Commit 8431633e authored by Blaise Li's avatar Blaise Li
Browse files

Script and links to start pipelines more easily.

parent 1bba523f
CLIP
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iCLIP.snakefile
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PRO-seq
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PRO-seq.snakefile
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RNA_Seq_Cecere
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CLIP
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iCLIP
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run_pipeline.sh
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run_pipeline.sh
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run_pipeline.sh
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run_pipeline.sh
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run_pipeline.sh
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run_pipeline.sh
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#!/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_pipeline.sh
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run_pipeline.sh
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small_RNA-seq.snakefile
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