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ensembl-gh-mirror
ensembl-hive
Commits
5de2091b
Commit
5de2091b
authored
Jul 05, 2017
by
Leo Gordon
Browse files
Dockerfile for running Hive scripts in a container, also the base for guiHive container
parent
d4940811
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# This is a Dockerfile to run eHive scripts (init_pipeline.pl, beekeeper.pl, runWorker.pl) in a container
#
# docker build -t ensembl-hive .
#
# docker run -it -e PATH=/repo/ensembl-hive/scripts:/bin:/usr/bin:/usr/local/bin:/sbin:/usr/sbin:/usr/local/sbin ensembl-hive # assume bash
# docker run -it -e PATH=/repo/ensembl-hive/scripts:/bin:/usr/bin:/usr/local/bin:/sbin:/usr/sbin:/usr/local/sbin ensembl-hive init_pipeline.pl Bio::EnsEMBL::Hive::Examples::LongMult::PipeConfig::LongMult_conf -pipeline_url $URL
# docker run -it -e PATH=/repo/ensembl-hive/scripts:/bin:/usr/bin:/usr/local/bin:/sbin:/usr/sbin:/usr/local/sbin ensembl-hive beekeeper.pl -url $URL -loop -sleep 0.2
# docker run -it -e PATH=/repo/ensembl-hive/scripts:/bin:/usr/bin:/usr/local/bin:/sbin:/usr/sbin:/usr/local/sbin ensembl-hive runWorker.pl -url $URL
FROM
ubuntu:16.04
RUN
mkdir
/repo
RUN
apt-get update
-y
\
&&
apt-get
install
git build-essential curl sqlite3 mysql-client libmariadb-client-lgpl-dev libpq-dev libexpat1-dev graphviz
-y
\
&&
apt-get
install
netcat.openbsd vim perl-doc
-y
\
&&
apt-get clean
&&
rm
-rf
/var/lib/apt/lists/
*
/tmp/
*
/var/tmp/
*
# RUN apt-get install iputils-ping net-tools apt-file -y
RUN
ln
-s
/usr/bin/mariadb_config /usr/bin/mysql_config
RUN
curl
-L
https://cpanmin.us | perl - App::cpanminus
RUN
cd
/repo
;
git clone https://github.com/Ensembl/ensembl-hive.git
RUN
cd
/repo/ensembl-hive
;
git checkout master
RUN
cpanm
--installdeps
--with-recommends
/repo/ensembl-hive
# for the processes you run in an interactive bash
RUN
echo
"export PATH=
$PATH
:/repo/ensembl-hive/scripts"
>>
/root/.bashrc
CMD
[ "/bin/bash" ]
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