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ensembl-gh-mirror
ensembl-hive
Commits
8474eaa6
Commit
8474eaa6
authored
Sep 20, 2017
by
Matthieu Muffato
Browse files
Added some installation scripts for Ubuntu. Will ease the definition of Dockerfiles
parent
22165755
Changes
5
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5 changed files
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65 additions
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30 deletions
+65
-30
docker/Dockerfile
docker/Dockerfile
+7
-30
docker/setup_cpan.Ubuntu-14.04.sh
docker/setup_cpan.Ubuntu-14.04.sh
+1
-0
docker/setup_cpan.Ubuntu-16.04.sh
docker/setup_cpan.Ubuntu-16.04.sh
+21
-0
docker/setup_os.Ubuntu-14.04.sh
docker/setup_os.Ubuntu-14.04.sh
+16
-0
docker/setup_os.Ubuntu-16.04.sh
docker/setup_os.Ubuntu-16.04.sh
+20
-0
No files found.
docker/Dockerfile
View file @
8474eaa6
...
...
@@ -17,40 +17,17 @@
FROM
ubuntu:16.04
RUN
apt-get update
-y
\
# Needed to clone the checkout, to use cpanm and forbasic help
&& apt-get install -y curl git perl-doc \
# Database-related dependencies
sqlite3 libdbd-sqlite3-perl postgresql-client libdbd-pg-perl mysql-client libdbd-mysql-perl libdbi-perl \
# Required Perl modules
libcapture-tiny-perl libdatetime-perl libhtml-parser-perl libjson-perl \
# Perl modules needed for the test-suite
libtest-exception-perl libtest-simple-perl libtest-warn-perl libtest-warnings-perl libtest-file-contents-perl libtest-perl-critic-perl libgraphviz-perl \
# Recommendations
libgetopt-argvfile-perl libchart-gnuplot-perl libbsd-resource-perl \
&& apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
## Useful for debugging
# RUN apt-get install netcat.openbsd vim perl-doc iputils-ping net-tools apt-file -y
RUN
ln
-s
/usr/bin/mariadb_config /usr/bin/mysql_config
# Install git
ARG
DEBIAN_FRONTEND=noninteractive
RUN
apt-get update
-y
&&
apt-get
install
-y
git
&&
apt-get clean
&&
rm
-rf
/var/lib/apt/lists/
*
/tmp/
*
/var/tmp/
*
# Clone the repo
RUN
mkdir
/repo
&&
git clone
-b
master https://github.com/Ensembl/ensembl-hive.git /repo/ensembl-hive
# Install all the dependencies
RUN
/repo/ensembl-hive/docker/setup_os.Ubuntu-16.04.sh
# Install the missing dependencies (if any)
# NOTE: buildDeps may have to be extended to include some lib*-dev packages
# such as libmariadb-client-lgpl-dev libpq-dev libsqlite3-dev libexpat1-dev
# The cpanm command is wrapped with apt-get install / purge to keep the
# image small
RUN
buildDeps
=
'
\
cpanminus
\
build-essential
\
'
\
&&
apt-get update
-y
\
&&
apt-get
install
-y
$buildDeps
\
&&
rm
-rf
/var/lib/apt/lists/
*
\
&&
cpanm
--installdeps
--with-recommends
/repo/ensembl-hive
\
&&
apt-get purge
-y
--auto-remove
$buildDeps
RUN
/repo/ensembl-hive/docker/setup_cpan.Ubuntu-16.04.sh /repo/ensembl-hive
ENV
PATH "/repo/ensembl-hive/scripts:$PATH"
ENV
PERL5LIB "/repo/ensembl-hive/modules:$PERL5LIB"
...
...
docker/setup_cpan.Ubuntu-14.04.sh
0 → 120000
View file @
8474eaa6
setup_cpan.Ubuntu-16.04.sh
\ No newline at end of file
docker/setup_cpan.Ubuntu-16.04.sh
0 → 100755
View file @
8474eaa6
#!/bin/bash
set
-e
# NOTE: buildDeps may have to be extended to include some lib*-dev packages
# such as libmariadb-client-lgpl-dev libpq-dev libsqlite3-dev libexpat1-dev
buildDeps
=
'
cpanminus
build-essential
'
apt-get update
-y
apt-get
install
-y
$buildDeps
for
arg
do
cpanm
--installdeps
--with-recommends
"
$arg
"
done
# Cleanup the cache and remove the build dependencies to reduce the disk footprint
rm
-rf
/var/lib/apt/lists/
*
apt-get purge
-y
--auto-remove
$buildDeps
docker/setup_os.Ubuntu-14.04.sh
0 → 100755
View file @
8474eaa6
#!/bin/bash
set
-e
apt-get update
apt-get
install
-y
curl perl-doc
\
sqlite3 libdbd-sqlite3-perl postgresql-client libdbd-pg-perl mysql-client libdbd-mysql-perl libdbi-perl
\
libcapture-tiny-perl libdatetime-perl libhtml-parser-perl libjson-perl
\
libtest-exception-perl libtest-simple-perl libtest-warn-perl libtest-warnings-perl libtest-file-contents-perl libtest-perl-critic-perl libgraphviz-perl
\
libgetopt-argvfile-perl libchart-gnuplot-perl libbsd-resource-perl
## Useful for debugging
#apt-get install -y netcat.openbsd vim perl-doc iputils-ping net-tools apt-file
apt-get clean
&&
rm
-rf
/var/lib/apt/lists/
*
/tmp/
*
/var/tmp/
*
docker/setup_os.Ubuntu-16.04.sh
0 → 100755
View file @
8474eaa6
#!/bin/bash
set
-e
apt-get update
apt-get
install
-y
curl perl-doc
\
sqlite3 libdbd-sqlite3-perl postgresql-client libdbd-pg-perl mysql-client libdbd-mysql-perl libdbi-perl
\
libcapture-tiny-perl libdatetime-perl libhtml-parser-perl libjson-perl libproc-daemon-perl
\
libtest-exception-perl libtest-simple-perl libtest-warn-perl libtest-warnings-perl libtest-file-contents-perl libtest-perl-critic-perl libgraphviz-perl
\
libgetopt-argvfile-perl libchart-gnuplot-perl libbsd-resource-perl
## Useful for debugging
#apt-get install -y netcat.openbsd vim perl-doc iputils-ping net-tools apt-file
# Cleanup the cache to reduce the disk footprint
apt-get clean
&&
rm
-rf
/var/lib/apt/lists/
*
/tmp/
*
/var/tmp/
*
# Needed for Perl DBI
ln
-s
/usr/bin/mariadb_config /usr/bin/mysql_config
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