTGID \
- --non-unique \
- --groups docker,fuse \
- arvbox
- useradd --home-dir /var/lib/arvados/git --uid $HOSTUID --gid $HOSTGID --non-unique git
- useradd --groups docker,fuse crunch
-
- chown arvbox:arvbox -R /usr/local /var/lib/arvados /var/lib/gems \
- /var/lib/passenger /var/lib/postgresql \
- /var/lib/nginx /var/log/nginx /etc/ssl/private
-
- mkdir -p /var/lib/gems/ruby/2.1.0
- chown arvbox:arvbox -R /var/lib/gems/ruby/2.1.0
-
- mkdir -p /tmp/crunch0 /tmp/crunch1
- chown crunch:crunch -R /tmp/crunch0 /tmp/crunch1
-
- echo "arvbox ALL=(crunch) NOPASSWD: ALL" >> /etc/sudoers
-fi
diff --git a/arvbox/lib/arvbox/docker/crunch-setup.sh b/arvbox/lib/arvbox/docker/crunch-setup.sh
deleted file mode 100755
index 178fec1..0000000
--- a/arvbox/lib/arvbox/docker/crunch-setup.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/bin/bash
-
-exec 2>&1
-set -eux -o pipefail
-
-. /usr/local/lib/arvbox/common.sh
-
-mkdir -p /var/lib/arvados/gostuff
-cd /var/lib/arvados/gostuff
-
-export GOPATH=$PWD
-mkdir -p "$GOPATH/src/git.curoverse.com"
-ln -sfn "/usr/src/arvados" "$GOPATH/src/git.curoverse.com/arvados.git"
-flock /var/lib/arvados/gostuff.lock go get -t "git.curoverse.com/arvados.git/services/crunchstat"
-install bin/crunchstat /usr/local/bin
-
-export ARVADOS_API_HOST=$localip:${services[api]}
-export ARVADOS_API_HOST_INSECURE=1
-export ARVADOS_API_TOKEN=$(cat /usr/src/arvados/services/api/superuser_token)
-export CRUNCH_JOB_BIN=/usr/src/arvados/sdk/cli/bin/crunch-job
-export PERLLIB=/usr/src/arvados/sdk/perl/lib
-export CRUNCH_TMP=/tmp/$1
-export CRUNCH_DISPATCH_LOCKFILE=/var/lock/$1-dispatch
-export CRUNCH_JOB_DOCKER_BIN=docker
-export HOME=/tmp/$1
-
-cd /usr/src/arvados/services/api
-exec bundle exec ./script/crunch-dispatch.rb development
diff --git a/arvbox/lib/arvbox/docker/fuse.conf b/arvbox/lib/arvbox/docker/fuse.conf
deleted file mode 100644
index a439ab8..0000000
--- a/arvbox/lib/arvbox/docker/fuse.conf
+++ /dev/null
@@ -1 +0,0 @@
-user_allow_other
diff --git a/arvbox/lib/arvbox/docker/gitolite.rc b/arvbox/lib/arvbox/docker/gitolite.rc
deleted file mode 100644
index 03c4b29..0000000
--- a/arvbox/lib/arvbox/docker/gitolite.rc
+++ /dev/null
@@ -1,213 +0,0 @@
-# This is based on the default Gitolite configuration file with the following
-# changes applied as described here:
-# http://doc.arvados.org/install/install-arv-git-httpd.html
-
-# 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 = (
-
- REPO_ALIASES => $repo_aliases,
-
- # ------------------------------------------------------------------
-
- # 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,
- # logging options
- # 1. leave this section as is for 'normal' gitolite logging (default)
- # 2. uncomment this line to log ONLY to syslog:
- # LOG_DEST => 'syslog',
- # 3. uncomment this line to log to syslog and the normal gitolite log:
- # LOG_DEST => 'syslog,normal',
- # 4. prefixing "repo-log," to any of the above will **also** log just the
- # update records to "gl-log" in the bare repo directory:
- # LOG_DEST => 'repo-log,normal',
- # LOG_DEST => 'repo-log,syslog',
- # LOG_DEST => 'repo-log,syslog,normal',
-
- # 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,
- },
-
- # enable caching (currently only Redis). PLEASE RTFM BEFORE USING!!!
- # CACHE => 'Redis',
-
- # ------------------------------------------------------------------
-
- # 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 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",
-
- # TTL for redis cache; PLEASE SEE DOCUMENTATION BEFORE UNCOMMENTING!
- # CACHE_TTL => 600,
-
- # ------------------------------------------------------------------
-
- # 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/non-core.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. See documentation in
- # sts.html for details on the following two choices.
- # "Shell $ENV{HOME}/.gitolite.shell-users",
- # 'Shell alice bob',
-
- # set default roles from lines like 'option default.roles-1 = ...', etc.
- # 'set-default-roles',
-
- # show more detailed messages on deny
- # 'expand-deny-messages',
-
- # show a message of the day
- # 'Motd',
-
- # system admin stuff
-
- # enable mirroring (don't forget to set the HOSTNAME too!)
- # 'Mirroring',
-
- # allow people to submit pub files with more than one key in them
- # 'ssh-authkeys-split',
-
- # selective read control hack
- # 'partial-copy',
-
- # manage local, gitolite-controlled, copies of read-only upstream repos
- # 'upstream',
-
- # updates 'description' file instead of 'gitweb.description' config item
- # 'cgit',
-
- # allow repo-specific hooks to be added
- # 'repo-specific-hooks',
-
- # performance, logging, monitoring...
-
- # be nice
- # 'renice 10',
-
- # log CPU times (user, system, cumulative user, cumulative system)
- # 'CpuTime',
-
- # syntactic_sugar for gitolite.conf and included files
-
- # allow backslash-escaped continuation lines in gitolite.conf
- # 'continuation-lines',
-
- # create implicit user groups from directory names in keydir/
- # 'keysubdirs-as-groups',
-
- # allow simple line-oriented macros
- # 'macros',
-
- # Kindergarten mode
-
- # disallow various things that sensible people shouldn't be doing anyway
- # 'Kindergarten',
- ],
-
-);
-
-# ------------------------------------------------------------------------------
-# per perl rules, this should be the last line in such a file:
-1;
-
-# Local variables:
-# mode: perl
-# End:
-# vim: set syn=perl:
diff --git a/arvbox/lib/arvbox/docker/keep-setup.sh b/arvbox/lib/arvbox/docker/keep-setup.sh
deleted file mode 100755
index b66463f..0000000
--- a/arvbox/lib/arvbox/docker/keep-setup.sh
+++ /dev/null
@@ -1,51 +0,0 @@
-#!/bin/bash
-
-exec 2>&1
-sleep 2
-set -eux -o pipefail
-
-. /usr/local/lib/arvbox/common.sh
-
-mkdir -p /var/lib/arvados/gostuff
-cd /var/lib/arvados/gostuff
-
-export GOPATH=$PWD
-mkdir -p "$GOPATH/src/git.curoverse.com"
-ln -sfn "/usr/src/arvados" "$GOPATH/src/git.curoverse.com/arvados.git"
-flock /var/lib/arvados/gostuff.lock go get -t "git.curoverse.com/arvados.git/services/keepstore"
-install bin/keepstore /usr/local/bin
-
-mkdir -p /var/lib/arvados/$1
-
-export ARVADOS_API_HOST=$localip:${services[api]}
-export ARVADOS_API_HOST_INSECURE=1
-export ARVADOS_API_TOKEN=$(cat /var/lib/arvados/superuser_token)
-
-set +e
-read -rd $'\000' keepservice <<EOF
-{
- "service_host":"$localip",
- "service_port":$2,
- "service_ssl_flag":false,
- "service_type":"disk"
-}
-EOF
-set -e
-
-if test -s /var/lib/arvados/$1-uuid ; then
- keep_uuid=$(cat /var/lib/arvados/$1-uuid)
- arv keep_service update --uuid $keep_uuid --keep-service "$keepservice"
-else
- UUID=$(arv --format=uuid keep_service create --keep-service "$keepservice")
- echo $UUID > /var/lib/arvados/$1-uuid
-fi
-
-set +e
-killall -HUP keepproxy
-
-exec /usr/local/bin/keepstore \
- -listen=:$2 \
- -enforce-permissions=true \
- -blob-signing-key-file=/var/lib/arvados/blob_signing_key \
- -max-buffers=20 \
- -volume=/var/lib/arvados/$1
diff --git a/arvbox/lib/arvbox/docker/logger b/arvbox/lib/arvbox/docker/logger
deleted file mode 100755
index a79a518..0000000
--- a/arvbox/lib/arvbox/docker/logger
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-exec svlogd -tt ./main
diff --git a/arvbox/lib/arvbox/docker/runit-docker/.gitignore b/arvbox/lib/arvbox/docker/runit-docker/.gitignore
deleted file mode 100644
index bbf313b..0000000
--- a/arvbox/lib/arvbox/docker/runit-docker/.gitignore
+++ /dev/null
@@ -1,32 +0,0 @@
-# Object files
-*.o
-*.ko
-*.obj
-*.elf
-
-# Precompiled Headers
-*.gch
-*.pch
-
-# Libraries
-*.lib
-*.a
-*.la
-*.lo
-
-# Shared objects (inc. Windows DLLs)
-*.dll
-*.so
-*.so.*
-*.dylib
-
-# Executables
-*.exe
-*.out
-*.app
-*.i*86
-*.x86_64
-*.hex
-
-# Debug files
-*.dSYM/
diff --git a/arvbox/lib/arvbox/docker/runit-docker/LICENSE b/arvbox/lib/arvbox/docker/runit-docker/LICENSE
deleted file mode 100644
index d158667..0000000
--- a/arvbox/lib/arvbox/docker/runit-docker/LICENSE
+++ /dev/null
@@ -1,28 +0,0 @@
-Copyright (c) 2015, Kosma Moczek
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-* Redistributions of source code must retain the above copyright notice, this
- list of conditions and the following disclaimer.
