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
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___________________________________________________________
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