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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
Nicola Soranzo
@nsoranzo
The size attribute of <param /> should be tagged as deprecated in https://docs.galaxyproject.org/en/latest/dev/schema.html#id39 , shouldn't it ?
It was removed from tools-iuc tools in galaxyproject/tools-iuc#268 thanks to @bgruening , but it keeps reappearing
Björn Grüning
@bgruening
@/all we have accumulated a lot of PR and great contributions. Can we all take some time and review them? Would be great! If you think we should have a Codefest for this let me know.
Anthony Bretaudeau
@abretaud
should we close all tool_dependencies.xml issues now that we've switched to conda? https://github.com/galaxyproject/tools-iuc/issues?q=is%3Aissue+is%3Aopen+label%3Atool_dependencies.xml
Marius van den Beek
@mvdbeek
yes please!
I've closed them and will add a new label (won't fix - deprecated tool dependencies)
Anthony Bretaudeau
@abretaud
good!
Björn Grüning
@bgruening
@mvdbeek do you think we can put all samtools tools in one folder and create a demultiplexing-suite without breaking the Shed-repos? This would make the macro handling easier I think.
Marius van den Beek
@mvdbeek
Sure, why not. But after the open PRs are merged
Björn Grüning
@bgruening
I haven't looked at it, sorry. I'm not sure this is possible - so if the tool-ids matching the repo names and so on. Just as an idea.
Nicola Soranzo
@nsoranzo
@hepcat72 Regarding your question from August 30th, it is actually already possible to add suggestions to a text form, see https://docs.galaxyproject.org/en/latest/dev/schema.html#id24
Marius van den Beek
@mvdbeek
can I get a merge on galaxyproject/tools-iuc#2066 ?
pvanheus
@pvanheus
hey IUC folks - I'm working on adding a data manager (data_manager_fetch_refseq), what should the contents of .shed.yml be? I see there is a checkbox about it on the checklist.
Marius van den Beek
@mvdbeek
You can copy and adjust it from another IUC tool
pvanheus
@pvanheus
Thanks @mvdbeek
btw when I try planemo test with the data manager it doesn't actually run any tests. I recall planemo didn't have support for testing data managers in the past - is that still the case?
Marius van den Beek
@mvdbeek
that's right
you can load the data manager in your galaxy instance though and then do run_tests.sh -data_managers.
that's for the dev branch only IIRC
pvanheus
@pvanheus
ok... I'll try that thanks. BTW what is the correct import order? it complains about from datetime import date being before import gzip (https://travis-ci.org/galaxyproject/tools-iuc/jobs/426136502) - which style is this?
Marius van den Beek
@mvdbeek
stdlib before project imports, from b import c after import x
should be the default flake8-import-order
pvanheus
@pvanheus
ok... so called "cryptography" style, thanks.
Jennifer Hillman-Jackson
@jennaj
@mvdbeek @nsoranzo A usage change/issue with SnpEff was reported at Galaxy Biostars. Is this a known? New requirement? Bug? https://biostar.usegalaxy.org/p/29336/
Jennifer Hillman-Jackson
@jennaj
I know there were some issues with the dataset building wrappers and related problems. These aren't on the public servers yet so I can't test in those environments quite yet. Help linking reported usage with the changes made would be appreciated.
Nicola Soranzo
@nsoranzo
@jennaj I cannot find "Parameter regulation" anywhere in the SnpEff eff tool
Jennifer Hillman-Jackson
@jennaj
it is under "Genome source" when either of the first two of the four options are chosen
I'm looking at version SnpEff eff: annotate variants (Galaxy Version 4.3+T.galaxy1) at .org & .eu -- not the new wrapper version released on the 9th in the MTS.
We probably need to update both servers .. issue may go away. There were several issues earlier. Could use https://test.galaxyproject.org/ -- I don't see it there yet
@davebx Is this something you could do?
Seems good to test it out on a public server environment to find out what is going on, test prior known problems, etc
Jennifer Hillman-Jackson
@jennaj
In particular the database build function was a problem for nested pre-indexed genomes
(bacterial, etc)
Too many tickets to link back easily -- seems easier to get this on a server for integration testing and kick the tires :)
Nicola Soranzo
@nsoranzo
For the second issue, uploading of snpeff database is not supported by the Galaxy datatype, see galaxyproject/galaxy#6666
Jennifer Hillman-Jackson
@jennaj
Right -- people were mostly trying that because the snpeff database builder tool wasn't pulling the correct database in many cases
None of this is new, but there isn't a clean usage path (yet -- maybe the new wrappers addressed prior problems)
Nicola Soranzo
@nsoranzo
The updated snpeff download should fix the downloads from SourceForge.
Jennifer Hillman-Jackson
@jennaj
Ok, good to know. We need to test that in the prod server environment. I'll request the tool updates
CareyLambert
@CareyLambert
Hi,
Just to clarify the problem I encountered. I'm using Galaxy Version 4.3+T.galaxy1. I had previously had success with the new version of snpEff build, which overcame the nested genomes problem, and then the resulting files worked with snpEff eff. However, recently doing this again requires a value in the regulation option where it previously did not. As a potential quick fix, does anyone know what are legal values for this? Thanks, Carey
pvanheus
@pvanheus
Hello there - is there anyone interested in reviewing #2069 - a data manager to download RefSeq data and add to the all_fasta table?
pvanheus
@pvanheus

