Script and links to start pipelines more easily.

CLIP-seq

+CLIP
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CLIP/iCLIP-seq.snakefile

+iCLIP.snakefile
\ No newline at end of file

GRO-seq

+PRO-seq
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PRO-seq/GRO-seq.snakefile

+PRO-seq.snakefile
\ No newline at end of file

RNA-seq

+RNA_Seq_Cecere
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iCLIP

+CLIP
\ No newline at end of file

iCLIP-seq

+iCLIP
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run_GRO-seq_pipeline

+run_pipeline.sh
\ No newline at end of file

run_PRO-seq_pipeline

+run_pipeline.sh
\ No newline at end of file

run_RNA-seq_pipeline

+run_pipeline.sh
\ No newline at end of file

run_Ribo-seq_pipeline

+run_pipeline.sh
\ No newline at end of file

run_iCLIP-seq_pipeline

+run_pipeline.sh
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run_iCLIP_pipeline

+run_pipeline.sh
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run_pipeline.sh

+#!/bin/bash
+# Usage: run_pipeline.sh [<snakefile>] <configuration_file> [extra arguments for snakemake]
+# If no snakefile is provided, the script should be called from one of its aliases.
+# Each alias will run a specific pipeline, depending on its name.
+
+# 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 "${SCRIPT}")
+
+# This script can be called from various symbolic links.
+# The name of the link determines which snakefile to use.
+# PRO-seq and GRO-seq are actually the same pipeline
+# similarly for sRNA-seq and small_RNA-seq
+# similarly for iCLIP-seq and iCLIP
+case "${PROGNAME}" in
+    "run_RNA-seq_pipeline")
+        snakefile="${BASEDIR}/RNA-seq/RNA-seq.snakefile"
+        ;;
+    "run_GRO-seq_pipeline")
+        snakefile="${BASEDIR}/PRO-seq/GRO-seq.snakefile"
+        ;;
+    "run_PRO-seq_pipeline")
+        snakefile="${BASEDIR}/PRO-seq/PRO-seq.snakefile"
+        ;;
+    "run_small_RNA-seq_pipeline")
+        snakefile="${BASEDIR}/small_RNA-seq/small_RNA-seq.snakefile"
+        ;;
+    "run_sRNA-seq_pipeline")
+        snakefile="${BASEDIR}/sRNA-seq/sRNA-seq.snakefile"
+        ;;
+    "run_iCLIP-seq_pipeline")
+        snakefile="${BASEDIR}/iCLIP-seq/iCLIP-seq.snakefile"
+        ;;
+    "run_iCLIP_pipeline")
+        snakefile="${BASEDIR}/iCLIP/iCLIP.snakefile"
+        ;;
+    "run_Ribo-seq_pipeline")
+        snakefile="${BASEDIR}/Ribo-seq/Ribo-seq.snakefile"
+        ;;
+    *)
+        snakefile="${1}"
+        shift
+        ;;
+esac
+
+configfile="${1}"
+shift
+
+if [ -e ${configfile} ]
+then
+    cmd="snakemake -s ${snakefile} --configfile ${configfile} $@"
+else
+    error_exit "Pipeline configuration file ${configfile} not found."
+fi
+echo ${cmd}
+eval ${cmd} || error_exit "${cmd} failed"
+
+exit 0

run_sRNA-seq_pipeline

+run_pipeline.sh
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run_small_RNA-seq_pipeline

+run_pipeline.sh
\ No newline at end of file

small_RNA-seq/sRNA-seq.snakefile

+small_RNA-seq.snakefile
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