[ARVADOS] updated: 18c93ee7a21912e9759b127a3ec73bb81c15f23d
git at public.curoverse.com
git at public.curoverse.com
Mon Jun 29 10:56:05 EDT 2015
Summary of changes:
docker/api/Dockerfile | 4 ++--
docker/base/Dockerfile | 13 ++++++++++---
docker/compute/Dockerfile | 6 +++---
docker/doc/Dockerfile | 4 ++--
docker/java-bwa-samtools/Dockerfile | 4 ++--
docker/keepproxy/Dockerfile | 4 ++--
docker/passenger/Dockerfile | 4 ++--
docker/postgresql/Dockerfile | 2 +-
docker/shell/Dockerfile | 4 ++--
docker/slurm/Dockerfile | 4 ++--
docker/workbench/Dockerfile | 4 ++--
11 files changed, 30 insertions(+), 23 deletions(-)
via 18c93ee7a21912e9759b127a3ec73bb81c15f23d (commit)
from b17c7d97723d99909868d3435b449ab4e95f1708 (commit)
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commit 18c93ee7a21912e9759b127a3ec73bb81c15f23d
Author: Nico Cesar <nico at curoverse.com>
Date: Mon Jun 29 10:53:18 2015 -0400
we need to manually install python-pyasn1=0.1.7 python-pyasn1-modules=0.0.5 because apt-get wont resolve correctly.
apt-get install are less quiet now too.
no issue #
diff --git a/docker/api/Dockerfile b/docker/api/Dockerfile
index 51d452b..758c015 100644
--- a/docker/api/Dockerfile
+++ b/docker/api/Dockerfile
@@ -4,8 +4,8 @@ FROM arvados/passenger
MAINTAINER Ward Vandewege <ward at curoverse.com>
# Install postgres and apache.
-RUN apt-get update -qq
-RUN apt-get install -qqy \
+RUN apt-get update -q
+RUN apt-get install -qy \
procps postgresql postgresql-server-dev-9.1 slurm-llnl munge \
supervisor sudo libwww-perl libio-socket-ssl-perl libcrypt-ssleay-perl \
libjson-perl cron openssh-server
diff --git a/docker/base/Dockerfile b/docker/base/Dockerfile
index 2347da3..e46cdd3 100644
--- a/docker/base/Dockerfile
+++ b/docker/base/Dockerfile
@@ -12,11 +12,18 @@ ENV DEBIAN_FRONTEND noninteractive
ADD apt.arvados.org.list /etc/apt/sources.list.d/
RUN apt-key adv --keyserver pool.sks-keyservers.net --recv 1078ECD7
-RUN apt-get update -qq
-
-RUN apt-get install -qqy apt-utils git curl \
+RUN apt-get update -q
+
+## 2015-06-29 nico
+## KNOWN BUG: python-oauth2client needs specific versions
+## python-pyasn1=0.1.7 python-pyasn1-modules=0.0.5
+## but apt-get doesn't resolv them correctly. we have to
+## do it by hand here (or add apt_preferences if it gets too hairy)
+RUN apt-get install -qy apt-utils git curl \
libcurl3 libcurl3-gnutls libcurl4-openssl-dev locales \
postgresql-server-dev-9.1 python-arvados-python-client
+ postgresql-server-dev-9.1 python-arvados-python-client \
+ python-google-api-python-client python-oauth2client python-pyasn1=0.1.7 python-pyasn1-modules=0.0.5
RUN gpg --keyserver pool.sks-keyservers.net --recv-keys D39DC0E3 && \
/bin/sed -ri 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && \
diff --git a/docker/compute/Dockerfile b/docker/compute/Dockerfile
index 402ed64..f2f48da 100644
--- a/docker/compute/Dockerfile
+++ b/docker/compute/Dockerfile
@@ -3,8 +3,8 @@
FROM arvados/slurm
MAINTAINER Ward Vandewege <ward at curoverse.com>
-RUN apt-get update -qq
-RUN apt-get install -qqy supervisor python-pip python-pyvcf python-gflags python-google-api-python-client python-virtualenv libattr1-dev libfuse-dev python-dev python-llfuse fuse crunchstat python-arvados-fuse cron dnsmasq
+RUN apt-get update -q
+RUN apt-get install -qy supervisor python-pip python-pyvcf python-gflags python-google-api-python-client python-virtualenv libattr1-dev libfuse-dev python-dev python-llfuse fuse crunchstat python-arvados-fuse cron dnsmasq
ADD fuse.conf /etc/fuse.conf
RUN chmod 644 /etc/fuse.conf
@@ -12,7 +12,7 @@ RUN chmod 644 /etc/fuse.conf
RUN /usr/local/rvm/bin/rvm-exec default gem install arvados-cli arvados
# Install Docker from the Arvados package repository (cf. arvados/base)
-RUN apt-get install -qqy iptables ca-certificates lxc apt-transport-https docker.io
+RUN apt-get install -qy iptables ca-certificates lxc apt-transport-https docker.io
RUN addgroup --gid 4005 crunch && mkdir /home/crunch && useradd --uid 4005 --gid 4005 crunch && usermod crunch -G fuse,docker && chown crunch:crunch /home/crunch
diff --git a/docker/doc/Dockerfile b/docker/doc/Dockerfile
