Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
  • 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
Helena Rasche
@erasche
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=256m; support was removed in 8.0

Downloading https://github.com/grails/grails-core/releases/download/v2.5.5/grails-2.5.5.zip to /apollo/.grails/wrapper/grails-2.5.5-download.zip

Exception in thread "main" java.net.NoRouteToHostException: Host is unreachable (Host unreachable)
Jennifer Hillman-Jackson
@jennaj
Alexia became an evil laughing sentient AI earlier this week. Maybe Judgement day has arrived, lol
Dave B.
@davebx
was that a terminator 2 reference?
Jennifer Hillman-Jackson
@jennaj
:)
Jennifer Hillman-Jackson
@jennaj
I can reach https://usegalaxy.eu now! Yea!
Jennifer Hillman-Jackson
@jennaj
meant to mention this before -- but really like the landing page .. news, etc but especially the "Currently Running and Queued Jobs" graphic!!
we get that question a lot for usegalaxy.org. anyone know if there are plans to put that on main as well? @natefoo? Or should I ask @tnabtaf?
workflow-of-the-month is also interesting
seems like user-related release highlights could be on main, and be super helpful to alert users about new functions. or add them to news and get it all rolled in that way
just tossing ideas - done now :clap:
Björn Grüning
@bgruening
thanks for the flowers :)
Dave B.
@davebx
ooh, fancy
Anton Nekrutenko
@nekrut
@jennaj :+1:
Nicola Soranzo
@nsoranzo
Should this be iuc?
If you prefer devteam the repos need to be created and permissions given to iuc
Dave B.
@davebx
I'm not sure - the other sam tools are all devteam, so by one viewpoint it makes sense to do the same for _fastx
on the other hand, what you said
Nicola Soranzo
@nsoranzo
samtools_bam_to_cram and samtools_cram_to_bam are already iuc-owned
I'm going to change the owner to iuc in a direct commit, if that's alright
Martin Cech
@martenson
+1 to iuc owmership
Dave B.
@davebx
works for me
Nicola Soranzo
@nsoranzo
Pushed
Nicola Soranzo
@nsoranzo
Travis successfully published it on TS
Jennifer Hillman-Jackson
@jennaj
team - longer conda paths are known to be a problem for some locals. What is the best working solution?
Jennifer Hillman-Jackson
@jennaj
John Chilton
@jmchilton
Though that doc is a bit dated, in some cases the conda recipe needs to be rebuilt.
Jennifer Hillman-Jackson
@jennaj
Tool that gave the error MACS2 (also happened with a 17.09 local I had earlier, can't recall which exact tool in that case) https://toolshed.g2.bx.psu.edu/view/iuc/macs2/cb785e26207c
thanks @jmchilton - if starting up Galaxy from scratch, but you have older conda/miniconda installed already, will that be updated when Galaxy starts or does the user need to do something active (remove/update conda?)
I had that problem in 17.09 (which I think the Q&A is also about). Not sure if just this tool being a problem or something more.
Nicola Soranzo
@nsoranzo
Conda needs to be updated manually at the moment
Jennifer Hillman-Jackson
@jennaj
Ah, ok, that's important, thank you @nsoranzo
Greg Von Kuster
@gregvonkuster
I'm working on the meme-chip tool for @bgruening which I'll contribute to tools-iuc. Currently all meme tools are located in the same directory in the repo, so they all share the same macros.xml, tool_data_table_conf.xml.sample, etc. But the meme-chip tool requires a different data table that I've named "meme_motif_databases". The dev version of the data manager for this data is here https://testtoolshed.g2.bx.psu.edu/view/iuc/data_manager_meme_motif_database_downloader/6d6b69ad6bdc. Should I place this new tool in a separate directory outside of meme (e.g., meme_chip)?
Marius van den Beek
@mvdbeek
so that's a data manager ? Those usually go to the data managers folder https://github.com/galaxyproject/tools-iuc/tree/master/data_managers
Greg Von Kuster
@gregvonkuster
there are 2 tools I'm discussing here: 1) the meme_motif_databases data manager tool which is required by 2) the meme_chip tool. The meme_motif_databases data manager tool is used to install the meme_motif_databases that are then used to populate a combination of 2 select lists in the meme_chip tool. I'm wondering if the iuc will approve separating out the meme_chip tool into a directory under the ~/tools directory which is separate from ~/tools/meme. The reason is that this new meme_chip tool does not use the all_fasta data table, and the 3 meme tools currently in the ~/tools/meme directory do not use the meme_motif_databases data table.
Marius van den Beek
@mvdbeek
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?