Installing Tool Dependencies
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 misilot@fit.edu<mailto:misilot@fit.edu>
Hello Tom, that page is very very outdated and I wouldn't trust it. Do you have any specific tools from that list that are giving you trouble? If not then I would ignore it completely. Majority of the tools are now installed through the Toolshed and dependencies are auto-managed by Galaxy's own Conda which should provide a much better experience. Martin p.s. from what page did you get to this list? On Mon, Jul 16, 2018 at 12:06 PM Tom Misilo <misilot@fit.edu> wrote:
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 <(321)%20674-8831>
Fax: 321-724-2559 <(321)%20724-2559>
misilot@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/
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Hi Martin, I will try and figure out where I came across the page (it may have been from Google). I am having trouble installing: BEAM, LPS, PASS, and GPASS. Conda cannot find any sources to install these packages. Thank you! Tom From: Martin Čech <marten@bx.psu.edu> Sent: Monday, July 16, 2018 12:42 PM To: Tom Misilo <misilot@fit.edu> Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Installing Tool Dependencies Hello Tom, that page is very very outdated and I wouldn't trust it. Do you have any specific tools from that list that are giving you trouble? If not then I would ignore it completely. Majority of the tools are now installed through the Toolshed and dependencies are auto-managed by Galaxy's own Conda which should provide a much better experience. Martin p.s. from what page did you get to this list? On Mon, Jul 16, 2018 at 12:06 PM Tom Misilo <misilot@fit.edu<mailto:misilot@fit.edu>> wrote: 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<tel:(321)%20674-8831> Fax: 321-724-2559<tel:(321)%20724-2559> misilot@fit.edu<mailto:misilot@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/
All the links to the sources are at the bottom of the page and seem to work, except of GPASS which is here: http://stat.psu.edu/~yuzhang/software/GPASS.tar I would double check with your users whether they actually need these tools, since they are fairly old. Martin On Mon, Jul 16, 2018 at 12:56 PM Tom Misilo <misilot@fit.edu> wrote:
Hi Martin,
I will try and figure out where I came across the page (it may have been from Google).
I am having trouble installing: BEAM, LPS, PASS, and GPASS. Conda cannot find any sources to install these packages.
Thank you!
Tom
*From:* Martin Čech <marten@bx.psu.edu> *Sent:* Monday, July 16, 2018 12:42 PM *To:* Tom Misilo <misilot@fit.edu> *Cc:* galaxy-dev@bx.psu.edu *Subject:* Re: [galaxy-dev] Installing Tool Dependencies
Hello Tom,
that page is very very outdated and I wouldn't trust it. Do you have any specific tools from that list that are giving you trouble? If not then I would ignore it completely.
Majority of the tools are now installed through the Toolshed and dependencies are auto-managed by Galaxy's own Conda which should provide a much better experience.
Martin
p.s. from what page did you get to this list?
On Mon, Jul 16, 2018 at 12:06 PM Tom Misilo <misilot@fit.edu> wrote:
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!
<https://maps.google.com/?q=150+W.+University+Blvd+%0D%0A+Melbourne,+FL+32901&entry=gmail&source=g>
Tom
Thomas Misilo
Network Engineer
Florida Institute of Technology
Evans Library
150 W. University Blvd <https://maps.google.com/?q=150+W.+University+Blvd+%0D%0A+Melbourne,+FL+32901&entry=gmail&source=g>
Melbourne, FL 32901 <https://maps.google.com/?q=150+W.+University+Blvd+%0D%0A+Melbourne,+FL+32901&entry=gmail&source=g>
Phone: 321-674-8831 <(321)%20674-8831>
Fax: 321-724-2559 <(321)%20724-2559>
misilot@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/
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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 misilot@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/
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 misilot@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/
___________________________________________________________ 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/
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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 misilot@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/
___________________________________________________________ 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/
participants (4)
-
Björn Grüning -
Gudrun Mareike Amedick -
Martin Čech -
Tom Misilo