Commit 7568d221 authored by Valentin Vautrot's avatar Valentin Vautrot

Creation of bismark definition file

parent df87ddf2
# bismark container definition file - see %help section
# Created : 2024-06-12
# Last updated : 2024-06-13
# authors : valentin.vautrot@u-bourgogne.fr
BootStrap: docker
From: ubuntu:22.04
%help
Description : This is a singularity/apptainer container packing bismark v0.24.2. It can be run by mounting a host bowtie2 installation directory, preferably towards /usr/bin/bowtie2/ destination to avoid PATH problems. Python2 is installed with the required librairies to run the miniconda version of bowtie2-2.3.2 present on the ccub.
exemple : singularity exec -e --bind /work/gad/shared/bin/bowtie2-2.3.2/:/usr/bin/bowtie2[:options],<python2_directory>:/usr/bin/python/ <path/to/this/container.sif> bismark [--<options>] --genome <path/to/bismark/converted/genome> <fastq.file>
Use "singularity test <path/to/this/container.sif>" to see --version calls of installed softwares.
This container has no runscripts.
Authors : valentin.vautrot@u-bourgogne.fr
%post
export DEBIAN_FRONTEND=noninteractive
apt-get update
apt-get install -y --no-install-recommends apt-utils
apt-get install -y --no-install-recommends \
locales \
language-pack-fr \
wget \
samtools \
python2.7 \
python2.7-dev \
perl \
libtbb2
# hisat2
ln -s /usr/bin/python2.7 /usr/bin/python
# get bismark code (no repo)
wget -P /usr/bin/bismark --no-check-certificate https://github.com/FelixKrueger/Bismark/archive/refs/tags/v0.24.2.tar.gz
tar -xvzf /usr/bin/bismark/v0.24.2.tar.gz -C /usr/bin/
rm -rf /usr/bin/bismark/
# create mount directory for bowtie2 bind, to avoid problems
mkdir /usr/bin/bowtie2
%environment
export PATH=${PATH}:/usr/bin/samtools/:/usr/bin/Bismark-0.24.2/:/usr/bin/bowtie2/:/usr/bin/python:/usr/bin/python2.7:/usr/lib/x86_64-linux-gnu/:/usr/lib/python2.7/
export PYTHON=/usr/bin/python
export LANGUAGE=fr_FR.UTF-8
export LC_ALL=fr_FR.UTF-8
export LANG=fr_FR.UTF-8
export LC_CTYPE=fr_FR.UTF-8
%test
samtools --version
echo "############################"
bismark --version
echo "############################"
echo "PATH variable : $PATH "
%labels
Author valentin.vautrot
container_version 0.1
Ubuntu_version 22.04
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