made the snakemake bash files submittable by qsub

ctanes · Jun 29, 2020 · 2845552 · 2845552
1 parent a96beee
commit 2845552
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Showing 2 changed files with 24 additions and 5 deletions.
diff --git a/dryrun_snakemake.bash b/dryrun_snakemake.bash
@@ -1,4 +1,15 @@
-#!/bin/bash
+#!/usr/bin/env bash
+
+#$ -cwd
+#$ -r n
+#$ -V
+#$ -l h_vmem=2G
+#$ -j y
+
+#Uncomment the next two lines if you want to 'qsub' this script
+#source ~/.bashrc #needed to make "conda" command to work
+#conda activate qiime2-snakemake
+
 set -xeuo pipefail
 
 if [ $# -ne 1 ]; then

diff --git a/run_snakemake.bash b/run_snakemake.bash
@@ -1,4 +1,15 @@
-#!/bin/bash
+#!/usr/bin/env bash
+
+#$ -cwd
+#$ -r n
+#$ -V
+#$ -l h_vmem=2G
+#$ -j y
+
+#Uncomment the next two lines if you want to 'qsub' this script
+#source ~/.bashrc #needed to make "conda" command to work
+#conda activate qiime2-snakemake
+
 set -xeuo pipefail
 
 if [ $# -ne 1 ]; then
@@ -8,9 +19,6 @@ fi
 
 CONFIG_FP=$1
 
-#source ~/.bashrc
-#conda activate qiime2-snakemake
-
 snakemake \
     --jobs 100 \
     --configfile ${CONFIG_FP} \