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

[Jochen Bick]

Thanks Dan,

I would like to have it as plain text but no as a separate file in the
history but more like the solution of bam and bai files. Do you know how
to do that?

Cheers Jochen

On 07.02.2017 21:26, Daniel Blankenberg wrote:
> Just a quick note, if you want svg to be rendered as a graphics correctly via 
> the eye preview, you’ll need to set “serve_xss_vulnerable_mimetypes = True" 
> in galaxy.ini. Otherwise it will appear as plaintext xml. But do be aware of 
> the security concerns if you change this setting.  Downloading/saving the svg 
> and then manually opening will work regardless.
> 
> 
> Thanks for using Galaxy,
> 
> Dan
> 

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

[Jochen Bick]

Hej Björn,

ok you were right... I had a tool issue.
Now its working.

Cheers Jochen

On 07.02.2017 21:17, Björn Grüning wrote:
> Hi,
> 
> just change it to svg. If the output is empty this could be a tool problem.
> 
> Ciao,
> Bjoern
> 
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Re: [galaxy-dev] Create a new datatype svg

[Daniel Blankenberg]

Just a quick note, if you want svg to be rendered as a graphics correctly via 
the eye preview, you’ll need to set “serve_xss_vulnerable_mimetypes = True" in 
galaxy.ini. Otherwise it will appear as plaintext xml. But do be aware of the 
security concerns if you change this setting.  Downloading/saving the svg and 
then manually opening will work regardless.


Thanks for using Galaxy,

Dan


> On Feb 7, 2017, at 3:17 PM, Björn Grüning  wrote:
> 
> Hi,
> 
> just change it to svg. If the output is empty this could be a tool problem.
> 
> Ciao,
> Bjoern
> 
> Am 07.02.2017 um 14:19 schrieb Jochen Bick:
>> Hi Björn,
>> 
>> thanks, so I just change the format to svg? or is there more to do?
>> The output appears to be empty?
>> 
>> Cheers Jochen
>> 
>> 
>> On 07.02.2017 13:34, Björn Grüning wrote:
>>> Hi Jochen,
>>> 
>>> svg is supported, see here:
>>> 
>>> https://github.com/galaxyproject/galaxy/blob/dev/config/datatypes_conf.xml.sample#L282
>>> 
>>> Cheers,
>>> Bjoern
>>> 
>>> Am 07.02.2017 um 12:45 schrieb Jochen Bick:
 Hi all,
 
 I'm working on a tool that will have svg as an output file. Is this data
 type already established? If not how do I start?
 
 Cheers Jochen
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Re: [galaxy-dev] Configuring Galaxy, Pulsar and Conda

[John Chilton]

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 

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

[Björn Grüning]

Hi,

just change it to svg. If the output is empty this could be a tool problem.

Ciao,
Bjoern

Am 07.02.2017 um 14:19 schrieb Jochen Bick:
> Hi Björn,
> 
> thanks, so I just change the format to svg? or is there more to do?
> The output appears to be empty?
> 
> Cheers Jochen
> 
> 
> On 07.02.2017 13:34, Björn Grüning wrote:
>> Hi Jochen,
>>
>> svg is supported, see here:
>>
>> https://github.com/galaxyproject/galaxy/blob/dev/config/datatypes_conf.xml.sample#L282
>>
>> Cheers,
>> Bjoern
>>
>> Am 07.02.2017 um 12:45 schrieb Jochen Bick:
>>> Hi all,
>>>
>>> I'm working on a tool that will have svg as an output file. Is this data
>>> type already established? If not how do I start?
>>>
>>> Cheers Jochen
>>> ___
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>>> 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/mailinglists/
>>>
> 
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Re: [galaxy-dev] Pulsar Metadata

[John Chilton]

I perhaps don't understand the question. As long as the "datasets" are
Galaxy datasets and they appear in the command-line specific by the
"command" block of your tool - it should be transmitted. When you say
a "dataset list of files" - do you mean (1) a Galaxy collection, (2) a
set of files selected with a 
block in your tool, or (3) do you have a special datatype that
references lists of paths on the file system not tracked by Galaxy?

