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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
Ghost
@ghost~5772e7e2c2f0db084a206e1b
both seems fine to me, but I think I prefer separating the directories
Greg Von Kuster
@gregvonkuster
ok, thanks!
I cannot see a way to make it work if keeping them all in the same directory. tool_data_table_conf.xml.sample cannot have differing entries IIRC.
Greg Von Kuster
@gregvonkuster
Ah, ok. But unless I hear differently, I still put meme_chip in a separate dir.
Nicola Soranzo
@nsoranzo
@jmchilton Are the log.info() calls in https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/tools.py#L373 leftovers or do you want to keep them?
John Chilton
@jmchilton
Ugh - those need to go
Nicola Soranzo
@nsoranzo
Thanks, I'll remove them (sorry for writing on the wrong chat)
John Chilton
@jmchilton
Thanks @nsoranzo !
Dave B.
@davebx
would it be bad or terrible to allow specifying a nonstandard conda channel in the requirement tag?
Björn Grüning
@bgruening
Dave we do have the IUC channel
for strange packages
Nicola Soranzo
@nsoranzo
@shiltemann Some Mothur tests failed after the PR was merged: https://travis-ci.org/galaxyproject/tools-iuc/jobs/355052918 , can you have a look?
I tried a restart, but that didn't help
Saskia Hiltemann
@shiltemann
@nsoranzo huh, weird, will have a look :)
Nicola Soranzo
@nsoranzo
Thanks!
Micropathology
@Micropathology
I'm getting tool errors with prokka and unicyler, are they working in 17.09?
Jennifer Hillman-Jackson
@jennaj
Is this the error? One of the dependencies needs to be manually updated. https://biostar.usegalaxy.org/p/27193/
Nicola Soranzo
@nsoranzo
@shiltemann Tests are now OK, but TS upload failed for some repos: https://travis-ci.org/galaxyproject/tools-iuc/jobs/355922400
E.g. for mothur_taxonomy-to-krona: Repository names must contain only lower-case letters, numbers and underscore.
Björn Grüning
@bgruening
@nsoranzo galaxyproject/tools-iuc#1783
Nicola Soranzo
@nsoranzo
I think that's the only one, except for suite_mothur which is a direct consequence
Björn Grüning
@bgruening
Think so too
Nicola Soranzo
@nsoranzo
Thanks, I'll keep an eye on the Travis build and merge later!
Jennifer Hillman-Jackson
@jennaj
Question about tool install issues in a Docker Galaxy. I pointed the admin/end-user here for help, but the Q&A could also happen at Biostars if someone has time. https://biostar.usegalaxy.org/p/27213/
Bruno Grande
@BrunoGrandePhD

Question about tool install issues in a Docker Galaxy. I pointed the admin/end-user here for help, but the Q&A could also happen at Biostars if someone has time. https://biostar.usegalaxy.org/p/27213/

I'm the affected user. I'll see if I can reproduce the issue on my MacBook to narrow it down to the Galaxy Docker Image or the Linux server where I first ran into tool installation problems. I'll update the Biostars post accordingly. Any suggestions in the meantime would be appreciated!

Björn Grüning
@bgruening
@brunogrande which version of Docker Galaxy is this?
Bruno Grande
@BrunoGrandePhD
I ran the docker run commands to instantiate the containers yesterday, so presumably the latest version.
Björn Grüning
@bgruening
And what was the image name? Any special tag you used?
Bruno Grande
@BrunoGrandePhD
I tried bgruening/galaxy-stable and quay.io/bgruening/galaxy-rna-workbench (no special tags) as well as older Galaxy Docker instances we already had running. The issue affected all of them as far as I can tell.
Björn Grüning
@bgruening
Wow, this is wired and you can not install a single tool. Not even something simple then https://toolshed.g2.bx.psu.edu/view/iuc/samtools_fastx/
?
Bruno Grande
@BrunoGrandePhD
Let me confirm.
Björn Grüning
@bgruening
just to make sure, if you open your galaxy and add a /api/verison to the URL, what do you see?
Bruno Grande
@BrunoGrandePhD
quay.io/bgruening/galaxy-rna-workbench:
{"extra": {}, "version_major": "17.09"}
bgruening/galaxy-stable:
{"version_major": "16.07"}
When I set up bgruening/galaxy-stable, it might have installed a cached version.
Screen Shot 2018-03-21 at 9.48.11 AM.png
I just tried installing samtools_fastx in my galaxy-rna-workbench instance and got this error.
Bruno Grande
@BrunoGrandePhD
I was able to instantiate a galaxy-rna-workbench container on my MacBook and install samtools_fastx and other tools. The issue seems to be related to the Linux server I'm using to run Docker. I'll try updating Docker. Any other suggestions?
Anton Nekrutenko
@nekrut
which envorimental variable contains the path to the current working directory?
Björn Grüning
@bgruening
$__tool_directory__/ ?
Anton Nekrutenko
@nekrut
not something `working_directory<?
Björn Grüning
@bgruening
I don't think we have such thing
you can use ./
or pwd
Anton Nekrutenko
@nekrut
./ does not work in my particualr case (snpEff bug)
so I need to tell it to look at the current directiry
I'll try $tool_directory/
Björn Grüning
@bgruening
so you need a full path?