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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
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    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
Martin Cech
@martenson
wrong channel :)
Marius van den Beek
@mvdbeek
oops
:D
M Bernt
@bernt-matthias

@jmchilton here are a few examples:

ctd/CVInspector.ctd:      <ITEMLIST name="ignore_cv" type="string" description="A list of CV identifiers 
which should be ignored." required="false" advanced="false">
ctd/CVInspector.ctd:        <LISTITEM value="UO"/>
ctd/CVInspector.ctd:        <LISTITEM value="PATO"/>
ctd/CVInspector.ctd:        <LISTITEM value="BTO"/>
ctd/CVInspector.ctd:      </ITEMLIST>
<ITEMLIST name="target_modifications" type="string" description="List the amino acids to be searched for and their mass modifications, specified using UniMod (www.unimod.org) terms, e.g. &apos;Carbamidomethyl (C)&apos;" required="false" advanced="false" restrictions="15N-oxobutanoic (N-term C),2-dimethylsuccinyl (C),2-monomethylsuccinyl (C),2-nitrobenzyl (Y),2-succinyl (C),2HPG (R),3-deoxyglucosone (R),3-phosphoglyceryl (K),3sulfo (N-term),4-ONE (C),4-ONE (H),4-ONE (K),4-ONE+Delta:H(-2)O(-1) (C),4-ONE+Delta:H(-2)O(-1) (H),4-ONE+Delta:H(-2)O(-1) (K),4AcAllylGal (C),a-type-ion (C-term),AccQTag (K),AccQTag (N-term),Acetyl (C),Acetyl (H),Acetyl (K),Acetyl (N-term),Acetyl (S),Acetyl (T),Acetyl (Y),Acetyl:13C(2) (K),Acetyl:2H(3) (H),Acetyl:2H(3) (K),Acetyl:2H(3) (N-term),Acetyl:2H(3)...">
        <LISTITEM value="Phospho (S)"/>
        <LISTITEM value="Phospho (T)"/>
        <LISTITEM value="Phospho (Y)"/>
</ITEMLIST>

Since both cases don't have restrictions we can't render them as <select> and repeats don't work, because I can't set the defaults.

My favorite solution would be a select where the user can add values.

The repeat units are very simple here, i.e. single string (but can be int,float as well)
@nsoranzo : btw: <param><value></value></param> does not work in a test :(
Nicola Soranzo
@nsoranzo
I only knew it would work for the help attribute.
John Chilton
@jmchilton
Thanks for the examples - yeah, that doesn't really fall nicely in the Galaxy tool framework at all. We probably want something like collection_type in the workflow editor - a free-form text box... but with multiple and suggestions.
Marius van den Beek
@mvdbeek

My favorite solution would be a select where the user can add values.

:+1: that would be nice

:D
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: twobit:{'path': 1, 'name': 0, 'value': 0} != twobit:{'value': 1, 'dbkey': 0, 'name': 1}"}
Nicola Soranzo
@nsoranzo
Trying to merge tools/extract_genomic_dna/tool_data_table_conf.xml.sample with Galaxy's config/tool_data_table_conf.xml.sample ?
Marius van den Beek
@mvdbeek
yes
probably a good check, but kind of surprising
there is a mismatch in the colum definition in extract_genomic_dna and the data manager
I suppose the data manager one should win
Nicola Soranzo
@nsoranzo
There's a definition also in Galaxy config/tool_data_table_conf.xml.sample , from which the data manager correctly derives.
Since 2015, commit galaxyproject/galaxy@30f1815
Marius van den Beek
@mvdbeek
does anyone know why we put emboss5 in the IUC conda channel ?
it’s pretty much the only package there that we still need in non-deprecated iuc tools
M Bernt
@bernt-matthias
Marius van den Beek
@mvdbeek
could be
I’ll open a PR, let’s see if it gets in
M Bernt
@bernt-matthias
Is this for the container tests? I remember that in the first iteration there was only one failing emboss tool which I tried to fix here galaxyproject/tools-iuc#2725.
Marius van den Beek
@mvdbeek
yeah, and now we need to build a container that includes the IUC channel, while we already had a container
that was emboss 5 only
Marius van den Beek
@mvdbeek
do all the emboss 5 tools need perl to run / should I add perl to the run requirements ?
M Bernt
@bernt-matthias
I think its only for the 4 perl script that are included in the galaxy wrappers. I guess requirements are fine.
Marius van den Beek
@mvdbeek
Marius van den Beek
@mvdbeek
@nsoranzo the old source tarball is at ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/EMBOSS-5.0.0.tar.gz, should we use that instead of cheating our way around the linter ?
Nicola Soranzo
@nsoranzo
So compile it?
The linter seems broken though, should_not_be_noarch_source when there is no noarch makes no sense
Marius van den Beek
@mvdbeek
yep
to both
Robert Leach
@hepcat72
Question, I added a new version of a tool to bioconda-recipes. I'd like my galaxy wrapper to use that new version (no interface changes to the wrapper - just a bug fix). I updated the version attribute of the requirement tag in the wrapper's xml, but when I run planemo serve, it's still using the older version. What change must I make to have it use the newer bioconda-recipes version? (Note, if I do conda install toolname on the command line, it installs the new version.)
Martin Cech
@martenson
@hepcat72 maybe some conda cache clearing is needed? It should work.
Robert Leach
@hepcat72
Hmmm. It's is still using version 2.006 instead of 2.0013. I think I probably need to bump the wrapper version. I was using some weird version spec and I see that the latest spec says that the <tool version attribute should be tool_version+wrapper_version. I only had wrapper_version.
Robert Leach
@hepcat72
Gee. It still uses 2.006. If I do a which on the tool before doing planemo serve, it's the correct version.
Martin Cech
@martenson
can you share the tool?
Robert Leach
@hepcat72
Sure, although I accidentally got it to run the new version - and I'm not sure why it worked. I accidentally ran planemo serve from the main tool repo directory instead of the specific tool directory and it happened to use the new version when I ran it. Now if I run it from either, it uses the new version. I don't understand it. https://github.com/hepcat72/robs_galaxy_tools/tree/vcfsc13/tools/vcfsamplecompare
Martin Cech
@martenson
sounds like it could be some caching issue
glad it works now
M Bernt
@bernt-matthias
Is it correct that for <param name="in" multiple="true"> there is atm no way to create a list with the same name of elements, i.e. like<collection name="out" type="list" structured_like="in" inherit_format="true">? Would be really handy.
Marius van den Beek
@mvdbeek
yes, that’s right, and I wouldn’t implement this. If you need to derive a structure you should use a collection input
M Bernt
@bernt-matthias
Hmm. Have to think about this.
Marius van den Beek
@mvdbeek
You can take a look around the code, you’ll see that multiple=“true” is very different from a collection input
It might be a nice project to replace that with implicit collection building, I think it could unify some code paths