From ca5b834f938130ad6b46cbdf1ae90b4d9c42d452 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 17 Apr 2019 09:23:40 +0200
Subject: [PATCH] add pbs script for in2p3

---
 src/nextflow.pbs | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 src/nextflow.pbs

diff --git a/src/nextflow.pbs b/src/nextflow.pbs
new file mode 100644
index 00000000..aa3d9c0b
--- /dev/null
+++ b/src/nextflow.pbs
@@ -0,0 +1,26 @@
+#!/bin/sh
+#####################################
+# job script example with GE options
+#####################################
+#$ -S "/usr/local/bin/bash -l"
+#$ -q demon
+#$ -P P_lbmc
+#$ -N nf_pipe
+#$ -o /sps/inter/lbmc/lmodolo/logs/
+#$ -e /sps/inter/lbmc/lmodolo/logs/
+#$ -r n       # relaunch y/n
+#$ -M laurent.modolo@ens-lyon.fr
+#$ -m be      ## send an email when the job starts and ends
+#$ -l os=cl7  ## choose OS
+#$ -l sps=1   ## acces /sps directory
+#####################################
+
+PIPELINE=/sps/lbmc/common/nextflow/src/nf_modules/kallisto/indexing.nf
+CONFIG=/sps/lbmc/common/nextflow/src/nf_modules/kallisto/indexing.config
+OPTIONx="--fasta \"data/tiny_dataset/fasta/tiny_v2.fasta\""
+
+time /pbs/throng/lbmc/cl7/nextflow/19.01/nextflow \
+-profile ccin2p3_conda \
+$PIPELINE \
+-c $CONFIG \
+$OPTIONS
-- 
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