-
-* Redistributions in binary form must reproduce the above copyright notice,
- this list of conditions and the following disclaimer in the documentation
- and/or other materials provided with the distribution.
-
-* Neither the name of runit-docker nor the names of its
- contributors may be used to endorse or promote products derived from
- this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
diff --git a/arvbox/lib/arvbox/docker/runit-docker/Makefile b/arvbox/lib/arvbox/docker/runit-docker/Makefile
deleted file mode 100644
index 9a28963..0000000
--- a/arvbox/lib/arvbox/docker/runit-docker/Makefile
+++ /dev/null
@@ -1,18 +0,0 @@
-CFLAGS=-std=c99 -Wall -O2 -fPIC -D_POSIX_SOURCE -D_GNU_SOURCE
-LDLIBS=-ldl
-
-PROGNAME=runit-docker
-
-all: $(PROGNAME).so
-
-%.so: %.c
- gcc -shared $(CFLAGS) $(LDLIBS) -o $@ $^
-
-install: runit-docker.so
- mkdir -p $(DESTDIR)/sbin
- mkdir -p $(DESTDIR)/lib
- install -m 755 $(PROGNAME) $(DESTDIR)/sbin/
- install -m 755 $(PROGNAME).so $(DESTDIR)/lib/
-
-clean:
- $(RM) $(PROGNAME).so
diff --git a/arvbox/lib/arvbox/docker/runit-docker/README.md b/arvbox/lib/arvbox/docker/runit-docker/README.md
deleted file mode 100644
index 1bcb8cc..0000000
--- a/arvbox/lib/arvbox/docker/runit-docker/README.md
+++ /dev/null
@@ -1,24 +0,0 @@
-# runit-docker
-
-Docker and `runsvdir` don't quite agree on what each signal means, causing
-TONS of frustration when attempting to use `runsvdir` as init under Docker.
-`runit-docker` is a plug'n'play adapter library which does signal translation
-without the overhead and nuisance of running a nanny process.
-
-## Features
-
-* Pressing Ctrl-C does a clean shutdown.
-* `docker stop` does a clean shutdown.
-
-Under the hood, `runit-docker` translates `SIGTERM` and `SIGINT` to `SIGHUP`.
-
-## Usage
-
-* Build with `make`, install with `make install`.
-* Add `CMD ["/sbin/runit-docker"]` to your `Dockerfile`.
-* Run `debian/rules clean build binary` to build a Debian package.
-
-## Author
-
-runit-docker was written by Kosma Moczek <kosma.moczek at pixers.pl> during a single Scrum
-planning meeting. Damn meetings.
diff --git a/arvbox/lib/arvbox/docker/runit-docker/debian/changelog b/arvbox/lib/arvbox/docker/runit-docker/debian/changelog
deleted file mode 100644
index 7d8689f..0000000
--- a/arvbox/lib/arvbox/docker/runit-docker/debian/changelog
+++ /dev/null
@@ -1,12 +0,0 @@
-runit-docker (1.1) unstable; urgency=low
-
- * Simplify logic.
- * Install for SIGINT as well.
-
- -- Kosma Moczek <kosma at kosma.pl> Mon, 11 May 2015 12:23:59 +0000
-
-runit-docker (1.0) unstable; urgency=low
-
- * Initial release
-
- -- Kosma Moczek <kosma at kosma.pl> Mon, 11 May 2015 12:23:59 +0000
diff --git a/arvbox/lib/arvbox/docker/runit-docker/debian/compat b/arvbox/lib/arvbox/docker/runit-docker/debian/compat
deleted file mode 100644
index ec63514..0000000
--- a/arvbox/lib/arvbox/docker/runit-docker/debian/compat
+++ /dev/null
@@ -1 +0,0 @@
-9
diff --git a/arvbox/lib/arvbox/docker/runit-docker/debian/control b/arvbox/lib/arvbox/docker/runit-docker/debian/control
deleted file mode 100644
index 4060915..0000000
--- a/arvbox/lib/arvbox/docker/runit-docker/debian/control
+++ /dev/null
@@ -1,14 +0,0 @@
-Source: runit-docker
-Section: contrib/admin
-Priority: optional
-Maintainer: Kosma Moczek <kosma at kosma.pl>
-Build-Depends: debhelper (>= 9)
-Standards-Version: 3.9.5
-Homepage: https://github.com/kosma/runit-docker
-#Vcs-Git: git://anonscm.debian.org/collab-maint/runit-docker.git
-#Vcs-Browser: http://anonscm.debian.org/?p=collab-maint/runit-docker.git;a=summary
-
-Package: runit-docker
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: painlessly use runit in Docker containers
diff --git a/arvbox/lib/arvbox/docker/runit-docker/debian/copyright b/arvbox/lib/arvbox/docker/runit-docker/debian/copyright
deleted file mode 100644
index 8679a6a..0000000
--- a/arvbox/lib/arvbox/docker/runit-docker/debian/copyright
+++ /dev/null
@@ -1,31 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: runit-docker
-Source: https://github.com/kosma/runit-docker
-
-Files: *
-Copyright: 2015 Kosma Moczek <kosma at kosma.pl>
-License: MIT
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions are met:
-
- * Redistributions of source code must retain the above copyright notice, this
- list of conditions and the following disclaimer.
-
- * Redistributions in binary form must reproduce the above copyright notice,
- this list of conditions and the following disclaimer in the documentation
- and/or other materials provided with the distribution.
-
- * Neither the name of runit-docker nor the names of its
- contributors may be used to endorse or promote products derived from
- this software without specific prior written permission.
-
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
- FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
- DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
- SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
- OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
- OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/arvbox/lib/arvbox/docker/runit-docker/debian/docs b/arvbox/lib/arvbox/docker/runit-docker/debian/docs
deleted file mode 100644
index b43bf86..0000000
--- a/arvbox/lib/arvbox/docker/runit-docker/debian/docs
+++ /dev/null
@@ -1 +0,0 @@
-README.md
diff --git a/arvbox/lib/arvbox/docker/runit-docker/debian/rules b/arvbox/lib/arvbox/docker/runit-docker/debian/rules
deleted file mode 100755
index ce15cce..0000000
--- a/arvbox/lib/arvbox/docker/runit-docker/debian/rules
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/usr/bin/make -f
-# See debhelper(7) (uncomment to enable)
-# output every command that modifies files on the build system.
-#DH_VERBOSE = 1
-
-# see EXAMPLES in dpkg-buildflags(1) and read /usr/share/dpkg/*
-DPKG_EXPORT_BUILDFLAGS = 1
-include /usr/share/dpkg/default.mk
-
-# see FEATURE AREAS in dpkg-buildflags(1)
-#export DEB_BUILD_MAINT_OPTIONS = hardening=+all
-
-# see ENVIRONMENT in dpkg-buildflags(1)
-# package maintainers to append CFLAGS
-#export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic
-# package maintainers to append LDFLAGS
-#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
-
-
-# main packaging script based on dh7 syntax
-%:
- dh $@
-
-# debmake generated override targets
-# This is example for Cmake (See http://bugs.debian.org/641051 )
-#override_dh_auto_configure:
-# dh_auto_configure -- \
-# -DCMAKE_LIBRARY_PATH=$(DEB_HOST_MULTIARCH)
-
-
-
-
diff --git a/arvbox/lib/arvbox/docker/runit-docker/debian/source/format b/arvbox/lib/arvbox/docker/runit-docker/debian/source/format
deleted file mode 100644
index 163aaf8..0000000
--- a/arvbox/lib/arvbox/docker/runit-docker/debian/source/format
+++ /dev/null
@@ -1 +0,0 @@
-3.0 (quilt)
diff --git a/arvbox/lib/arvbox/docker/runit-docker/runit-docker b/arvbox/lib/arvbox/docker/runit-docker/runit-docker
deleted file mode 100755
index fdbaad5..0000000
--- a/arvbox/lib/arvbox/docker/runit-docker/runit-docker
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/sh
-
-export LD_PRELOAD=/lib/runit-docker.so
-exec runsvdir /etc/service
diff --git a/arvbox/lib/arvbox/docker/runit-docker/runit-docker.c b/arvbox/lib/arvbox/docker/runit-docker/runit-docker.c
deleted file mode 100644
index 825a35f..0000000
--- a/arvbox/lib/arvbox/docker/runit-docker/runit-docker.c
+++ /dev/null
@@ -1,32 +0,0 @@
-#include <signal.h>
-#include <dlfcn.h>
-#include <stdlib.h>
-
-
-int sigaction(int signum, const struct sigaction *act, struct sigaction *oldact)
-{
- static int (*real_sigaction)(int signum, const struct sigaction *act, struct sigaction *oldact) = NULL;
-
- // Retrieve the real sigaction we just shadowed.
