Random tools?
What is the risk if it is wrongly annotated? It has no impact on Galaxy's functionality now, does it?
Problem report when installing samtools from MTS with certain versions of ubunto as the OS. Known? Could someone help troubleshoot? https://biostar.usegalaxy.org/p/28213/
@nsoranzo The user replied at https://biostar.usegalaxy.org/p/28213/. They are trying to install an older version that is required by other tools as a dependency. Would you be able to help with a reply?
I'm running the test command on a tool I've been working on but it fails each time saying "History item different than expected, difference (using diff):". My output when I execute the command myself appears to have an extra space at the beginning of each line so I'm fairly certain that's what's causing my issue. Is there a way I can tell the test to ignore the spaces?
for example searching with a regex in your expected output
Hi, we have a homemade tool that we try to update (to integrate in toolshed by the end hopefully!) written in PERL. One script.pl A, calling one script.pl B requiring one module.pm asking for dependency as use Statistics::R. In the tool.xml, I added dependency : <requirement type="package" version="0.34" >perl-statistics-r</requirement>. Dependency is well installed as I can see in the admin interface. However, I have the error "Can't locate Statistics/R.pm in @INC ... " unless I add at the begining of script.pl B the 2 libraries from _conda folder : use lib "/storage/galaxydev/aubi/deps/_conda/envs/mulled-v1-a13c90f5fb8d14af93747bd7e50940f3368a06c26204eb3e68d6595d645d5073/lib/perl5/site_perl/5.22.0";
use lib "/storage/galaxydev/aubi/deps/_conda/envs/mulled-v1-a13c90f5fb8d14af93747bd7e50940f3368a06c26204eb3e68d6595d645d5073/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi";
use lib "/storage/galaxydev/aubi/deps/_conda/envs/mulled-v1-a13c90f5fb8d14af93747bd7e50940f3368a06c26204eb3e68d6595d645d5073/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi";
any clue on how can I solve this problem ?
@davebx fire away! I'm working on fixing this diffbind control file issue atm https://github.com/galaxyproject/usegalaxy-playbook/issues/127#issuecomment-395073384
Any plans to wraps Trinity's "SuperTranscript" utility for Galaxy? Or did I miss it in the MTS? Question asked here about it: https://biostar.usegalaxy.org/p/28312
there's a broken link in the toolshed for iuc's package_graphicsmagick_1_3_20 (latest version):
http://sourceforge.net/projects/graphicsmagick/files/graphicsmagick/1.3.20/GraphicsMagick-1.3.20.tar.gz
which has since been fixed in the tools-iuc repo of galaxy:
https://github.com/galaxyproject/tools-iuc/blob/1fe103338548dd65731a5a0887be59745370debd/packages/package_graphicsmagick_1_3_20/tool_dependencies.xml#L6
what's the cause of the disparity, and is there a way to update the toolshed.g2.bx.psu.edu version? thanks!
What is the decision for GATK 4? Will it be wrapped? I didn't find anything in tools-iuc but may have missed it. Question about if & status asked at Biostars today: https://biostar.usegalaxy.org/p/28327/
Linked the reply back here since I wasn't sure and though you all might know more, but please comment back at the message board if you prefer. Thanks!
in case anyone is around: I'm looking to doing some work on the picard tools since they do not use $TEMP but rather a
/tmp based path, yielding out-of-disk errors on my system. They are originally from devteam and do not follow IUC recommendations. I'm wondering how much to change though...
and should follow more or less our guideline, if not feel free to change this :)
Yes I know they are in IUC, not quite following the guidelines. The way Galaxy sets up its temporary directories seems very very complicated and relies on much barely documented code (e.g. https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tools/parser/interface.py#L99 and https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/__init__.py#L1663)
bottom line seems to be that if the admin sets TEMP via
<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).
@nsoranzo hey there I'm struggling with starting "planemo serve" with TEMP set to something with a space in - but I can't use 'TMP_DIR=\$TEMP' because then
$TEMP doesn't get expanded. I'm thinking that "TMP_DIR='\$TEMP'" should work but like I said I'm having trouble testing... I might need to inject a job_conf.xml that sets '$TEMP' to such a pathological value. How are you doing your testing?
$ . ~/miniconda3/bin/activate __picard@2.18.2
$ 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:/usr/users/ga002/soranzon/miniconda3/envs/__picard@2.18.2/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 soranzon@localhost.localdomain 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
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