Pulsar doesn't really have an API to expose these things to your tools
- as long as you are sticking to Galaxy's abstractions these things
should just work. If you have tools or datatypes that reference
arbitrary other files on the file system (like 3 above) that is going
to break some Galaxy abstractions including Pulsar, quota tracking,
purging datasets, object stores, etc

-John

On Thu, Feb 2, 2017 at 8:49 AM, Joseph Brent Greer
 wrote:
>
>
> Hi All,
>
>
>
> We’ve been using Pulsar to send jobs to our cluster on campus. Generally we
> send a dataset list of files over. We’re wondering if there is a way to get
> the metadata for the files after they’ve been sent to the cluster. We’re
> specifically trying to find the filepaths of the files before they were
> through Pulsar to the cluster.
>
>
>
> Any guidance would be great.
>
>
>
> Thanks,
>
>
>
> Joe
>
>
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Re: [galaxy-dev] Issue when using xsendfile with galaxy release_16.07

[SAPET, Frederic]

Hello

I can still reproduce this issue with release_16.10

I'm unable to preview some files (txt, pasted entry) until I have changed their 
type (ie : to tabular).

I've switch off the feature but it seems to be better regarding performances so 
if you could help me to find why it doesn't work it would be nice.

Thank you.

Fred

De : galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] De la part 
de SAPET, Frederic
Envoyé : mercredi 24 août 2016 17:19
À : galaxy-dev@lists.galaxyproject.org
Objet : [galaxy-dev] Issue when using xsendfile with galaxy release_16.07

Hello

I'm trying the latest Galaxy (git status gives me : # On branch release_16.07)

I've set the xsend option in galaxy.ini (in order to run Galaxy behind a web 
server proxy, and apply all methods described here : 
https://wiki.galaxyproject.org/Admin/Config/ApacheProxy)
apache_xsendfile = True

HTML, gff3,tabular files are just fine but the preview of some other files 
(txt, csv)  is broken on the interface.

When I want to preview a txt file :
Not Found
The requested URL /datasets/fd1df6a9052810d5/display/ was not found on this 
server.

And apache says :
[Thu Aug 18 15:33:48 2016] [error] [client 192.168.29.12] (13)Permission 
denied: xsendfile: cannot open file: 
/softs/bioinfo/galaxy-prod/database/files/000/dataset_19.dat, referer: http:

But it looks like this is not really a problem related to access.
Indeed, from the same file, I switch it from txt to tabular (edit attributes), 
the preview works.

Are you able to reproduce the behavior ?
The same problem occurs on release_16.01.
It's fine with  the release v15.05 which is my production server right now.

Fred

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[galaxy-dev] SLURM configuration problem

[Leonor Palmeira]

Dear all,

we have setup a Galaxy instance on a virtual machine, and we want to be
able to submit jobs to our HPC system (SLURM).

Currently, we do not understand how to define that jobs will be sent to
the HPC cluster.

We have set :

export $DRMAA_LIBRARY_PATH=/var/lib/libdrmaa.so

This is our config/job_conf.xml :













-P all_5hrs




And the output of "sh run.sh" :


galaxy.jobs.manager DEBUG 2017-02-07 15:50:39,962 Starting job handler

galaxy.jobs INFO 2017-02-07 15:50:39,962 Handler 'main' will load all
configured runner plugins

galaxy.jobs.runners.state_handler_factory DEBUG 2017-02-07 15:50:39,971
Loaded 'failure' state handler from module
galaxy.jobs.runners.state_handlers.resubmit

pulsar.managers.util.drmaa DEBUG 2017-02-07 15:50:39,975 Initializing
DRMAA session from thread MainThread

Traceback (most recent call last):

  File
"/home/mass/GAL/APP/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line
55, in paste_app_factory

app = galaxy.app.UniverseApplication( global_conf=global_conf,
**kwargs )