- if (real_sigaction == NULL) {
- real_sigaction = (void *) dlsym(RTLD_NEXT, "sigaction");
- // Prevent further shadowing in children.
- unsetenv("LD_PRELOAD");
- }
-
- if (signum == SIGTERM) {
- // Skip this handler, it doesn't do what we want.
- return 0;
- }
-
- if (signum == SIGHUP) {
- // Install this handler for others as well.
- real_sigaction(SIGTERM, act, oldact);
- real_sigaction(SIGINT, act, oldact);
- }
-
- // Forward the call the the real sigaction.
- return real_sigaction(signum, act, oldact);
-}
-
-// vim: ts=2 sw=2 et
diff --git a/arvbox/lib/arvbox/docker/runsu.sh b/arvbox/lib/arvbox/docker/runsu.sh
deleted file mode 100755
index 1557d09..0000000
--- a/arvbox/lib/arvbox/docker/runsu.sh
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/bin/sh
-
-HOSTUID=$(ls -nd /usr/src/arvados | sed 's/ */ /' | cut -d' ' -f4)
-HOSTGID=$(ls -nd /usr/src/arvados | sed 's/ */ /' | cut -d' ' -f5)
-
-flock /var/lib/arvados/createusers.lock /usr/local/lib/arvbox/createusers.sh
-
-export HOME=/var/lib/arvados
-
-if test -z "$1" ; then
- exec chpst -u arvbox:arvbox:docker $0-service
-else
- exec chpst -u arvbox:arvbox:docker $@
-fi
diff --git a/arvbox/lib/arvbox/docker/service/api/log/main/.gitstub b/arvbox/lib/arvbox/docker/service/api/log/main/.gitstub
deleted file mode 100644
index e69de29..0000000
diff --git a/arvbox/lib/arvbox/docker/service/api/log/run b/arvbox/lib/arvbox/docker/service/api/log/run
deleted file mode 120000
index d6aef4a..0000000
--- a/arvbox/lib/arvbox/docker/service/api/log/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/logger
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/api/run b/arvbox/lib/arvbox/docker/service/api/run
deleted file mode 120000
index a388c8b..0000000
--- a/arvbox/lib/arvbox/docker/service/api/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/runsu.sh
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/api/run-service b/arvbox/lib/arvbox/docker/service/api/run-service
deleted file mode 100755
index 058939c..0000000
--- a/arvbox/lib/arvbox/docker/service/api/run-service
+++ /dev/null
@@ -1,102 +0,0 @@
-#!/bin/bash
-
-exec 2>&1
-set -ex -o pipefail
-
-. /usr/local/lib/arvbox/common.sh
-
-cd /usr/src/arvados/services/api
-export RAILS_ENV=development
-
-run_bundler --without=development
-bundle exec passenger start --runtime-check-only --runtime-dir=/var/lib/passenger
-
-if test "$1" = "--only-deps" ; then
- exit
-fi
-
-set -u
-
-if ! test -s /var/lib/arvados/api_uuid_prefix ; then
- ruby -e 'puts "#{rand(2**64).to_s(36)[0,5]}"' > /var/lib/arvados/api_uuid_prefix
-fi
-uuid_prefix=$(cat /var/lib/arvados/api_uuid_prefix)
-
-if ! test -s /var/lib/arvados/api_secret_token ; then
- ruby -e 'puts rand(2**400).to_s(36)' > /var/lib/arvados/api_secret_token
-fi
-secret_token=$(cat /var/lib/arvados/api_secret_token)
-
-if ! test -s /var/lib/arvados/blob_signing_key ; then
- ruby -e 'puts rand(2**400).to_s(36)' > /var/lib/arvados/blob_signing_key
-fi
-blob_signing_key=$(cat /var/lib/arvados/blob_signing_key)
-
-# self signed key will be created by SSO server script.
-test -s /var/lib/arvados/self-signed.key
-
-sso_app_secret=$(cat /var/lib/arvados/sso_app_secret)
-
-if test -s /var/lib/arvados/vm-uuid ; then
- vm_uuid=$(cat /var/lib/arvados/vm-uuid)
-else
- vm_uuid=$uuid_prefix-2x53u-$(ruby -e 'puts rand(2**400).to_s(36)[0,15]')
- echo $vm_uuid > /var/lib/arvados/vm-uuid
-fi
-
-cat >config/application.yml <<EOF
-development:
- uuid_prefix: $uuid_prefix
- secret_token: $secret_token
- blob_signing_key: $blob_signing_key
- sso_app_secret: $sso_app_secret
- sso_app_id: arvados-server
- sso_provider_url: "https://$localip:${services[sso]}"
- sso_insecure: true
- workbench_address: "http://$localip/"
- git_repo_ssh_base: "git@$localip:"
- git_repo_https_base: "http://$localip:${services[arv-git-httpd]}/"
- new_users_are_active: true
- auto_admin_first_user: true
- auto_setup_new_users: true
- auto_setup_new_users_with_vm_uuid: $vm_uuid
- auto_setup_new_users_with_repository: true
- default_collection_replication: 1
-EOF
-
-(cd config && /usr/local/lib/arvbox/application_yml_override.py)
-
-if ! test -f /var/lib/arvados/api_database_pw ; then
- ruby -e 'puts rand(2**128).to_s(36)' > /var/lib/arvados/api_database_pw
-fi
-database_pw=$(cat /var/lib/arvados/api_database_pw)
-
-if ! (psql postgres -c "\du" | grep "^ arvados ") >/dev/null ; then
- psql postgres -c "create user arvados with password '$database_pw'"
- psql postgres -c "ALTER USER arvados CREATEDB;"
-fi
-
-sed "s/password:.*/password: $database_pw/" <config/database.yml.example >config/database.yml
-
-if ! test -f /var/lib/arvados/api_database_setup ; then
- bundle exec rake db:setup
- touch /var/lib/arvados/api_database_setup
-fi
-
-if ! test -s /var/lib/arvados/superuser_token ; then
- bundle exec ./script/create_superuser_token.rb > /var/lib/arvados/superuser_token
-fi
-
-rm -rf tmp
-
-bundle exec rake db:migrate
-
-set +u
-if test "$1" = "--only-setup" ; then
- exit
-fi
-
-ARVADOS_WEBSOCKETS=1 exec bundle exec passenger start --port=${services[api]} \
- --runtime-dir=/var/lib/passenger \
- --ssl --ssl-certificate=/var/lib/arvados/self-signed.pem \
- --ssl-certificate-key=/var/lib/arvados/self-signed.key
diff --git a/arvbox/lib/arvbox/docker/service/arv-git-httpd/log/main/.gitstub b/arvbox/lib/arvbox/docker/service/arv-git-httpd/log/main/.gitstub
deleted file mode 100644
index e69de29..0000000
diff --git a/arvbox/lib/arvbox/docker/service/arv-git-httpd/log/run b/arvbox/lib/arvbox/docker/service/arv-git-httpd/log/run
deleted file mode 120000
index d6aef4a..0000000
--- a/arvbox/lib/arvbox/docker/service/arv-git-httpd/log/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/logger
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/arv-git-httpd/run b/arvbox/lib/arvbox/docker/service/arv-git-httpd/run
deleted file mode 120000
index a388c8b..0000000
--- a/arvbox/lib/arvbox/docker/service/arv-git-httpd/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/runsu.sh
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/arv-git-httpd/run-service b/arvbox/lib/arvbox/docker/service/arv-git-httpd/run-service
deleted file mode 100755
index 854464e..0000000
--- a/arvbox/lib/arvbox/docker/service/arv-git-httpd/run-service
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/bin/bash
-
-exec 2>&1
-set -eux -o pipefail
-
-. /usr/local/lib/arvbox/common.sh
-
-mkdir -p /var/lib/arvados/gostuff
-cd /var/lib/arvados/gostuff
-
-export GOPATH=$PWD
-mkdir -p "$GOPATH/src/git.curoverse.com"
-ln -sfn "/usr/src/arvados" "$GOPATH/src/git.curoverse.com/arvados.git"
-flock /var/lib/arvados/gostuff.lock go get -t "git.curoverse.com/arvados.git/services/arv-git-httpd"
-install bin/arv-git-httpd /usr/local/bin
-
-export ARVADOS_API_HOST=$localip:${services[api]}
-export ARVADOS_API_HOST_INSECURE=1
-export GITOLITE_HTTP_HOME=/var/lib/arvados/git
-export GL_BYPASS_ACCESS_CHECKS=1
-export PATH="$PATH:/var/lib/arvados/git/bin"
-cd ~git
-
-exec /usr/local/bin/arv-git-httpd \
- -address=:${services[arv-git-httpd]} \
- -git-command=/usr/share/gitolite3/gitolite-shell \
- -repo-root=/var/lib/arvados/git/repositories
diff --git a/arvbox/lib/arvbox/docker/service/crunch-dispatch-local/log/main/.gitstub b/arvbox/lib/arvbox/docker/service/crunch-dispatch-local/log/main/.gitstub
