Mercurial > repos > elixir-it > covacs_apply_recalibrator

annotate mv_untar_gatk.sh @ 2:f47e8d9b7f2e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author elixir-it
date Wed, 02 Oct 2019 04:29:44 -0400
parents 48dc4c9bc497
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c785cec34cdc Uploaded
elixir-it
parents:
diff changeset
1 #!/bin/bash
c785cec34cdc Uploaded
elixir-it
parents:
diff changeset
2 #if the .jar file is not present in the conda_prefix the script search the tar.gz in the conda_prefix of the vm
c785cec34cdc Uploaded
elixir-it
parents:
diff changeset
3 #and untar the archive
2
f47e8d9b7f2e Uploaded
elixir-it
parents: 1
diff changeset
4 if [ ! -f $CONDA_PREFIX/../../GenomeAnalysisTK.jar ] ; then
f47e8d9b7f2e Uploaded
elixir-it
parents: 1
diff changeset
5 echo start untar ;
1
48dc4c9bc497 Uploaded
elixir-it
parents: 0
diff changeset
6 tar -jxvf $CONDA_PREFIX/../../GenomeAnalysis*.tar.bz2 --strip-components=1 -C $CONDA_PREFIX/../../ 2> log_tar
2
f47e8d9b7f2e Uploaded
elixir-it
parents: 1
diff changeset
7 echo all done
0
c785cec34cdc Uploaded
elixir-it
parents:
diff changeset
8 else
1
48dc4c9bc497 Uploaded
elixir-it
parents: 0
diff changeset
9 echo GATK is present
0
c785cec34cdc Uploaded
elixir-it
parents:
diff changeset
10 fi
1
48dc4c9bc497 Uploaded
elixir-it
parents: 0
diff changeset
11