Mercurial > repos > chrisw > monorail_test

annotate run_mr_snakemake.sh @ 39:6c879705d61b draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author chrisw
date Wed, 20 Nov 2019 02:56:18 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
39
6c879705d61b Uploaded
chrisw
parents:
diff changeset
1 #!/bin/bash
6c879705d61b Uploaded
chrisw
parents:
diff changeset
2
6c879705d61b Uploaded
chrisw
parents:
diff changeset
3 snakefile=$1
6c879705d61b Uploaded
chrisw
parents:
diff changeset
4 numprocs=$2
6c879705d61b Uploaded
chrisw
parents:
diff changeset
5 ref=$3
6c879705d61b Uploaded
chrisw
parents:
diff changeset
6 exon_bed=$4
6c879705d61b Uploaded
chrisw
parents:
diff changeset
7 output=$5
6c879705d61b Uploaded
chrisw
parents:
diff changeset
8 temp=$6
6c879705d61b Uploaded
chrisw
parents:
diff changeset
9 genome=$7
6c879705d61b Uploaded
chrisw
parents:
diff changeset
10 inputs=$8
6c879705d61b Uploaded
chrisw
parents:
diff changeset
11 compressed=$9
6c879705d61b Uploaded
chrisw
parents:
diff changeset
12
6c879705d61b Uploaded
chrisw
parents:
diff changeset
13 if [[ -n "$compressed" ]]; then
6c879705d61b Uploaded
chrisw
parents:
diff changeset
14 comp_str="compressed=1"
6c879705d61b Uploaded
chrisw
parents:
diff changeset
15 fi
6c879705d61b Uploaded
chrisw
parents:
diff changeset
16
6c879705d61b Uploaded
chrisw
parents:
diff changeset
17 snakemake --snakefile "$snakefile" -j $numprocs --config inputs=$inputs $comp_str ref=$ref exon_bed=$exon_bed output=$output temp=$temp genome=$genome