deleted file mode 100644
index e69de29..0000000
diff --git a/arvbox/lib/arvbox/docker/service/crunch-dispatch-local/log/run b/arvbox/lib/arvbox/docker/service/crunch-dispatch-local/log/run
deleted file mode 120000
index d6aef4a..0000000
--- a/arvbox/lib/arvbox/docker/service/crunch-dispatch-local/log/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/logger
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/crunch-dispatch-local/run b/arvbox/lib/arvbox/docker/service/crunch-dispatch-local/run
deleted file mode 120000
index a388c8b..0000000
--- a/arvbox/lib/arvbox/docker/service/crunch-dispatch-local/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/runsu.sh
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/crunch-dispatch-local/run-service b/arvbox/lib/arvbox/docker/service/crunch-dispatch-local/run-service
deleted file mode 100755
index 211b438..0000000
--- a/arvbox/lib/arvbox/docker/service/crunch-dispatch-local/run-service
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/bin/bash
-
-exec 2>&1
-set -eux -o pipefail
-
-. /usr/local/lib/arvbox/common.sh
-
-mkdir -p /var/lib/arvados/gostuff
-cd /var/lib/arvados/gostuff
-
-export GOPATH=$PWD
-mkdir -p "$GOPATH/src/git.curoverse.com"
-ln -sfn "/usr/src/arvados" "$GOPATH/src/git.curoverse.com/arvados.git"
-flock /var/lib/arvados/gostuff.lock go get -t "git.curoverse.com/arvados.git/services/crunch-run"
-flock /var/lib/arvados/gostuff.lock go get -t "git.curoverse.com/arvados.git/services/crunch-dispatch-local"
-install bin/crunch-run bin/crunch-dispatch-local /usr/local/bin
-
-export ARVADOS_API_HOST=$localip:${services[api]}
-export ARVADOS_API_HOST_INSECURE=1
-export ARVADOS_API_TOKEN=$(cat /var/lib/arvados/superuser_token)
-
-exec /usr/local/bin/crunch-dispatch-local -crunch-run-command=/usr/local/bin/crunch-run
diff --git a/arvbox/lib/arvbox/docker/service/crunch-dispatch0/log/main/.gitstub b/arvbox/lib/arvbox/docker/service/crunch-dispatch0/log/main/.gitstub
deleted file mode 100644
index e69de29..0000000
diff --git a/arvbox/lib/arvbox/docker/service/crunch-dispatch0/log/run b/arvbox/lib/arvbox/docker/service/crunch-dispatch0/log/run
deleted file mode 120000
index d6aef4a..0000000
--- a/arvbox/lib/arvbox/docker/service/crunch-dispatch0/log/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/logger
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/crunch-dispatch0/run b/arvbox/lib/arvbox/docker/service/crunch-dispatch0/run
deleted file mode 120000
index a388c8b..0000000
--- a/arvbox/lib/arvbox/docker/service/crunch-dispatch0/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/runsu.sh
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/crunch-dispatch0/run-service b/arvbox/lib/arvbox/docker/service/crunch-dispatch0/run-service
deleted file mode 100755
index fa3a73a..0000000
--- a/arvbox/lib/arvbox/docker/service/crunch-dispatch0/run-service
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-exec /usr/local/lib/arvbox/crunch-setup.sh crunch0
diff --git a/arvbox/lib/arvbox/docker/service/crunch-dispatch1/log/main/.gitstub b/arvbox/lib/arvbox/docker/service/crunch-dispatch1/log/main/.gitstub
deleted file mode 100644
index e69de29..0000000
diff --git a/arvbox/lib/arvbox/docker/service/crunch-dispatch1/log/run b/arvbox/lib/arvbox/docker/service/crunch-dispatch1/log/run
deleted file mode 120000
index d6aef4a..0000000
--- a/arvbox/lib/arvbox/docker/service/crunch-dispatch1/log/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/logger
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/crunch-dispatch1/run b/arvbox/lib/arvbox/docker/service/crunch-dispatch1/run
deleted file mode 120000
index a388c8b..0000000
--- a/arvbox/lib/arvbox/docker/service/crunch-dispatch1/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/runsu.sh
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/crunch-dispatch1/run-service b/arvbox/lib/arvbox/docker/service/crunch-dispatch1/run-service
deleted file mode 100755
index 6430e9c..0000000
--- a/arvbox/lib/arvbox/docker/service/crunch-dispatch1/run-service
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/sh
-sleep 1
-exec /usr/local/lib/arvbox/crunch-setup.sh crunch1
diff --git a/arvbox/lib/arvbox/docker/service/doc/log/main/.gitstub b/arvbox/lib/arvbox/docker/service/doc/log/main/.gitstub
deleted file mode 100644
index e69de29..0000000
diff --git a/arvbox/lib/arvbox/docker/service/doc/log/run b/arvbox/lib/arvbox/docker/service/doc/log/run
deleted file mode 120000
index d6aef4a..0000000
--- a/arvbox/lib/arvbox/docker/service/doc/log/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/logger
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/doc/run b/arvbox/lib/arvbox/docker/service/doc/run
deleted file mode 120000
index a388c8b..0000000
--- a/arvbox/lib/arvbox/docker/service/doc/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/runsu.sh
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/doc/run-service b/arvbox/lib/arvbox/docker/service/doc/run-service
deleted file mode 100755
index acbe21c..0000000
--- a/arvbox/lib/arvbox/docker/service/doc/run-service
+++ /dev/null
@@ -1,41 +0,0 @@
-#!/bin/bash
-
-exec 2>&1
-set -ex -o pipefail
-
-. /usr/local/lib/arvbox/common.sh
-
-cd /usr/src/arvados/doc
-run_bundler --without=development
-
-if test "$1" = "--only-deps" ; then
- exit
-fi
-
-set -u
-
-cat <<EOF >/var/lib/arvados/doc-nginx.conf
-worker_processes auto;
-pid /var/lib/arvados/doc-nginx.pid;
-daemon off;
-
-events {
- worker_connections 64;
-}
-
-http {
- include /etc/nginx/mime.types;
- default_type application/octet-stream;
- server {
- listen ${services[doc]} default_server;
- listen [::]:${services[doc]} default_server;
- root /usr/src/arvados/doc/.site;
- index index.html;
- server_name _;
- }
-}
-EOF
-
-bundle exec rake generate baseurl=http://$localip:${services[doc]} arvados_api_host=$localip:${services[api]} arvados_workbench_host=http://$localip
-
-exec nginx -c /var/lib/arvados/doc-nginx.conf
diff --git a/arvbox/lib/arvbox/docker/service/docker/log/main/.gitstub b/arvbox/lib/arvbox/docker/service/docker/log/main/.gitstub
deleted file mode 100644
index e69de29..0000000
diff --git a/arvbox/lib/arvbox/docker/service/docker/log/run b/arvbox/lib/arvbox/docker/service/docker/log/run
deleted file mode 120000
index d6aef4a..0000000
--- a/arvbox/lib/arvbox/docker/service/docker/log/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/logger
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/docker/run b/arvbox/lib/arvbox/docker/service/docker/run
deleted file mode 100755
index 1ecdc16..0000000
--- a/arvbox/lib/arvbox/docker/service/docker/run
+++ /dev/null
@@ -1,102 +0,0 @@
-#!/bin/bash
-
-# Taken from https://github.com/jpetazzo/dind
-
-exec 2>&1
-
-# Ensure that all nodes in /dev/mapper correspond to mapped devices currently loaded by the device-mapper kernel driver
-dmsetup mknodes
-
-: {LOG:=stdio}
-
-# First, make sure that cgroups are mounted correctly.
-CGROUP=/sys/fs/cgroup
-[ -d $CGROUP ] || mkdir $CGROUP
-
-if mountpoint -q $CGROUP ; then
- break
-else
- mount -n -t tmpfs -o uid=0,gid=0,mode=0755 cgroup $CGROUP
-fi
-
-if ! mountpoint -q $CGROUP ; then
- echo "Could not find or mount cgroups. Tried /sys/fs/cgroup and /cgroup. Did you use --privileged?"