hello IUC folks.... this is not about a IUC tool but perhaps some people here have seen this... I've got a data manager in testtoolshed, data_manager_shapeit_reference, to which I am trying to add a new column... however when I try and shed_update I get this error:

$ planemo shed_update --shed_target testtoolshed
cd '/home/pvh/Documents/code/SANBI/CPGR/data_managers/data_manager_shapeit_ref' && git rev-parse HEAD
cd '/home/pvh/Documents/code/SANBI/CPGR/data_managers/data_manager_shapeit_ref' && git diff --quiet
Could not update data_manager_shapeit_reference
Unexpected HTTP status code: 500: {"err_msg": "Error attempting to parse file tool_data_table_conf.xml.sample: Merging tabular data tables with non matching columns is not allowed: shapeit_ref:{'path': 2, 'reference_prefix': 3, 'name': 1, 'value': 0, 'map_prefix': 4} != shapeit_ref:{'name': 1, 'value': 0, 'sample_prefix': 5, 'path': 2, 'reference_prefix': 3, 'map_prefix': 4}"}
Repository metadata updated successfully for repository 'data_manager_shapeit_reference' on the test Tool Shed.
Failed to update repository contents for repository 'data_manager_shapeit_reference' on the test Tool Shed.

Anyone seen something this this / know how to fix this?

Steffen Neumann
@sneumann
Evening', I am about to add a new tool to IUC, currently still in https://github.com/sneumann/tools-iuc/tree/feature/addMetFrag/tools/metfrag . I can't get planemo test to finish, I am getting this result: https://msbi.ipb-halle.de/~sneumann/tool_test_output.html . The tool has exit code 0 when running the command line metfrag ParameterFile='/tmp/tmpY2Mq2g/files/000/dataset_1.dat' ResultsFile='/tmp/tmpY2Mq2g/files/000/dataset_3.dat' LocalDatabasePath="/tmp/tmpY2Mq2g/files/000/dataset_2.dat" manually. It does write to stderr, and likely I failled to tell Galaxy that only exit code is relevant to detect failure. Any ideas ?
Björn Grüning
@bgruening
Steffen Neumann
@sneumann
Nope, neither <command detect_errors="exit_code"> nor aggressive worked, I also explicitly set profile <tool id="metfrag-cli-batch" name="metfrag-cli-batch" version="0.3" profile="16.04"> . The https://msbi.ipb-halle.de/~sneumann/tool_test_output.html shows a python exception without any informative hint. Maybe too late for hacking. Good night for now.
Björn Grüning
@bgruening
Stupid question, does the expected output file exists?
Can you give us a link to the wrapper, so I can run it locally?