CHRUdeLille/vep_containers:92
$ singularity pull shub://CHRUdeLille/vep_containers:92
Singularity Recipe
#!/bin/bash
#
# Christophe Demay <christophe.demay@chru-lille.fr>
# 2018/04/24: initial version
BootStrap: docker
From: phusion/baseimage:0.10.1
%labels
MAINTAINER christophe.demay@chru-lille.fr
VERSION 92.1
%environment
PATH=/opt/vep/src/ensembl-vep:$PATH
LC_ALL=en_US.UTF-8
LANGUAGE=en_US.UTF-8
%help
__ _______ ____ ___ ____ _
\ \ / / ____| _ \ / _ \___ \ / |
\ \ / /| _| | |_) | | (_) |__) | | |
\ V / | |___| __/ \__, / __/ _| |
\_/ |_____|_| /_/_____(_)_|
Singularity container for VEP 92.1 <https://github.com/Ensembl/ensembl-vep> application. Documentation available at http://www.ensembl.org/info/docs/tools/vep/script/index.html
Cache folder is not included in the container. You have to bind folder containing the cache and add it with the '--cache' option.
%post
apt-get update
apt-get -y install apache2 \
build-essential \
cpanminus \
curl \
git \
libmysqlclient-dev \
libpng12-dev \
libssl-dev \
locales \
manpages \
mysql-client \
openssl \
perl \
perl-base \
unzip \
wget
locale-gen en_US.UTF-8
export LANGUAGE=en_US.UTF-8
export LANG=en_US.UTF-8
export LC_ALL=en_US.UTF-8
locale-gen en_US.UTF-8
dpkg-reconfigure locales
cpanm DBI DBD::mysql
git config --global http.postBuffer 524288000
mkdir -p /opt/vep/src
cd /opt/vep/src
git clone -b release/92 https://github.com/Ensembl/ensembl.git
git clone -b release/92 https://github.com/Ensembl/ensembl-vep.git
ensembl-vep/travisci/get_dependencies.sh
export PERL5LIB=$PERL5LIB:/opt/vep/src/bioperl-live-release-1-6-924
export KENT_SRC=/opt/vep/src/kent-335_base/src
KENT_SRC=/opt/vep/src/kent-335_base/src
export HTSLIB_DIR=/opt/vep/src/htslib
export MACHTYPE=x86_64
export CFLAGS="-fPIC"
export DEPS=/opt/vep/src
cd /opt/vep/src
ensembl-vep/travisci/build_c.sh
cd $HTSLIB_DIR
make install
cd /opt/vep/src
git clone https://github.com/bioperl/bioperl-ext.git
cd bioperl-ext
git reset --hard 1b59725
cd Bio/Ext/Align/
perl -pi -e"s|(cd libs.+)CFLAGS=\\\'|\$1CFLAGS=\\\'-fPIC |" Makefile.PL
perl Makefile.PL
make
make install
cd /opt/vep/src
cpanm --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile .
cpanm --installdeps --with-recommends --notest --cpanfile ensembl-vep/cpanfile .
echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen && \
locale-gen en_US.utf8 && \
/usr/sbin/update-locale LANG=en_US.UTF-8
cd /opt/vep/src/ensembl-vep
chmod u+x *.pl
./INSTALL.pl -a a -l
Collection
- Name: CHRUdeLille/vep_containers
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/CHRUdeLille-vep_containers-92 |
collection name | CHRUdeLille/vep_containers |
branch | master |
tag | 92 |
commit | 47fe6250bd25423975a75ac155054542adf39b8a |
version (container hash) | 150a3ed01b55e76ffd3eec42caae290e |
build date | 2018-05-25T13:57:39.227Z |
size (MB) | 1627 |
size (bytes) | 622215199 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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