- exit 1
-fi
-
-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 "$FD>&-"
- ;;
- esac
-done
-popd >/dev/null
-
-
-# If a pidfile is still around (for example after a container restart),
-# delete it so that docker can start.
-rm -rf /var/run/docker.pid
-
-read pid cmd state ppid pgrp session tty_nr tpgid rest < /proc/self/stat
-trap "kill -TERM -$pgrp; exit" EXIT TERM KILL SIGKILL SIGTERM SIGQUIT
-
-if ! docker daemon --storage-driver=overlay $DOCKER_DAEMON_ARGS ; then
- docker daemon $DOCKER_DAEMON_ARGS
-fi
diff --git a/arvbox/lib/arvbox/docker/service/gitolite/log/main/.gitstub b/arvbox/lib/arvbox/docker/service/gitolite/log/main/.gitstub
deleted file mode 100644
index e69de29..0000000
diff --git a/arvbox/lib/arvbox/docker/service/gitolite/log/run b/arvbox/lib/arvbox/docker/service/gitolite/log/run
deleted file mode 120000
index d6aef4a..0000000
--- a/arvbox/lib/arvbox/docker/service/gitolite/log/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/logger
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/gitolite/run b/arvbox/lib/arvbox/docker/service/gitolite/run
deleted file mode 120000
index a388c8b..0000000
--- a/arvbox/lib/arvbox/docker/service/gitolite/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/runsu.sh
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/gitolite/run-service b/arvbox/lib/arvbox/docker/service/gitolite/run-service
deleted file mode 100755
index e0e8771..0000000
--- a/arvbox/lib/arvbox/docker/service/gitolite/run-service
+++ /dev/null
@@ -1,116 +0,0 @@
-#!/bin/bash
-
-exec 2>&1
-set -eux -o pipefail
-
-. /usr/local/lib/arvbox/common.sh
-
-mkdir -p /var/lib/arvados/git
-
-export ARVADOS_API_HOST=$localip:${services[api]}
-export ARVADOS_API_HOST_INSECURE=1
-export ARVADOS_API_TOKEN=$(cat /var/lib/arvados/superuser_token)
-
-export USER=git
-export USERNAME=git
-export LOGNAME=git
-export HOME=/var/lib/arvados/git
-
-cd ~arvbox
-
-mkdir -p ~arvbox/.ssh ~git/.ssh
-chmod 0700 ~arvbox/.ssh ~git/.ssh
-
-if ! test -s ~arvbox/.ssh/id_rsa ; then
- ssh-keygen -t rsa -P '' -f .ssh/id_rsa
- cp ~arvbox/.ssh/id_rsa ~arvbox/.ssh/id_rsa.pub ~git/.ssh
-fi
-
-if test -s ~arvbox/.ssh/known_hosts ; then
- ssh-keygen -f ".ssh/known_hosts" -R localhost
-fi
-
-if ! test -f /var/lib/arvados/gitolite-setup ; then
- cd ~git
-
- # Do a no-op login to populate known_hosts
- # with the hostkey, so it won't try to ask
- # about it later.
- cp .ssh/id_rsa.pub .ssh/authorized_keys
- ssh -o stricthostkeychecking=no git at localhost true
- rm .ssh/authorized_keys
-
- cp /usr/local/lib/arvbox/gitolite.rc .gitolite.rc
-
- gitolite setup -pk .ssh/id_rsa.pub
-
- if ! test -d gitolite-admin ; then
- git clone git at localhost:gitolite-admin
- fi
-
- cd gitolite-admin
- git config user.email arvados
- git config user.name arvados
- git config push.default simple
- git push
-
- touch /var/lib/arvados/gitolite-setup
-else
- # Do a no-op login to populate known_hosts
- # with the hostkey, so it won't try to ask
- # about it later. Don't run anything,
- # get the default gitolite behavior.
- ssh -o stricthostkeychecking=no git at localhost
-fi
-
-prefix=$(arv --format=uuid user current | cut -d- -f1)
-
-if ! test -s /var/lib/arvados/arvados-git-uuid ; then
- repo_uuid=$(arv --format=uuid repository create --repository "{\"owner_uuid\":\"$prefix-tpzed-000000000000000\", \"name\":\"arvados\"}")
- echo $repo_uuid > /var/lib/arvados/arvados-git-uuid
-fi
-
-repo_uuid=$(cat /var/lib/arvados/arvados-git-uuid)
-
-if ! test -s /var/lib/arvados/arvados-git-link-uuid ; then
- all_users_group_uuid="$prefix-j7d0g-fffffffffffffff"
-
- set +e
- read -rd $'\000' newlink <<EOF
-{
- "tail_uuid":"$all_users_group_uuid",
- "head_uuid":"$repo_uuid",
- "link_class":"permission",
- "name":"can_read"
-}
-EOF
- set -e
- link_uuid=$(arv --format=uuid link create --link "$newlink")
- echo $link_uuid > /var/lib/arvados/arvados-git-link-uuid
-fi
-
-if ! test -d /var/lib/arvados/git/repositories/$repo_uuid.git ; then
- git clone --bare /usr/src/arvados /var/lib/arvados/git/repositories/$repo_uuid.git
-else
- git --git-dir=/var/lib/arvados/git/repositories/$repo_uuid.git fetch -f /usr/src/arvados master:master
-fi
-
-cd /usr/src/arvados/services/api
-export RAILS_ENV=development
-
-git_user_key=$(cat ~git/.ssh/id_rsa.pub)
-
-cat > config/arvados-clients.yml <<EOF
-development:
- gitolite_url: /var/lib/arvados/git/repositories/gitolite-admin.git
- gitolite_tmp: /var/lib/arvados/git
- arvados_api_host: $localip:${services[api]}
- arvados_api_token: "$ARVADOS_API_TOKEN"
- arvados_api_host_insecure: true
- gitolite_arvados_git_user_key: "$git_user_key"
-EOF
-
-while true ; do
- bundle exec script/arvados-git-sync.rb development
- sleep 120
-done
diff --git a/arvbox/lib/arvbox/docker/service/keep-web/log/main/.gitstub b/arvbox/lib/arvbox/docker/service/keep-web/log/main/.gitstub
deleted file mode 100644
index e69de29..0000000
diff --git a/arvbox/lib/arvbox/docker/service/keep-web/log/run b/arvbox/lib/arvbox/docker/service/keep-web/log/run
deleted file mode 120000
index d6aef4a..0000000
--- a/arvbox/lib/arvbox/docker/service/keep-web/log/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/logger
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/keep-web/run b/arvbox/lib/arvbox/docker/service/keep-web/run
deleted file mode 120000
index a388c8b..0000000
--- a/arvbox/lib/arvbox/docker/service/keep-web/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/runsu.sh
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/keep-web/run-service b/arvbox/lib/arvbox/docker/service/keep-web/run-service
deleted file mode 100755
index a2c6aa1..0000000
--- a/arvbox/lib/arvbox/docker/service/keep-web/run-service
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/bin/bash
-
-exec 2>&1
-set -eux -o pipefail
-
-. /usr/local/lib/arvbox/common.sh
-
-mkdir -p /var/lib/arvados/gostuff
-cd /var/lib/arvados/gostuff
-
-export GOPATH=$PWD
-mkdir -p "$GOPATH/src/git.curoverse.com"
-ln -sfn "/usr/src/arvados" "$GOPATH/src/git.curoverse.com/arvados.git"
-flock /var/lib/arvados/gostuff.lock go get -t "git.curoverse.com/arvados.git/services/keep-web"
-install bin/keep-web /usr/local/bin
-
-export ARVADOS_API_HOST=$localip:${services[api]}
-export ARVADOS_API_HOST_INSECURE=1
-export ARVADOS_API_TOKEN=$(cat /var/lib/arvados/superuser_token)
-
-exec /usr/local/bin/keep-web -trust-all-content -listen=:${services[keep-web]}
diff --git a/arvbox/lib/arvbox/docker/service/keepproxy/log/main/.gitstub b/arvbox/lib/arvbox/docker/service/keepproxy/log/main/.gitstub
deleted file mode 100644
index e69de29..0000000
diff --git a/arvbox/lib/arvbox/docker/service/keepproxy/log/run b/arvbox/lib/arvbox/docker/service/keepproxy/log/run
deleted file mode 120000
index d6aef4a..0000000
--- a/arvbox/lib/arvbox/docker/service/keepproxy/log/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/logger
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/keepproxy/run b/arvbox/lib/arvbox/docker/service/keepproxy/run
deleted file mode 120000
index a388c8b..0000000
--- a/arvbox/lib/arvbox/docker/service/keepproxy/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/runsu.sh
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/keepproxy/run-service b/arvbox/lib/arvbox/docker/service/keepproxy/run-service
deleted file mode 100755
index 413a67e..0000000
--- a/arvbox/lib/arvbox/docker/service/keepproxy/run-service
+++ /dev/null
@@ -1,41 +0,0 @@
-#!/bin/bash
-
-exec 2>&1
-sleep 2
-set -eux -o pipefail
-
-. /usr/local/lib/arvbox/common.sh
-
-mkdir -p /var/lib/arvados/gostuff
-cd /var/lib/arvados/gostuff
-
-export GOPATH=$PWD
-mkdir -p "$GOPATH/src/git.curoverse.com"
-ln -sfn "/usr/src/arvados" "$GOPATH/src/git.curoverse.com/arvados.git"
-flock /var/lib/arvados/gostuff.lock go get -t "git.curoverse.com/arvados.git/services/keepproxy"
-install bin/keepproxy /usr/local/bin
