there's a broken link in the toolshed for iuc's
package_graphicsmagick_1_3_20 (latest version):
which has since been fixed in the tools-iuc repo of galaxy:
what's the cause of the disparity, and is there a way to update the toolshed.g2.bx.psu.edu version? thanks!
/tmpbased path, yielding out-of-disk errors on my system. They are originally from
devteamand do not follow IUC recommendations. I'm wondering how much to change though...
<env>statements in job_conf.xml it will get copied into the job environment (which is something I rely on in the draft version of my wrapper).
$TEMPdoesn't get expanded. I'm thinking that "TMP_DIR='\$TEMP'" should work but like I said I'm having trouble testing... I might need to inject a
job_conf.xmlthat sets '$TEMP' to such a pathological value. How are you doing your testing?
$ . ~/miniconda3/bin/activate firstname.lastname@example.org $ TEMP=/tmp/picard\ tmp/ $ picard BamIndexStats VALIDATION_STRINGENCY=LENIENT `if [ -n "$TEMP" ]; then echo 'TMP_DIR=$TEMP'; fi` I=1.bam 23:01:03.883 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/email@example.com/share/picard-2.18.2-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Mon Jun 18 23:01:03 BST 2018] BamIndexStats INPUT=1.bam TMP_DIR=[/tmp/picard tmp] VALIDATION_STRINGENCY=LENIENT VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Mon Jun 18 23:01:03 BST 2018] Executing as firstname.lastname@example.org on Linux 4.4.0-128-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_121-b15; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.2-SNAPSHOT ...