Creation of bismark definition file

bismark_0.24.2.def

+# 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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