index d890710..1492675 100644
--- a/docker/doc/Dockerfile
+++ b/docker/doc/Dockerfile
@@ -5,8 +5,8 @@ maintainer Ward Vandewege <ward at curoverse.com>
# Install packages
RUN /bin/mkdir -p /usr/src/arvados && \
- apt-get update -qq && \
- apt-get install -qqy curl procps apache2-mpm-worker
+ apt-get update -q && \
+ apt-get install -qy curl procps apache2-mpm-worker
ADD generated/doc.tar.gz /usr/src/arvados/
diff --git a/docker/java-bwa-samtools/Dockerfile b/docker/java-bwa-samtools/Dockerfile
index 713ef21..2a73977 100644
--- a/docker/java-bwa-samtools/Dockerfile
+++ b/docker/java-bwa-samtools/Dockerfile
@@ -3,8 +3,8 @@ MAINTAINER Peter Amstutz <peter.amstutz at curoverse.com>
USER root
-RUN apt-get update -qq
-RUN apt-get install -qqy openjdk-7-jre-headless && \
+RUN apt-get update -q
+RUN apt-get install -qy openjdk-7-jre-headless && \
cd /tmp && \
curl --location http://cache.arvados.org/sourceforge.net/project/bio-bwa/bwa-0.7.9a.tar.bz2 -o bwa-0.7.9a.tar.bz2 && \
tar xjf bwa-0.7.9a.tar.bz2 && \
diff --git a/docker/keepproxy/Dockerfile b/docker/keepproxy/Dockerfile
index 78e82b9..e8df168 100644
--- a/docker/keepproxy/Dockerfile
+++ b/docker/keepproxy/Dockerfile
@@ -2,8 +2,8 @@
FROM arvados/debian:wheezy
MAINTAINER Ward Vandewege <ward at curoverse.com>
-RUN apt-get update -qq
-RUN apt-get install -qqy ca-certificates
+RUN apt-get update -q
+RUN apt-get install -qy ca-certificates
ADD generated/bin/keepproxy /usr/local/bin/
ADD generated/run-keepproxy /usr/local/bin/
diff --git a/docker/passenger/Dockerfile b/docker/passenger/Dockerfile
index 5e0fd76..77aeb66 100644
--- a/docker/passenger/Dockerfile
+++ b/docker/passenger/Dockerfile
@@ -5,8 +5,8 @@ MAINTAINER Ward Vandewege <ward at curoverse.com>
# Install packages and build the passenger apache module
-RUN apt-get update -qq
-RUN apt-get install -qqy \
+RUN apt-get update -q
+RUN apt-get install -qy \
apt-utils git curl procps apache2-mpm-worker \
libcurl4-openssl-dev apache2-threaded-dev \
libapr1-dev libaprutil1-dev
diff --git a/docker/postgresql/Dockerfile b/docker/postgresql/Dockerfile
index 8a59acf..a99a886 100644
--- a/docker/postgresql/Dockerfile
+++ b/docker/postgresql/Dockerfile
@@ -19,7 +19,7 @@ ENV ARVADOS_PROD_USER arvados
ENV ARVADOS_PROD_PW dummy_pw
# Install postgres and apache
-RUN apt-get -q -y install procps postgresql postgresql-server-dev-9.1
+RUN apt-get install -qy procps postgresql postgresql-server-dev-9.1
# Configure databases and users.
ADD postgresql.conf /etc/postgresql/9.1/main/
diff --git a/docker/shell/Dockerfile b/docker/shell/Dockerfile
index 8235159..8f0ed41 100644
--- a/docker/shell/Dockerfile
+++ b/docker/shell/Dockerfile
@@ -3,8 +3,8 @@
FROM arvados/base
MAINTAINER Ward Vandewege <ward at curoverse.com>
-RUN apt-get update -qq
-RUN apt-get install -qqy \
+RUN apt-get update -q
+RUN apt-get install -qy \
python-pip python-pyvcf python-gflags python-google-api-python-client \
python-virtualenv libattr1-dev libfuse-dev python-dev python-llfuse fuse \
crunchstat python-arvados-fuse cron vim supervisor openssh-server
diff --git a/docker/slurm/Dockerfile b/docker/slurm/Dockerfile
index 7e4284f..28a3c3b 100644
--- a/docker/slurm/Dockerfile
+++ b/docker/slurm/Dockerfile
@@ -3,8 +3,8 @@
FROM arvados/base
MAINTAINER Ward Vandewege <ward at curoverse.com>
-RUN apt-get update -qq
-RUN apt-get install -qqy slurm-llnl munge
+RUN apt-get update -q
+RUN apt-get install -qy slurm-llnl munge
ADD munge.key /etc/munge/
RUN chown munge:munge /etc/munge/munge.key && chmod 600 /etc/munge/munge.key
diff --git a/docker/workbench/Dockerfile b/docker/workbench/Dockerfile
index 2e2a782..148153a 100644
--- a/docker/workbench/Dockerfile
+++ b/docker/workbench/Dockerfile
@@ -4,8 +4,8 @@ FROM arvados/passenger
MAINTAINER Ward Vandewege <ward at curoverse.com>
# We need graphviz for the provenance graphs
-RUN apt-get update -qq
-RUN apt-get install -qqy graphviz
+RUN apt-get update -q
+RUN apt-get install -qy graphviz
# Update Arvados source
RUN /bin/mkdir -p /usr/src/arvados/apps
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