Mercurial > repos > bgruening > interproscan

diff interproscan.xml @ 9:c55643c3d813 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 38c5ce62205ebeda50bedd83dd55737aef339468"
author: iuc
date: Fri, 11 Feb 2022 17:20:19 +0000
parents: 1207025b9b9c
children: 98cafcbd2578
--- a/interproscan.xml	Thu Jan 27 09:46:37 2022 +0000
+++ b/interproscan.xml	Fri Feb 11 17:20:19 2022 +0000
@@ -16,6 +16,9 @@
 &&
 sed 's|^\(data.directory=\).*$|\1${database.fields.path}/data|' \$(dirname \$(readlink -f \$(command -v interproscan.sh)))/interproscan.properties > \$HOME/.interproscan-5/interproscan.properties
 &&
+## Java doesn't read the HOME env var
+export _JAVA_OPTIONS=-Duser.home=\$HOME
+&&
 
 ## Now run interproscan
 interproscan.sh
@@ -31,7 +34,7 @@
 #else:
     --applications ${','.join($applications)}
 #end if
---tempdir \$TEMP
+--tempdir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
 
 $pathways
 $goterms
author	iuc
date	Fri, 11 Feb 2022 17:20:19 +0000
parents	1207025b9b9c
children	98cafcbd2578