Re: [galaxy-dev] regarding tool dependencies

[Martin Čech]

Hello Nir,

the tool publishing  process looks like this: tools for Galaxy are
contributed by developers like you to the Tool Shed
https://toolshed.g2.bx.psu.edu/ which serves as an 'appstore' for Galaxies
worldwide. Any Galaxy administrator can then instal the tool. Some tools
have dependencies, yours seem to depend on R. The recommended way to have
Galaxy installed these dependencies for you is to use Conda (list of some
available R packages here: https://anaconda.org/r/repo?type=conda). To
learn more about Conda please visit
https://docs.galaxyproject.org/en/master/admin/conda_faq.html

Alternatively, when you do not care about sharing your tool, and you do not
need to track reproducibility you can add any tool to Galaxy locally (add
the .xml wrapper and point tool_conf.xml at it and restart Galaxy). When
the tool is executed and no dependencies are found Galaxy will look for its
executable and if it is on the $PATH it will just use it.

Please let us know if you have more questions.

Thanks for using Galaxy,

Martin


On Thu, Feb 9, 2017 at 11:01 AM Nir Shachaf 
wrote:

> Dear Galaxy-dev team,
>
> As a research scientist in the dept. of Plant Sciences I would like to
> contribute a tool to the 'Metabolomics' tool-box under Galaxy. The tool is
> principally written in R, with some dependencies (namely: R>=3.x, and
> several R packages). Following the documentation in:
>
> https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies
>
> https://wiki.galaxyproject.org/Admin/Config/ToolDependencies
>
> I admit I get confused by the numerous possibilities offered by the
> framework. My main concern is to be able to link the Galaxy server to tools
> already installed on my development environment, and NOT to depend on the
> tools available in the tool-shed repository (as many are not there, and
> there are specific versions requirements).
>
> Could you kindly direct me to the relevant solution, or a user's-list
> post, if applicable?
>
> Many thanks in advance,
> Nir Shachaf,
> Plant Sciences Dept.,
> Weizmann Inst. of Science,
> Rehovot, Israel.
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[galaxy-dev] regarding tool dependencies

[Nir Shachaf]

Dear Galaxy-dev team,

As a research scientist in the dept. of Plant Sciences I would like to 
contribute a tool to the 'Metabolomics' tool-box under Galaxy. The tool is 
principally written in R, with some dependencies (namely: R>=3.x, and several R 
packages). Following the documentation in:

https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies

https://wiki.galaxyproject.org/Admin/Config/ToolDependencies

I admit I get confused by the numerous possibilities offered by the framework. 
My main concern is to be able to link the Galaxy server to tools already 
installed on my development environment, and NOT to depend on the tools 
available in the tool-shed repository (as many are not there, and there are 
specific versions requirements).

Could you kindly direct me to the relevant solution, or a user's-list post, if 
applicable?

Many thanks in advance,
Nir Shachaf,
Plant Sciences Dept.,
Weizmann Inst. of Science,
Rehovot, Israel.
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[galaxy-dev] Newline characters for txt files

[Lawrence, Cris W]

I have observed that when I upload a file with CRLF line endings into Galaxy 
and then later download it, the endings have changed to UNIX (LF only).  I also 
observed that an uploaded file containing CR only line endings in Galaxy 
downloads to a file again with LF only line endings.  These file types are txt. 
 Just want to confirm - does Galaxy scrub line endings?

- Cris
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Re: [galaxy-dev] Configuring Galaxy, Pulsar and Conda

[ric]

Hi John, thank you for your help.
Now it works!



Il 07/02/2017 21:20, John Chilton ha scritto:

Hello,

Thanks for working on this - Pulsar still hasn't quite caught up with
Galaxy in terms of support for Conda but we are getting there. So I
noticed two things that should help today when I was trying to
recreate your problem - the first is that Conda support in Pulsar
requires this PR (https://github.com/galaxyproject/pulsar/pull/126)
which isn't part of 0.7.3 - the pulsar you are targeting. I did an
update of Pulsar though so that should help - release 0.7.4 should be
available as of today.

Additionally, I noticed that the default for the Pulsar client option
"dependency_resolution" in Galaxy was broken. So to get this to work
at all - you will need to update your job_conf.xml and specify that
Pulsar should resolve dependencies and not Galaxy. This means adding
remote to your Pulsar
destination. I opened a Pull Request here for the Galaxy change - so
hopefully this will be the default by the time 17.01 is released.

The logs should make it clear if there are additional problems after
those changes I think. One think I would recommend is adding a
versionless Conda resolver also - so you may want to make that
dependency resolvers file look like this instead:


 
 


This may not be strictly needed based on the tools you are attempting
to get this to work for though.

Thanks for your patience and let me know how it goes.

