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  • Jan 31 2019 17:58
    jorgemachucav starred galaxyproject/tools-iuc
  • Jan 31 2019 17:45
    bebatut opened #2270
  • Jan 31 2019 16:18
    cpreviti synchronize #2267
  • Jan 31 2019 14:15
    cpreviti synchronize #2267
  • Jan 31 2019 12:42
    bernt-matthias review_requested #2269
  • Jan 31 2019 12:42
    bernt-matthias edited #2269
  • Jan 31 2019 12:41
    bernt-matthias edited #2269
  • Jan 31 2019 12:40
    bernt-matthias synchronize #2269
  • Jan 31 2019 12:13
    cpreviti commented #2267
  • Jan 31 2019 12:07
    nsoranzo commented #2267
  • Jan 31 2019 12:01
    cpreviti synchronize #2267
  • Jan 31 2019 11:21
    cpreviti synchronize #2267
  • Jan 31 2019 09:47
    cpreviti synchronize #2267
  • Jan 31 2019 09:27
    cpreviti synchronize #2267
  • Jan 30 2019 20:38
    bernt-matthias commented #2131
  • Jan 30 2019 20:19
    hepcat72 commented #2239
  • Jan 30 2019 19:50
    lparsons commented #2239
  • Jan 30 2019 18:36
    bgruening commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2267
Jennifer Hillman-Jackson
@jennaj
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/
Nicola Soranzo
@nsoranzo
Would need to know exactly which Tool Shed package this "samtools" is
Jennifer Hillman-Jackson
@jennaj
I'll add a comment asking for more details .. the post has very few details
Nicola Soranzo
@nsoranzo
Thanks!
Jennifer Hillman-Jackson
@jennaj
@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?
Nicola Soranzo
@nsoranzo
The easiest solution is to update the tool to use conda dependencies by default. In the mean time it should be possible to uninstall package_samtools_1_2 and install samtools 1.2 from conda
nickeener
@nickeener
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?
Björn Grüning
@bgruening
you could use a different test
for example searching with a regex in your expected output
Dave B.
@davebx
@mblue9 I have an idea that could fix the filenames in diffbind while keeping the informative column headers, unless you're still working on this
Nicola Soranzo
@nsoranzo
@davebx Maybe galaxyproject/tools-iuc#1923 ?
Dave B.
@davebx
based on 1923, yes
Nadia Goué
@nagoue
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";
any clue on how can I solve this problem ?
mblue9
@mblue9
@davebx fire away! I'm working on fixing this diffbind control file issue atm https://github.com/galaxyproject/usegalaxy-playbook/issues/127#issuecomment-395073384
Jennifer Hillman-Jackson
@jennaj
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
luke
@luke-c-sargent

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!

Martin Cech
@martenson
@luke-c-sargent I am not sure the repos with packages are autoupdated
Martin Cech
@martenson
there for sure were not at the time of this change (2015) galaxyproject/tools-iuc#213
Nicola Soranzo
@nsoranzo
@luke-c-sargent ToolShed repo updated. For which tool do you need it? It's time to condafy it!
Nicola Soranzo
@nsoranzo
@martenson Packages are auto-pushed to the TTS and MTS like tool repos since galaxyproject/tools-iuc#1229
Jennifer Hillman-Jackson
@jennaj
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!
Björn Grüning
@bgruening
Jen please ask @davebx
Jennifer Hillman-Jackson
@jennaj
Thanks for the pointer, wasn't sure who was taking this on
Dave B.
@davebx
GATK 4 will be wrapped, but it might have to be after GCC
Jennifer Hillman-Jackson
@jennaj
Great, thanks for update dave
Martin Cech
@martenson
would be great if they wrapped it themselves now when they are open source
Dave B.
@davebx
that would be nice
pvanheus
@pvanheus
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...
Björn Grüning
@bgruening
they are already ported to IUC
and should follow more or less our guideline, if not feel free to change this :)
pvanheus
@pvanheus
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).
pvanheus
@pvanheus
@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?
Nicola Soranzo
@nsoranzo
From the command-line, no Planemo:
$ . ~/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
...
pvanheus
@pvanheus
does that actually create files in '/tmp/picard tmp' or does it create '/tmp/picard' ?
Nicola Soranzo
@nsoranzo
Creates '/tmp/picard tmp', not sure if it creates any file there for this particular command though
pvanheus
@pvanheus
Good. I am somewhat surprised that it works but I'll make the change.
Nicola Soranzo
@nsoranzo
Wait, you said that this fails in Planemo, right?
pvanheus
@pvanheus
if I set TEMP to a value with a space, it fails in planemo because Galaxy itself fails.
Nicola Soranzo
@nsoranzo
Ah, OK, that doesn't surprise me too much :D
pvanheus
@pvanheus
I can imagine a way of an admin injecting a path with a space into TEMP while keeping Galaxy safe frm such a path but it would be rather obtuse.
Nicola Soranzo
@nsoranzo
Do you have a traceback for the Galaxy crash? Would be good to fix this someday.
actually it is planemo failing not Galaxy...
and now #1944 is ready for a merge I think :)
John Chilton
@jmchilton
Yeah - looks like Planemo breaks if galaxy_root contains a space. We probably just need to quote something in the shell commands we execute