Hi, I found the source of the tools. I think.
tool_conf.xml.sample from release_18.05 contains this:
<section id="hgv" name="Phenotype Association">
<tool file="evolution/codingSnps.xml" />
<tool file="evolution/add_scores.xml" />
<tool file="phenotype_association/sift.xml" />
<tool file="phenotype_association/linkToGProfile.xml" />
<tool file="phenotype_association/linkToDavid.xml" />
<tool file="phenotype_association/ldtools.xml" />
<tool file="phenotype_association/pass.xml" />
<tool file="phenotype_association/gpass.xml" />
<tool file="phenotype_association/beam.xml" />
<tool file="phenotype_association/lps.xml" />
<tool file="phenotype_association/master2pg.xml" />
</section>
There are the four tools. If I delete the section entirely, they disappear from
the dependencies list.
Since those tools weren't requested by "my" scientists and therefore probably
aren't used, this would explain why it doesn't cause any trouble. It
also explains why they popped up so suddenly, the section isn't part of the
file in release_18.01.
Kind regards
Gudrun
Am Mittwoch, den 18.07.2018, 09:12 +0200 schrieb Björn Grüning:
> Hi Gudrun,
>
> it seems this PASS tool is not yet available as Conda package.
>
> Do you know which ToolShed repo this is, you might want to contact the
> developer and ask for an upgrade to conda.
>
> > I don't know where they come from, I didn't install them explicitly.
>
> This is scary. Can you investigate here a little bit. Maybe some `suite`
> you have installed that had a dependency on PASS?
>
> Ciao,
> Bjoern
>
> Am 18.07.2018 um 09:07 schrieb Gudrun Mareike Amedick:
> >
> > Hi,
> >
> > I have those four tools, too. And they won't install properly. I don't
> > know where they come from, I didn't install them explicitly. They just
> > popped
> > up in my dependencies list. I've chosen to ignore them, since they don't
> > seem to cause any trouble. But if anyone had this problem too and solved
> > this, I'd be glad for pointers.
> >
> > If I try to install them I get the following log:
> >
> > galaxy.tools.deps.conda_util DEBUG 2018-07-17 10:39:17,261 [p:805,w:1,m:0]
> > [uWSGIWorker1Core0] Executing command:
> > /srv/galaxy/database/dependencies/_conda/bin/conda create -y
> > --override-channels --channel iuc --channel bioconda --channel conda-forge
> > --channel
> > defaults --name __pass@_uv_ pass
> > Fetching package metadata ...............
> >
> > PackageNotFoundError: Packages missing in current channels:
> >
> > - pass
> >
> > We have searched for the packages in the following channels:
> >
> > - https://conda.anaconda.org/iuc/linux-64
> > - https://conda.anaconda.org/iuc/noarch
> > - https://conda.anaconda.org/bioconda/linux-64
> > - https://conda.anaconda.org/bioconda/noarch
> > - https://conda.anaconda.org/conda-forge/linux-64
> > - https://conda.anaconda.org/conda-forge/noarch
> > - https://repo.continuum.io/pkgs/free/linux-64
> > - https://repo.continuum.io/pkgs/free/noarch
> > - https://repo.continuum.io/pkgs/r/linux-64
> > - https://repo.continuum.io/pkgs/r/noarch
> > - https://repo.continuum.io/pkgs/pro/linux-64
> > - https://repo.continuum.io/pkgs/pro/noarch
> >
> >
> > Kind regards
> >
> > GudrunAm Donnerstag, den 12.07.2018, 20:19 +0000 schrieb Tom
> > Misilo:
> > >
> > > Hello,
> > >
> > > I am trying to help a research here at Florida Tech setup Galaxy locally
> > > to process their data. However, I am running into a problem installing
> > > some
> > > tool dependencies was on this page
> > > (https://moin.galaxyproject.org/Admin/Tools/ToolDependencies).
> > >
> > > For example, I am trying to install BEAM, LPS, PASS, and GPASS. However,
> > > I cannot find in the documentation for either the tools themselves or
> > > on
> > > Galaxy on how to set these tools up for use in Galaxy. Would you be able
> > > to assist in this matter?
> > >
> > > Thank you!
> > > Tom
> > >
> > > Thomas Misilo
> > > Network Engineer
> > > Florida Institute of Technology
> > > Evans Library
> > > 150 W. University Blvd
> > > Melbourne, FL 32901
> > > Phone: 321-674-8831
> > > Fax: 321-724-2559
> > > misi...@fit.edu
> > >
> > > ___________________________________________________________
> > > Please keep all replies on the list by using "reply all"
> > > in your mail client. To manage your subscriptions to this
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> > > https://lists.galaxyproject.org/
> > >
> > > To search Galaxy mailing lists use the unified search at:
> > > http://galaxyproject.org/search/
> > >
> > >
> > > ___________________________________________________________
> > > Please keep all replies on the list by using "reply all"
> > > in your mail client. To manage your subscriptions to this
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> > >
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