-
-export ARVADOS_API_HOST=$localip:${services[api]}
-export ARVADOS_API_HOST_INSECURE=1
-export ARVADOS_API_TOKEN=$(cat /var/lib/arvados/superuser_token)
-
-set +e
-read -rd $'\000' keepservice <<EOF
-{
- "service_host":"$localip",
- "service_port":${services[keepproxy]},
- "service_ssl_flag":false,
- "service_type":"proxy"
-}
-EOF
-set -e
-
-if test -s /var/lib/arvados/keepproxy-uuid ; then
- keep_uuid=$(cat /var/lib/arvados/keepproxy-uuid)
- arv keep_service update --uuid $keep_uuid --keep-service "$keepservice"
-else
- UUID=$(arv --format=uuid keep_service create --keep-service "$keepservice")
- echo $UUID > /var/lib/arvados/keepproxy-uuid
-fi
-
-exec /usr/local/bin/keepproxy -listen=:${services[keepproxy]}
diff --git a/arvbox/lib/arvbox/docker/service/keepstore0/log/main/.gitstub b/arvbox/lib/arvbox/docker/service/keepstore0/log/main/.gitstub
deleted file mode 100644
index e69de29..0000000
diff --git a/arvbox/lib/arvbox/docker/service/keepstore0/log/run b/arvbox/lib/arvbox/docker/service/keepstore0/log/run
deleted file mode 120000
index d6aef4a..0000000
--- a/arvbox/lib/arvbox/docker/service/keepstore0/log/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/logger
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/keepstore0/run b/arvbox/lib/arvbox/docker/service/keepstore0/run
deleted file mode 120000
index a388c8b..0000000
--- a/arvbox/lib/arvbox/docker/service/keepstore0/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/runsu.sh
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/keepstore0/run-service b/arvbox/lib/arvbox/docker/service/keepstore0/run-service
deleted file mode 100755
index cf411e4..0000000
--- a/arvbox/lib/arvbox/docker/service/keepstore0/run-service
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/bash
-. /usr/local/lib/arvbox/common.sh
-exec /usr/local/lib/arvbox/keep-setup.sh keep0 ${services[keepstore0]}
diff --git a/arvbox/lib/arvbox/docker/service/keepstore1/log/main/.gitstub b/arvbox/lib/arvbox/docker/service/keepstore1/log/main/.gitstub
deleted file mode 100644
index e69de29..0000000
diff --git a/arvbox/lib/arvbox/docker/service/keepstore1/log/run b/arvbox/lib/arvbox/docker/service/keepstore1/log/run
deleted file mode 120000
index d6aef4a..0000000
--- a/arvbox/lib/arvbox/docker/service/keepstore1/log/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/logger
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/keepstore1/run b/arvbox/lib/arvbox/docker/service/keepstore1/run
deleted file mode 120000
index a388c8b..0000000
--- a/arvbox/lib/arvbox/docker/service/keepstore1/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/runsu.sh
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/keepstore1/run-service b/arvbox/lib/arvbox/docker/service/keepstore1/run-service
deleted file mode 100755
index 8d34d06..0000000
--- a/arvbox/lib/arvbox/docker/service/keepstore1/run-service
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/bash
-. /usr/local/lib/arvbox/common.sh
-exec /usr/local/lib/arvbox/keep-setup.sh keep1 ${services[keepstore1]}
diff --git a/arvbox/lib/arvbox/docker/service/postgres/log/main/.gitstub b/arvbox/lib/arvbox/docker/service/postgres/log/main/.gitstub
deleted file mode 100644
index e69de29..0000000
diff --git a/arvbox/lib/arvbox/docker/service/postgres/log/run b/arvbox/lib/arvbox/docker/service/postgres/log/run
deleted file mode 120000
index d6aef4a..0000000
--- a/arvbox/lib/arvbox/docker/service/postgres/log/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/logger
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/postgres/run b/arvbox/lib/arvbox/docker/service/postgres/run
deleted file mode 100755
index 4918bd7..0000000
--- a/arvbox/lib/arvbox/docker/service/postgres/run
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/bin/bash
-
-flock /var/lib/arvados/createusers.lock /usr/local/lib/arvbox/createusers.sh
-
-. /usr/local/lib/arvbox/common.sh
-
-chown -R $PGUSER:$PGGROUP /var/lib/postgresql
-chown -R $PGUSER:$PGGROUP /var/run/postgresql
-chown -R $PGUSER:$PGGROUP /etc/postgresql
-chown -R $PGUSER:$PGGROUP /etc/ssl/private
-
-exec chpst -u $PGUSER:$PGGROUP $0-service
diff --git a/arvbox/lib/arvbox/docker/service/postgres/run-service b/arvbox/lib/arvbox/docker/service/postgres/run-service
deleted file mode 100755
index a05be62..0000000
--- a/arvbox/lib/arvbox/docker/service/postgres/run-service
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/bin/bash
-
-exec 2>&1
-set -eux -o pipefail
-
-if ! test -d /var/lib/postgresql/9.4/main ; then
- /usr/lib/postgresql/9.4/bin/initdb -D /var/lib/postgresql/9.4/main
- sh -c "while ! (psql postgres -c'\du' | grep '^ arvbox ') >/dev/null ; do createuser -s arvbox ; sleep 1 ; done" &
-fi
-mkdir -p /var/run/postgresql/9.4-main.pg_stat_tmp
-
-rm -f /var/lib/postgresql/9.4/main/postmaster.pid
-
-exec /usr/lib/postgresql/9.4/bin/postgres -D /var/lib/postgresql/9.4/main -c config_file=/etc/postgresql/9.4/main/postgresql.conf
diff --git a/arvbox/lib/arvbox/docker/service/ready/run b/arvbox/lib/arvbox/docker/service/ready/run
deleted file mode 120000
index a388c8b..0000000
--- a/arvbox/lib/arvbox/docker/service/ready/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/runsu.sh
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/ready/run-service b/arvbox/lib/arvbox/docker/service/ready/run-service
deleted file mode 100755
index f560de0..0000000
--- a/arvbox/lib/arvbox/docker/service/ready/run-service
+++ /dev/null
@@ -1,96 +0,0 @@
-#!/bin/bash
-
-. /usr/local/lib/arvbox/common.sh
-
-set -eu -o pipefail
-
-if ! [[ -d /tmp/arvbox-ready ]] ; then
- echo
- echo "Arvados-in-a-box starting"
- echo
- echo "Note: if this is a fresh arvbox installation, it may take 10-15 minutes (or longer) to download and"
- echo "install dependencies. Use \"arvbox log\" to monitor the progress of specific services."
- echo
- mkdir -p /tmp/arvbox-ready
-fi
-
-sleep 3
-
-waiting=""
-
-for s in "${!services[@]}"
-do
- if ! [[ -f /tmp/arvbox-ready/$s ]] ; then
- if nc -z localhost ${services[$s]} ; then
- echo "$s is ready at $localip:${services[$s]}"
- touch /tmp/arvbox-ready/$s
- else
- waiting="$waiting $s"
- fi
- fi
-done
-
-if ! docker version >/dev/null 2>/dev/null ; then
- waiting="$waiting docker"
-fi
-
-if ! which arv >/dev/null ; then
- waiting="$waiting sdk"
-elif ! which arv-get >/dev/null ; then
- waiting="$waiting sdk"
-fi
-
-if ! (ps x | grep -v grep | grep "crunch-dispatch") > /dev/null ; then
- waiting="$waiting crunch-dispatch"
-fi
-
-export ARVADOS_API_HOST=$localip:${services[api]}
-export ARVADOS_API_HOST_INSECURE=1
-
-vm_ok=0
-if test -s /var/lib/arvados/vm-uuid -a -s /var/lib/arvados/superuser_token; then
- vm_uuid=$(cat /var/lib/arvados/vm-uuid)
- export ARVADOS_API_TOKEN=$(cat /var/lib/arvados/superuser_token)
- if (which arv && arv virtual_machine get --uuid $vm_uuid) >/dev/null 2>/dev/null ; then
- vm_ok=1
- fi
-fi
-
-if test $vm_ok = 0 ; then
- waiting="$waiting vm"
-fi
-
-if ! [[ -z "$waiting" ]] ; then
- if ps x | grep -v grep | grep "bundle install" > /dev/null; then
- gemcount=$(ls /var/lib/gems/ruby/2.1.0/gems 2>/dev/null | wc -l)
-
- gemlockcount=0
- for l in /usr/src/arvados/services/api/Gemfile.lock \
- /usr/src/arvados/apps/workbench/Gemfile.lock \
- /usr/src/sso/Gemfile.lock ; do
- gc=$(cat $l \
- | grep -vE "(GEM|PLATFORMS|DEPENDENCIES|$^|remote:|specs:)" \
- | sed 's/^ *//' | sed 's/(.*)//' | sed 's/ *$//' | sort | uniq | wc -l)
- gemlockcount=$(($gemlockcount + $gc))
- done
- waiting="$waiting (installing ruby gems $gemcount/$gemlockcount)"
- fi
-
- if ps x | grep -v grep | grep "c++.*/var/lib/passenger" > /dev/null ; then
- waiting="$waiting (compiling passenger)"
- fi
-
- if ps x | grep -v grep | grep "pip install" > /dev/null; then
- waiting="$waiting (installing python packages)"
- fi
- echo " Waiting for$waiting ..."
