From 12db624ed883f2038db4b4786a9c55bd45f71e4f Mon Sep 17 00:00:00 2001
From: Cedric Midoux <cedric.midoux@inra.fr>
Date: Wed, 24 Jul 2019 17:26:08 +0200
Subject: [PATCH] update jobscript.sh with snakemake-5.4.5

---
 RunSnake.sh                         | 12 ++++++++----
 RunSnake_create-envs.sh             | 13 +++++++++++++
 RunSnake_graph.sh                   |  6 ++++--
 RunSnake_printshellcmds-forceall.sh |  5 +++--
 RunSnake_printshellcmds.sh          |  5 +++--
 RunSnake_report.sh                  |  6 ++++--
 jobscript.sh                        |  3 ++-
 7 files changed, 37 insertions(+), 13 deletions(-)
 create mode 100755 RunSnake_create-envs.sh

diff --git a/RunSnake.sh b/RunSnake.sh
index ef02cd6..8bb0b5e 100755
--- a/RunSnake.sh
+++ b/RunSnake.sh
@@ -1,16 +1,20 @@
+#!/bin/bash
+export PYTHONPATH=''
+source activate snakemake-5.4.5
+
 mkdir -p ./.log/out/ ./.log/err/
-#PYTHONPATH=''
-source /usr/local/genome/Anaconda3-5.1.0/envs/snakemake-5.2.0/snakemake-5.2.0_conda
 
 snakemake \
 --snakefile $1 \
 --jobscript jobscript.sh \
 --cluster-config cluster.json \
---cluster "qsub -V -cwd -N {rule} -o {cluster.out} -e {cluster.err} -q {cluster.queue} -pe thread {threads} {cluster.cluster}" \
+--cluster "qsub -V -cwd -R y -N {rule} -o {cluster.out} -e {cluster.err} -q {cluster.queue} -pe thread {threads} {cluster.cluster}" \
 --keep-going \
 --jobs 80 \
+--use-conda \
+--conda-prefix /projet/maiage/save/cmidoux/environments/ \
 --wait-for-files \
 --latency-wait 150 \
+--use-conda \
 --verbose \
 --printshellcmds
-
diff --git a/RunSnake_create-envs.sh b/RunSnake_create-envs.sh
new file mode 100755
index 0000000..ddf5ce6
--- /dev/null
+++ b/RunSnake_create-envs.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+export PYTHONPATH=''
+source activate snakemake-5.4.5
+
+snakemake \
+--snakefile $1 \
+--use-conda \
+--conda-prefix /projet/maiage/save/cmidoux/environments/ \
+--create-envs-only \
+--jobscript jobscript.sh \
+--cluster-config cluster.json \
+--printshellcmds \
+--verbose
diff --git a/RunSnake_graph.sh b/RunSnake_graph.sh
index bb04f3a..c59a79f 100755
--- a/RunSnake_graph.sh
+++ b/RunSnake_graph.sh
@@ -1,6 +1,8 @@
+#!/bin/bash
+export PYTHONPATH=''
+source activate snakemake-5.4.5
+
 mkdir -p report/
-PYTHONPATH=''
-source /usr/local/genome/Anaconda3-5.1.0/envs/snakemake-5.2.0/snakemake-5.2.0_conda
 
 snakemake \
 --snakefile $1 \
diff --git a/RunSnake_printshellcmds-forceall.sh b/RunSnake_printshellcmds-forceall.sh
index 4a1d2a0..d64095a 100755
--- a/RunSnake_printshellcmds-forceall.sh
+++ b/RunSnake_printshellcmds-forceall.sh
@@ -1,5 +1,6 @@
-PYTHONPATH=''
-source /usr/local/genome/Anaconda3-5.1.0/envs/snakemake-5.2.0/snakemake-5.2.0_conda
+#!/bin/bash
+export PYTHONPATH=''
+source activate snakemake-5.4.5
 
 snakemake \
 --snakefile $1 \
diff --git a/RunSnake_printshellcmds.sh b/RunSnake_printshellcmds.sh
index b024c72..c80fc48 100755
--- a/RunSnake_printshellcmds.sh
+++ b/RunSnake_printshellcmds.sh
@@ -1,5 +1,6 @@
-PYTHONPATH=''
-source /usr/local/genome/Anaconda3-5.1.0/envs/snakemake-5.2.0/snakemake-5.2.0_conda
+#!/bin/bash
+export PYTHONPATH=''
+source activate snakemake-5.4.5
 
 snakemake \
 --snakefile $1 \
diff --git a/RunSnake_report.sh b/RunSnake_report.sh
index 7979ecb..bac4fc4 100755
--- a/RunSnake_report.sh
+++ b/RunSnake_report.sh
@@ -1,6 +1,8 @@
+#!/bin/bash
+export PYTHONPATH=''
+source activate snakemake-5.4.5
+
 mkdir -p report/
-PYTHONPATH=''
-source /usr/local/genome/Anaconda3-5.1.0/envs/snakemake-5.2.0/snakemake-5.2.0_conda
 
 snakemake \
 --snakefile $1 \
diff --git a/jobscript.sh b/jobscript.sh
index 0ab5620..abc387d 100644
--- a/jobscript.sh
+++ b/jobscript.sh
@@ -1,4 +1,5 @@
 #!/bin/sh
 # properties = {properties}
-source /usr/local/genome/Anaconda3-5.1.0/envs/snakemake-5.2.0/snakemake-5.2.0_conda
+export PYTHONPATH=''
+source activate snakemake-5.4.5
 {exec_job}
-- 
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