Installing Tool Dependencies

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Installing Tool Dependencies

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

[hidden email]

 


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Re: Installing Tool Dependencies

Martin Čech
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that page is very very outdated and I wouldn't trust it.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 <[hidden email]> 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: <a href="tel:(321)%20674-8831" value="+13216748831" target="_blank">321-674-8831

Fax: <a href="tel:(321)%20724-2559" value="+13217242559" target="_blank">321-724-2559

[hidden email]

 

___________________________________________________________
Please keep all replies on the list by using "reply all"
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and other Galaxy lists, please use the interface at:
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___________________________________________________________
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Re: Installing Tool Dependencies

Tom Misilo

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 <[hidden email]>
Sent: Monday, July 16, 2018 12:42 PM
To: Tom Misilo <[hidden email]>
Cc: [hidden email]
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 <[hidden email]> 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: <a href="tel:(321)%20674-8831" target="_blank">321-674-8831

Fax: <a href="tel:(321)%20724-2559" target="_blank">321-724-2559

[hidden email]

 

___________________________________________________________
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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Re: Installing Tool Dependencies

Martin Čech
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 <[hidden email]> 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 <[hidden email]>
Sent: Monday, July 16, 2018 12:42 PM
To: Tom Misilo <[hidden email]>
Cc: [hidden email]
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 <[hidden email]> 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: <a href="tel:(321)%20674-8831" target="_blank">321-674-8831

Fax: <a href="tel:(321)%20724-2559" target="_blank">321-724-2559

[hidden email]

 

___________________________________________________________
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:
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Re: Installing Tool Dependencies

Gudrun Mareike Amedick
In reply to this post by Tom Misilo
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
> [hidden email]
>  
> ___________________________________________________________
> 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/

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Re: Installing Tool Dependencies

Björn Grüning-3
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
>> [hidden email]
>>  
>> ___________________________________________________________
>> 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/
___________________________________________________________
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:
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Re: Installing Tool Dependencies

Gudrun Mareike Amedick
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
> > > [hidden email]
> > >   
> > > ___________________________________________________________
> > > 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/
___________________________________________________________
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:
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