- exit 1
-fi
-
-echo
-echo "Your Arvados-in-a-box is ready!"
-echo "Workbench is running at http://$localip"
-
-rm -r /tmp/arvbox-ready
-
-sv stop ready >/dev/null
diff --git a/arvbox/lib/arvbox/docker/service/sdk/log/main/.gitstub b/arvbox/lib/arvbox/docker/service/sdk/log/main/.gitstub
deleted file mode 100644
index e69de29..0000000
diff --git a/arvbox/lib/arvbox/docker/service/sdk/log/run b/arvbox/lib/arvbox/docker/service/sdk/log/run
deleted file mode 120000
index d6aef4a..0000000
--- a/arvbox/lib/arvbox/docker/service/sdk/log/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/logger
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/sdk/run b/arvbox/lib/arvbox/docker/service/sdk/run
deleted file mode 100755
index 816b166..0000000
--- a/arvbox/lib/arvbox/docker/service/sdk/run
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/sh
-set -e
-
-/usr/local/lib/arvbox/runsu.sh $0-service
-sv stop sdk
diff --git a/arvbox/lib/arvbox/docker/service/sdk/run-service b/arvbox/lib/arvbox/docker/service/sdk/run-service
deleted file mode 100755
index b51f0fc..0000000
--- a/arvbox/lib/arvbox/docker/service/sdk/run-service
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/bin/bash
-
-exec 2>&1
-set -eux -o pipefail
-
-. /usr/local/lib/arvbox/common.sh
-
-mkdir -p ~/.pip /var/lib/arvados/pip
-cat > ~/.pip/pip.conf <<EOF
-[global]
-download_cache = /var/lib/arvados/pip
-EOF
-
-cd /usr/src/arvados/sdk/cli
-run_bundler --binstubs=$PWD/binstubs
-ln -sf /usr/src/arvados/sdk/cli/binstubs/arv /usr/local/bin/arv
-
-cd /usr/src/arvados/sdk/python
-python setup.py sdist
-pip_install $(ls dist/arvados-python-client-*.tar.gz | tail -n1)
-
-cd /usr/src/arvados/services/fuse
-python setup.py sdist
-pip_install $(ls dist/arvados_fuse-*.tar.gz | tail -n1)
diff --git a/arvbox/lib/arvbox/docker/service/slurmctld/log/main/.gitstub b/arvbox/lib/arvbox/docker/service/slurmctld/log/main/.gitstub
deleted file mode 100644
index e69de29..0000000
diff --git a/arvbox/lib/arvbox/docker/service/slurmctld/log/run b/arvbox/lib/arvbox/docker/service/slurmctld/log/run
deleted file mode 120000
index d6aef4a..0000000
--- a/arvbox/lib/arvbox/docker/service/slurmctld/log/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/logger
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/slurmctld/run b/arvbox/lib/arvbox/docker/service/slurmctld/run
deleted file mode 100755
index bd75bd0..0000000
--- a/arvbox/lib/arvbox/docker/service/slurmctld/run
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/bin/bash
-
-exec 2>&1
-set -eux -o pipefail
-
-. /usr/local/lib/arvbox/common.sh
-
-cat > /etc/slurm-llnl/slurm.conf <<EOF
-ControlMachine=$HOSTNAME
-ControlAddr=$HOSTNAME
-AuthType=auth/munge
-DefaultStorageLoc=/var/log/slurm-llnl
-SelectType=select/cons_res
-SelectTypeParameters=CR_CPU_Memory
-SlurmUser=arvbox
-SlurmdUser=arvbox
-SlurmctldPort=7002
-SlurmctldTimeout=300
-SlurmdPort=7003
-SlurmdSpoolDir=/var/tmp/slurmd.spool
-SlurmdTimeout=300
-StateSaveLocation=/var/tmp/slurm.state
-NodeName=$HOSTNAME
-PartitionName=compute State=UP Default=YES Nodes=$HOSTNAME
-EOF
-
-mkdir -p /var/run/munge
-
-/usr/sbin/munged -f
-
-exec /usr/sbin/slurmctld -v -D
diff --git a/arvbox/lib/arvbox/docker/service/slurmd/log/main/.gitstub b/arvbox/lib/arvbox/docker/service/slurmd/log/main/.gitstub
deleted file mode 100644
index e69de29..0000000
diff --git a/arvbox/lib/arvbox/docker/service/slurmd/log/run b/arvbox/lib/arvbox/docker/service/slurmd/log/run
deleted file mode 120000
index d6aef4a..0000000
--- a/arvbox/lib/arvbox/docker/service/slurmd/log/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/logger
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/slurmd/run b/arvbox/lib/arvbox/docker/service/slurmd/run
deleted file mode 100755
index 865a7e6..0000000
--- a/arvbox/lib/arvbox/docker/service/slurmd/run
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-
-exec 2>&1
-set -eux -o pipefail
-
-exec /usr/local/lib/arvbox/runsu.sh /usr/sbin/slurmd -v -D
diff --git a/arvbox/lib/arvbox/docker/service/ssh/log/main/.gitstub b/arvbox/lib/arvbox/docker/service/ssh/log/main/.gitstub
deleted file mode 100644
index e69de29..0000000
diff --git a/arvbox/lib/arvbox/docker/service/ssh/log/run b/arvbox/lib/arvbox/docker/service/ssh/log/run
deleted file mode 120000
index d6aef4a..0000000
--- a/arvbox/lib/arvbox/docker/service/ssh/log/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/logger
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/ssh/run b/arvbox/lib/arvbox/docker/service/ssh/run
deleted file mode 100755
index 0f23542..0000000
--- a/arvbox/lib/arvbox/docker/service/ssh/run
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/bin/bash
-
-exec 2>&1
-set -eux -o pipefail
-
-if ! test -d /var/run/sshd ; then
- mkdir /var/run/sshd
- chmod 0755 /var/run/sshd
-fi
-/usr/sbin/sshd -D
diff --git a/arvbox/lib/arvbox/docker/service/sso/log/main/.gitstub b/arvbox/lib/arvbox/docker/service/sso/log/main/.gitstub
deleted file mode 100644
index e69de29..0000000
diff --git a/arvbox/lib/arvbox/docker/service/sso/log/run b/arvbox/lib/arvbox/docker/service/sso/log/run
deleted file mode 120000
index d6aef4a..0000000
--- a/arvbox/lib/arvbox/docker/service/sso/log/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/logger
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/sso/run b/arvbox/lib/arvbox/docker/service/sso/run
deleted file mode 120000
index a388c8b..0000000
--- a/arvbox/lib/arvbox/docker/service/sso/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/runsu.sh
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/sso/run-service b/arvbox/lib/arvbox/docker/service/sso/run-service
deleted file mode 100755
index da413e0..0000000
--- a/arvbox/lib/arvbox/docker/service/sso/run-service
+++ /dev/null
@@ -1,87 +0,0 @@
-#!/bin/bash
-
-exec 2>&1
-set -ex -o pipefail
-
-. /usr/local/lib/arvbox/common.sh
-
-cd /usr/src/sso
-export RAILS_ENV=development
-
-run_bundler --without=development
-bundle exec passenger start --runtime-check-only --runtime-dir=/var/lib/passenger
-
-if test "$1" = "--only-deps" ; then
- exit
-fi
-
-set -u
-
-if ! test -s /var/lib/arvados/sso_uuid_prefix ; then
- ruby -e 'puts "#{rand(2**64).to_s(36)[0,5]}"' > /var/lib/arvados/sso_uuid_prefix
-fi
-uuid_prefix=$(cat /var/lib/arvados/sso_uuid_prefix)
-
-if ! test -s /var/lib/arvados/sso_secret_token ; then
- ruby -e 'puts rand(2**400).to_s(36)' > /var/lib/arvados/sso_secret_token
-fi
-secret_token=$(cat /var/lib/arvados/sso_secret_token)
-
-if ! test -s /var/lib/arvados/self-signed.key ; then
- openssl req -new -x509 -nodes -out /var/lib/arvados/self-signed.pem -keyout /var/lib/arvados/self-signed.key -days 365 -subj '/CN=localhost'
-fi
-
-cat >config/application.yml <<EOF
-development:
- uuid_prefix: $uuid_prefix
- secret_token: $secret_token
- default_link_url: "http://$localip"
- allow_account_registration: true
-EOF
-
-(cd config && /usr/local/lib/arvbox/application_yml_override.py)
-
-if ! test -f /var/lib/arvados/sso_database_pw ; then
- ruby -e 'puts rand(2**128).to_s(36)' > /var/lib/arvados/sso_database_pw
-fi
-database_pw=$(cat /var/lib/arvados/sso_database_pw)
-
-if ! (psql postgres -c "\du" | grep "^ arvados_sso ") >/dev/null ; then
- psql postgres -c "create user arvados_sso with password '$database_pw'"
- psql postgres -c "ALTER USER arvados_sso CREATEDB;"
-fi
-
-sed "s/password:.*/password: $database_pw/" <config/database.yml.example >config/database.yml
-
-if ! test -f /var/lib/arvados/sso_database_setup ; then
- bundle exec rake db:setup
-
- if ! test -s /var/lib/arvados/sso_app_secret ; then
- ruby -e 'puts rand(2**400).to_s(36)' > /var/lib/arvados/sso_app_secret
- fi
- app_secret=$(cat /var/lib/arvados/sso_app_secret)
-
- bundle exec rails console <<EOF
-c = Client.new
-c.name = "joshid"
-c.app_id = "arvados-server"
-c.app_secret = "$app_secret"
-c.save!
