Re: [galaxy-dev] 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:

  













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 + 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/
> > > 
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> > >    http://galaxyproject.org/search/
> > > 
> > > 
> > > ___
> > > Please keep all replies on the list by using "reply all"
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> > > 
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Re: [galaxy-dev] Installing Tool Dependencies

[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 + 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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Re: [galaxy-dev] Installing Tool Dependencies

[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 + 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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Re: [galaxy-dev] 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 
Sent: Monday, July 16, 2018 12:42 PM
To: Tom Misilo 
Cc: galaxy-...@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 
mailto:misi...@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
Fax: 321-724-2559
misi...@fit.edu<mailto:misi...@fit.edu>

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Re: [galaxy-dev] 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  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 
> *Sent:* Monday, July 16, 2018 12:42 PM
> *To:* Tom Misilo 
> *Cc:* galaxy-...@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  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=gmail=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=gmail=g>
>
> Melbourne, FL 32901
> <https://maps.google.com/?q=150+W.+University+Blvd+%0D%0A+Melbourne,+FL+32901=gmail=g>
>
> Phone: 321-674-8831 <(321)%20674-8831>
>
> Fax: 321-724-2559 <(321)%20724-2559>
>
> 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:
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>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/
>
>
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Re: [galaxy-dev] 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  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>
>
> misi...@fit.edu
>
>
> ___
> Please keep all replies on the list by using "reply all"
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>
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[galaxy-dev] 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
misi...@fit.edu

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Re: [galaxy-dev] installing tool dependencies

[Jochen Bick]

Hej Marius,


> what version of galaxy are you running?

we are running 15.10 but it will be updated next Monday.

> When you are doing this you should have a traceback in your logs,
> this would be helpful to understand what is going on.

ok I will check the logs for the error.

> 
> When you say "I installed a bunch of tools at the same time",
> did you really trigger multiple installations at the same time,
> or did you install a suite of tools?
> I don't think the install framework can handle parallel installations
> (well).
> It may work once in a while, but you're better of installing things
> sequentially.

thats true. I guess that was the reason on all the errors.

Thanks Jochen
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Re: [galaxy-dev] installing tool dependencies

[Marius van den Beek]

Hello Jochen,

what version of galaxy are you running?
When you are doing this you should have a traceback in your logs,
this would be helpful to understand what is going on.

When you say "I installed a bunch of tools at the same time",
did you really trigger multiple installations at the same time,
or did you install a suite of tools?
I don't think the install framework can handle parallel installations
(well).
It may work once in a while, but you're better of installing things
sequentially.

Best,
Marius


On 12 January 2017 at 10:47, Jochen Bick  wrote:

> Hi,
>
> I installed a bunch of tools at the same time and ran into some errors.
> After repairing those tools some of the dependencies installations did
> not work. If I try to repair the tools again I also get this error message:
>
> Internal Server Error
> Galaxy was unable to successfully complete your request
>
> An error occurred.
> This may be an intermittent problem due to load or other unpredictable
> factors, reloading the page may address the problem.
>
> The error has been logged to our team.
>
>
> the tool I tried is called:
> Name:
> camera_annotate
> Description:
> [Metabolomics][W4M][LC-MS] CAMERA R Package - Annotation - Returns
> annotation results (isotope peaks, adducts and fragments)
>
> Maybe anyone has an idea how to solve this. Thanks in advance
>
>
> Cheers Jochen
>
>
> --
> ETH Zurich
> *Jochen Bick*
> Animal Physiology
> Institute of Agricultural Sciences
> Postal address: Universitätstrasse 2 / LFW B 58.1
> Office: Tannenstrasse 1 / TAN D 6.2
> 8092 Zurich, Switzerland
>
> Phone +41 44 632 28 25
> jochen.b...@usys.ethz.ch 
> www.ap.ethz.ch
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[galaxy-dev] installing tool dependencies

[Jochen Bick]

Hi,

I installed a bunch of tools at the same time and ran into some errors.
After repairing those tools some of the dependencies installations did
not work. If I try to repair the tools again I also get this error message:

Internal Server Error
Galaxy was unable to successfully complete your request

An error occurred.
This may be an intermittent problem due to load or other unpredictable
factors, reloading the page may address the problem.

The error has been logged to our team.


the tool I tried is called:
Name:
camera_annotate
Description:
[Metabolomics][W4M][LC-MS] CAMERA R Package - Annotation - Returns
annotation results (isotope peaks, adducts and fragments)

Maybe anyone has an idea how to solve this. Thanks in advance


Cheers Jochen


-- 
ETH Zurich
*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 58.1
Office: Tannenstrasse 1 / TAN D 6.2
8092 Zurich, Switzerland

Phone +41 44 632 28 25
jochen.b...@usys.ethz.ch 
www.ap.ethz.ch
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