Grelot/bioinfo_singularity_recipes:grindermbb
$ singularity pull shub://Grelot/bioinfo_singularity_recipes:grindermbb
Singularity Recipe
BootStrap: debootstrap
OSVersion: xenial
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
%runscript
echo "Opening container...ubuntu xenial: grinder, bioperl"
%labels
MAINTAINER Pierre-Edouard_GUERIN
INSTITUTE CNRS
TEAM Biogeographie_Ecologie_Vertebres
BUILD 1.0
SINGULARITY_VERSION 2.4.2-dist
GRINDER 0.5.3
PERL 5.22.1
%post
mv /etc/apt/sources.list /etc/apt/sources.list.bak
echo "deb http://us.archive.ubuntu.com/ubuntu/ xenial main restricted universe multiverse
deb-src http://us.archive.ubuntu.com/ubuntu/ xenial main restricted universe multiverse
deb http://us.archive.ubuntu.com/ubuntu/ xenial-security main restricted universe multiverse
deb http://us.archive.ubuntu.com/ubuntu/ xenial-updates main restricted universe multiverse
deb http://us.archive.ubuntu.com/ubuntu/ xenial-proposed main restricted universe multiverse
deb http://us.archive.ubuntu.com/ubuntu/ xenial-backports main restricted universe multiverse
deb-src http://us.archive.ubuntu.com/ubuntu/ xenial-security main restricted universe multiverse
deb-src http://us.archive.ubuntu.com/ubuntu/ xenial-updates main restricted universe multiverse
deb-src http://us.archive.ubuntu.com/ubuntu/ xenial-proposed main restricted universe multiverse
deb-src http://us.archive.ubuntu.com/ubuntu/ xenial-backports main restricted universe multiverse" >> /etc/apt/sources.list
## MBB config
mkdir -p /share/apps/bin
mkdir /share/apps/lib
mkdir /share/apps/gridengine
mkdir /share/bio
mkdir -p /opt/gridengine
mkdir -p /export/scrach
mkdir -p /usr/lib64
/usr/sbin/groupadd --system --gid 400 sge
/usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
ln -s /bin/bash /bin/mbb_bash
ln -s /bin/bash /bin/isem_bash
## git, make, wget
apt-get -y --force-yes update
apt-get -y --force-yes install build-essential
apt-get -y --force-yes install git
apt install wget
yes | apt-get install autoconf autogen
## pigz
yes | apt install pigz
## PERL
apt-get install -y --force-yes perl
echo "en_US.UTF-8 UTF-8" > /etc/locale.gen
echo "fr_FR.UTF-8 UTF-8" >> /etc/locale.gen
locale-gen
## BIO-PERL
yes | perl -MCPAN -e 'upgrade'
yes | apt-get install bioperl
## GRINDER
git clone -b master https://github.com/zyxue/biogrinder.git
cd biogrinder
yes | perl Makefile.PL
yes | make
yes | make install
cd ..
Collection
- Name: Grelot/bioinfo_singularity_recipes
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/Grelot-bioinfo_singularity_recipes-grindermbb |
collection name | Grelot/bioinfo_singularity_recipes |
branch | master |
tag | grindermbb |
commit | 7cccd77fc568a429087033060a5d974ea6dd4e16 |
version (container hash) | 4f62a40c87a7cb665a2d816433fb23bb |
build date | 2020-09-23T14:43:31.978Z |
size (MB) | 2189 |
size (bytes) | 816168991 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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