-EOF
-
- touch /var/lib/arvados/sso_database_setup
-fi
-
-rm -rf tmp
-
-bundle exec rake db:migrate
-
-set +u
-if test "$1" = "--only-setup" ; then
- exit
-fi
-
-exec bundle exec passenger start --port=${services[sso]} \
- --runtime-dir=/var/lib/passenger \
- --ssl --ssl-certificate=/var/lib/arvados/self-signed.pem \
- --ssl-certificate-key=/var/lib/arvados/self-signed.key
diff --git a/arvbox/lib/arvbox/docker/service/vm/log/main/.gitstub b/arvbox/lib/arvbox/docker/service/vm/log/main/.gitstub
deleted file mode 100644
index e69de29..0000000
diff --git a/arvbox/lib/arvbox/docker/service/vm/log/run b/arvbox/lib/arvbox/docker/service/vm/log/run
deleted file mode 120000
index d6aef4a..0000000
--- a/arvbox/lib/arvbox/docker/service/vm/log/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/logger
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/vm/run b/arvbox/lib/arvbox/docker/service/vm/run
deleted file mode 100755
index 0c10cb0..0000000
--- a/arvbox/lib/arvbox/docker/service/vm/run
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/bin/bash
-set -e
-
-. /usr/local/lib/arvbox/common.sh
-
-git config --system "credential.http://$localip:${services[arv-git-httpd]}/.username" none
-git config --system "credential.http://$localip:${services[arv-git-httpd]}/.helper" '!cred(){ cat >/dev/null; if [ "$1" = get ]; then echo password=$ARVADOS_API_TOKEN; fi; };cred'
-
-/usr/local/lib/arvbox/runsu.sh $0-service
-
-cd /usr/src/arvados/services/login-sync
-
-export ARVADOS_API_HOST=$localip:${services[api]}
-export ARVADOS_API_HOST_INSECURE=1
-export ARVADOS_API_TOKEN=$(cat /var/lib/arvados/superuser_token)
-export ARVADOS_VIRTUAL_MACHINE_UUID=$(cat /var/lib/arvados/vm-uuid)
-
-while true ; do
- bundle exec arvados-login-sync
- sleep 120
-done
diff --git a/arvbox/lib/arvbox/docker/service/vm/run-service b/arvbox/lib/arvbox/docker/service/vm/run-service
deleted file mode 100755
index fb209f5..0000000
--- a/arvbox/lib/arvbox/docker/service/vm/run-service
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/bin/bash
-
-exec 2>&1
-sleep 2
-set -ex -o pipefail
-
-. /usr/local/lib/arvbox/common.sh
-
-cd /usr/src/arvados/services/login-sync
-run_bundler
-
-if test "$1" = "--only-deps" ; then
- exit
-fi
-
-set -u
-
-export ARVADOS_API_HOST=$localip:${services[api]}
-export ARVADOS_API_HOST_INSECURE=1
-export ARVADOS_API_TOKEN=$(cat /var/lib/arvados/superuser_token)
-export ARVADOS_VIRTUAL_MACHINE_UUID=$(cat /var/lib/arvados/vm-uuid)
-
-set +e
-read -rd $'\000' vm <<EOF
-{
- "uuid": "$ARVADOS_VIRTUAL_MACHINE_UUID",
- "hostname":"$localip"
-}
-EOF
-set -e
-
-if arv virtual_machine get --uuid $ARVADOS_VIRTUAL_MACHINE_UUID ; then
- arv virtual_machine update --uuid $ARVADOS_VIRTUAL_MACHINE_UUID --virtual-machine "$vm"
-else
- arv virtual_machine create --virtual-machine "$vm"
-fi
diff --git a/arvbox/lib/arvbox/docker/service/workbench/log/main/.gitstub b/arvbox/lib/arvbox/docker/service/workbench/log/main/.gitstub
deleted file mode 100644
index e69de29..0000000
diff --git a/arvbox/lib/arvbox/docker/service/workbench/log/run b/arvbox/lib/arvbox/docker/service/workbench/log/run
deleted file mode 120000
index d6aef4a..0000000
--- a/arvbox/lib/arvbox/docker/service/workbench/log/run
+++ /dev/null
@@ -1 +0,0 @@
-/usr/local/lib/arvbox/logger
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/workbench/run b/arvbox/lib/arvbox/docker/service/workbench/run
deleted file mode 100755
index 6ac0476..0000000
--- a/arvbox/lib/arvbox/docker/service/workbench/run
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/bin/sh
-set -e
-
-/usr/local/lib/arvbox/runsu.sh $0-service $1
-
-cd /usr/src/arvados/apps/workbench
-
-rm -rf tmp
-mkdir tmp
-chown arvbox:arvbox tmp
-
-if test "$1" != "--only-deps" ; then
- exec bundle exec passenger start --port 80 \
- --user arvbox --runtime-dir=/var/lib/passenger
-fi
diff --git a/arvbox/lib/arvbox/docker/service/workbench/run-service b/arvbox/lib/arvbox/docker/service/workbench/run-service
deleted file mode 100755
index 850022a..0000000
--- a/arvbox/lib/arvbox/docker/service/workbench/run-service
+++ /dev/null
@@ -1,40 +0,0 @@
-#!/bin/bash
-
-exec 2>&1
-set -ex -o pipefail
-
-. /usr/local/lib/arvbox/common.sh
-
-cd /usr/src/arvados/apps/workbench
-export RAILS_ENV=development
-
-run_bundler --without=development
-bundle exec passenger start --runtime-check-only --runtime-dir=/var/lib/passenger
-
-if test "$1" = "--only-deps" ; then
- exit
-fi
-
-set -u
-
-if ! test -s /var/lib/arvados/workbench_secret_token ; then
- ruby -e 'puts rand(2**400).to_s(36)' > /var/lib/arvados/workbench_secret_token
-fi
-secret_token=$(cat /var/lib/arvados/workbench_secret_token)
-
-if ! test -s self-signed.key ; then
- openssl req -new -x509 -nodes -out self-signed.pem -keyout self-signed.key -days 365 -subj '/CN=localhost'
-fi
-
-cat >config/application.yml <<EOF
-development:
- secret_token: $secret_token
- arvados_login_base: https://$localip:${services[api]}/login
- arvados_v1_base: https://$localip:${services[api]}/arvados/v1
- arvados_insecure_https: true
- keep_web_download_url: http://$localip:${services[keep-web]}/c=%{uuid_or_pdh}
- keep_web_url: http://$localip:${services[keep-web]}/c=%{uuid_or_pdh}
- arvados_docsite: http://$localip:${services[doc]}/
-EOF
-
-(cd config && /usr/local/lib/arvbox/application_yml_override.py)
diff --git a/arvbox/lib/arvbox/docker/waitforpostgres.sh b/arvbox/lib/arvbox/docker/waitforpostgres.sh
deleted file mode 100755
index 84d9904..0000000
--- a/arvbox/lib/arvbox/docker/waitforpostgres.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/sh
-while ! psql postgres -c\\du >/dev/null 2>/dev/null ; do
- sleep 1
-done
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