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 > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/
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