Script to run interactive shell in the container.

singularity/Makefile

@@ -6,10 +6,11 @@ endif
 
 all: run_pipeline
 
-install: run_pipeline
+install: run_pipeline run_pipeline.sh workflows_shell.sh
 	install -d $(PREFIX)_$(VERSION)/bin
 	install run_pipeline $(PREFIX)_$(VERSION)/bin/.
 	install run_pipeline.sh $(PREFIX)_$(VERSION)/bin/.
+	install workflows_shell.sh $(PREFIX)_$(VERSION)/bin/.
 	for datatype in sRNA-seq smallRNA-seq RNA-seq GRO-seq PRO-seq Degradome-seq Ribo-seq iCLIP-seq iCLIP; \
 	do \
 	    ln -sf $(PREFIX)_$(VERSION)/bin/run_pipeline.sh $(PREFIX)_$(VERSION)/bin/run_$${datatype}_pipeline; \

singularity/run_pipeline.def

@@ -34,6 +34,8 @@ From:python:3.7-buster
 
 %post
 	apt-get -y update
+	# Useful for interactive work using the container
+	apt-get -y install vim
 	# run_pipeline.sh (and maybe other tools) needs bc
 	apt-get -y install bc rsync
 	apt-get -y install bedops bedtools bowtie2 cutadapt subread hisat2 parallel samtools

singularity/workflows_shell.sh

+#!/bin/bash -l
+# Usage: workflows_shell.sh
+# Run an interactive shell in the same container that is used for the workflows.
+
+# http://linuxcommand.org/wss0150.php
+PROGNAME=$(basename "${0}")
+
+function error_exit
+{
+#	----------------------------------------------------------------
+#	Function for exit due to fatal program error
+#		Accepts 1 argument:
+#			string containing descriptive error message
+#	----------------------------------------------------------------
+    echo "${PROGNAME}: ${1:-"Unknown Error"}" 1>&2
+    exit 1
+}
+
+# https://stackoverflow.com/a/1638397/1878788
+# Absolute path to this script
+SCRIPT=$(readlink -f "${0}")
+# Absolute path this script is in
+BASEDIR=$(dirname "${SCRIPT}")
+container="${BASEDIR}/run_pipeline"
+
+
+# Do we have singularity?
+singularity --version 2> /dev/null && have_singularity=1
+
+if [ ! ${have_singularity} ]
+then
+    install_doc="https://sylabs.io/guides/3.4/user-guide/quick_start.html#quick-installation-steps"
+    # Do we have an environment modules system?
+    module --version 2> /dev/null && have_modules=1
+    if [ ${have_modules} ]
+    then
+        module load singularity || error_exit "singularity is needed to run the pipelines (see ${install_doc})"
+    else
+        error_exit "singularity is needed to run the pipelines (see ${install_doc})"
+    fi
+fi
+
+if [ ! -e ${container} ]
+then
+    if [ -e ${BASEDIR}/run_pipeline.def ]
+    then
+        echo "The container was not found. Trying to build it. This may take quite some time and requires sudoer's rights."
+        sudo singularity build ${BASEDIR}/run_pipeline ${BASEDIR}/run_pipeline.def || error_exit "The container could not be built."
+    else
+        error_exit "The container was not found, nor a definition file to build it."
+    fi
+fi
+
+# -B /pasteur will mount /pasteur in the container
+# so that it finds the Genome configuration and gene lists
+# that are expected to be in a specific location there.
+singularity shell -B /pasteur -B /run/shm:/run/shm ${container} $@