-John



On Fri, Feb 3, 2017 at 6:18 AM, ric  wrote:

Hi,
I'm tryng to configure a Pulsar server to resolve dependencies using Conda
but unfortunately it does not work.
When I try to execute, for example, bowtie2, the standard error in the
Galaxy machine says: "/home/galaxy/pulsar/files/staging/67/command.sh: line
60: bowtie2-build: command not found" because Conda in the Pulsar machine
does not download this dependency.

Here is my app.yml:

dependency_resolvers_config_file: dependency_resolvers_conf.xml


My dependency_resolvers_conf.xml


 



The log of the Galaxy server:

galaxy.tools DEBUG 2017-01-19 14:50:18,910 Validated and populated state for
tool request (97.265 ms)
galaxy.tools.actions INFO 2017-01-19 14:50:19,069 Handled output named
output for tool toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0
(81.926 ms)
galaxy.tools.actions INFO 2017-01-19 14:50:19,113 Added output datasets to
history (43.950 ms)
galaxy.tools.actions INFO 2017-01-19 14:50:19,179 Verified access to
datasets for
Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0]
(33.690 ms)
galaxy.tools.actions INFO 2017-01-19 14:50:19,180 Setup for job
Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0]
complete, ready to flush (66.261 ms)
galaxy.tools.actions INFO 2017-01-19 14:50:19,240 Flushed transaction for
job
Job[id=67,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0]
(59.840 ms)
galaxy.tools.execute DEBUG 2017-01-19 14:50:19,240 Tool
[toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0] created job
[67] (296.972 ms)
galaxy.tools.execute DEBUG 2017-01-19 14:50:19,266 Executed 1 job(s) for
tool toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0 request:
(355.402 ms)
156.148.160.117 - - [19/Jan/2017:14:50:18 +0200] "POST /api/tools HTTP/1.1"
200 - "http://156.148.120.96:8080/; "Mozilla/5.0 (X11; Linux x86_64)
AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:50:19 +0200] "GET /api/webhooks/tool
HTTP/1.1" 200 - "http://156.148.120.96:8080/; "Mozilla/5.0 (X11; Linux
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87
Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:50:19 +0200] "GET
/api/histories/1cd8e2f6b131e891/contents?details=b847e822bdc195d0%2C40876639881ca029%2C915ae9a80309f157%2Cfd767e8b7355e21a%2C9ce617df390851fc%2C3cc0effd29705aa3%2Cb701da857886499b=hid=dev=update_time-ge=deleted=purged=2017-01-19T12%3A11%3A40.000Z=False=False
HTTP/1.1" 200 - "http://156.148.120.96:8080/; "Mozilla/5.0 (X11; Linux
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87
Safari/537.36"
galaxy.jobs DEBUG 2017-01-19 14:50:19,912 (67) Working directory for job is:
/home/galaxy/galaxy_test_pulsar/database/jobs_directory/000/67
galaxy.jobs.handler DEBUG 2017-01-19 14:50:19,931 (67) Dispatching to pulsar
runner
galaxy.jobs DEBUG 2017-01-19 14:50:20,013 (67) Persisting job destination
(destination id: remote_cluster)
galaxy.jobs.runners DEBUG 2017-01-19 14:50:20,044 Job [67] queued (112.446
ms)
galaxy.jobs.handler INFO 2017-01-19 14:50:20,090 (67) Job dispatched
galaxy.jobs.runners.pulsar INFO 2017-01-19 14:50:20,205 pulsar_version is
0.7.3
galaxy.util.object_wrapper WARNING 2017-01-19 14:50:20,644 Unable to create
dynamic subclass for , None: metaclass conflict: the
metaclass of a derived class must be a (non-strict) subclass of the
metaclasses of all its bases
galaxy.tools.deps DEBUG 2017-01-19 14:50:20,820 Find 

Re: [galaxy-dev] Create a new datatype svg

[Peter Cock]

Hmm. I wonder if a composite datatype would work here?

https://wiki.galaxyproject.org/Admin/Datatypes/Composite%20Datatypes

Peter

On Thu, Feb 9, 2017 at 9:25 AM, Jochen Bick  wrote:
> Hi Dan,
>
> I understand the option with this specific flag. What I mean is that for
> example the file format bam has two file in one save button. So if you
> click on save you can either save the bam file or the bai file. I would
> liek to have the same feature with my png and svg. So that I have just
> one item in the history showing the png and if you click on save you
> have the option to also save svg.
>
> Cheers Jochen
> ___
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Re: [galaxy-dev] Create a new datatype svg

[Jochen Bick]

Hi Dan,

I understand the option with this specific flag. What I mean is that for
example the file format bam has two file in one save button. So if you
click on save you can either save the bam file or the bai file. I would
liek to have the same feature with my png and svg. So that I have just
one item in the history showing the png and if you click on save you
have the option to also save svg.

Cheers Jochen
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