  File "/home/mass/GAL/APP/galaxy/lib/galaxy/app.py", line 170, in __init__

self.job_manager = manager.JobManager( self )

  File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/manager.py", line 23,
in __init__

self.job_handler = handler.JobHandler( app )

  File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/handler.py", line 32,
in __init__

self.dispatcher = DefaultJobDispatcher( app )

  File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/handler.py", line 723,
in __init__

self.job_runners = self.app.job_config.get_job_runner_plugins(
self.app.config.server_name )

  File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/__init__.py", line
687, in get_job_runner_plugins

rval[id] = runner_class( self.app, runner[ 'workers' ],
**runner.get( 'kwds', {} ) )

  File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/runners/drmaa.py",
line 88, in __init__

self.ds = DrmaaSessionFactory().get()

  File
"/usr/local/lib/python2.7/dist-packages/pulsar/managers/util/drmaa/__init__.py",
line 31, in get

return DrmaaSession(session_constructor, **kwds)

  File
"/usr/local/lib/python2.7/dist-packages/pulsar/managers/util/drmaa/__init__.py",
line 49, in __init__

DrmaaSession.session.initialize()

  File "/usr/local/lib/python2.7/dist-packages/drmaa/session.py", line
257, in initialize

py_drmaa_init(contactString)

  File "/usr/local/lib/python2.7/dist-packages/drmaa/wrappers.py", line
73, in py_drmaa_init

return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer))

  File "/usr/local/lib/python2.7/dist-packages/drmaa/errors.py", line
151, in error_check

raise _ERRORS[code - 1](error_string)

InternalException: code 1: cell directory
"/usr/lib/gridengine-drmaa/default" doesn't exist

Could anyone point us in the right direction?
This would be greatly appreciated.

Best regards
Leonor

-- 
Leonor Palmeira | PhD
Associate Scientist
Department of Human Genetics
CHU de Liège | Domaine Universitaire du Sart-Tilman
4000 Liège | BELGIQUE
Tél: +32-4-366.91.41
Fax: +32-4-366.72.61
e-mail: lpalme...@chu.ulg.ac.be
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Re: [galaxy-dev] Request more details from Nikolaos Tur about pyBamTools & pyBamParser dependency packages message

[Jennifer Hsieh]

Thanks so much guys,
I'll test it out again this weekend.
Looking forward to it :)

Best,
Jen

On 6 Feb 2017 7:23 p.m., "Peter Briggs" 
wrote:

> Hello Dan
>
> Thanks for merging in the changes, just to let you know that these
> packages seem to install okay for me now from the toolshed - much
> appreciated!
>
> Best wishes
>
> Peter
>
> --
> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>
> --
> *From:* Daniel Blankenberg [d...@bx.psu.edu]
> *Sent:* Friday, February 03, 2017 2:46 PM
> *To:* Jennifer Hsieh
> *Cc:* Nikolaos Tur; Galaxy Dev List; Peter Briggs
> *Subject:* Re: [galaxy-dev] Request more details from Nikolaos Tur about
> pyBamTools & pyBamParser dependency packages message
>
> Hi all,
>
> These packages should now install correctly from the toolshed with Peter’s
> PR. Please let me know if you encounter additional issues.
>
>
>
> Thanks for using Galaxy,
>
> Dan
>
> On Jan 31, 2017, at 10:47 PM, Jennifer Hsieh 
> wrote:
>
> Thank so much!
> This is exactly what I needed.
> What a gem :)
>
> Best,
> Jen
>
> On Tue, Jan 31, 2017 at 3:48 PM, Nikolaos Tur  w
> rote:
>
>> Hi,
>>
>> sorry for long delay answer. Solution which Peter suggested is absolutely
>> right - owner of packages has to add changes.
>> Because I did not have any reaction to my message but needed quick
>> solution and wanted to stay in consistent with
>> standard Galaxy installation procedure and neither do any fork of
>> Daniel's packages and setup then local toolsched
>> repository for tools or install these packages locally, I did some trick.
>>
>> First I installed these packages. Installation of course failed. Then I
>> open them in web interface, uninstalled them,
>> modified  tool_dependencies.xml files (see below) and installed them
>> again from the web interface.
>> Sorry if I miss something that was several months ago.
>>
>> shell_command was modified.
>>
>> ...
>> 
>> hg clone -r ba0341816b15fff5e0a554658d6579
>> a60e1b12b1 https://bitbucket.org/dan/pybamtools pyBamTools
>> $INSTALL_DIR/lib/python
>> export 
>> PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python
>> && sed -i '/use_setuptools()/ s/^/#/' setup.py && sed -i '/from
>> distribute_setup import use_set
>> uptools/ s/^/#/' setup.py && python setup.py install --home
>> $INSTALL_DIR
>> 
>> > action="prepend_to">$INSTALL_DIR/lib/python
>> 
>> 
>> ...
>>
>> instead of
>>
>> export 
>> PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python
>> && python setup.py install --home $INSTALL_DIR
>>
>> Idea I think is clear, after clone of tools, modify first setup.py files
>> and then compile and install.
>>
>> Hope it can be useful,
>> Nikolaos.
>>
>> On Tue, Jan 10, 2017 at 12:54 PM, Jennifer Hsieh > com> wrote:
>>
>>> Hi Peter,
>>> Thank you so much.
>>> I'll see what I can figure out with these pull requests. I'm still quite
>>> inexperienced with these types of files. This is probably a good
>>> opportunity to learn some new code/structures.
>>> If I can't manage to figure it out, I hope there's another variant
>>> caller with different dependencies I can use for my project.
>>>
>>> Best,
>>> Jen
>>>
>>>
>>> On 9 Jan 2017 4:06 p.m., "Peter Briggs" 
>>> wrote:
>>>
>>> Hello Jennifer
>>>
>>> I came across the same problem with the naive variant caller at the end
>>> of last year, when trying to upgrade our local Galaxy instance.
>>>
>>> As you describe, the issue is actually with the two dependency packages:
>>>
>>> -- package_pybamparser_0_0_1
>>> -- package_pybamtools_0_0_2
>>>
>>> I think I found the same solution as Nikolaos to the underlying problem
>>> (i.e. the setup.py files in these two packages are no longer compatible
>>> with the newer versions of the Python 'setuptools'), but I didn't have time
>>> to follow it up then.
>>>
>>> I've now submitted pull requests with my attempted fixes on the
>>> Bitbucket repositories which hold the source code for the dependencies
>>> (URLs below), so at least you can see how I've tried to address the
>>> problem. However I don't know of an easy way to apply these changes inside
>>> the Galaxy context - my hope is that the tool maintainer (Daniel
>>> Blankenberg, cc'ed) will take a look and update the dependencies on the
>>> toolshed.
>>>
>>> Not sure if this helps - maybe someone else on this list has a way to
>>> apply the patches directly?
>>>
>>> Best wishes
>>>
>>> Peter
>>>
>>> Pull request URLs:
>>>
>>> -- https://bitbucket.org/dan/pybamtools/pull-requests/1/
>>> -- https://bitbucket.org/dan/pybamparser/pull-requests/3/
>>>
>>>
>>>
>>> On 06/01/17 14:50, Jennifer Hsieh wrote:
>>>
 Hi,
 I've installed a local instance of Galaxy (on Ubuntu 16.04, python
 2.7.12) and have run in to this exact problem
 (posted by Nikolaos
 Tur 

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

[Jochen Bick]

Hi Björn,

thanks, so I just change the format to svg? or is there more to do?
The output appears to be empty?

Cheers Jochen


On 07.02.2017 13:34, Björn Grüning wrote:
> Hi Jochen,
> 
> svg is supported, see here:
> 
> https://github.com/galaxyproject/galaxy/blob/dev/config/datatypes_conf.xml.sample#L282
> 
> Cheers,
> Bjoern
> 
> Am 07.02.2017 um 12:45 schrieb Jochen Bick:
>> Hi all,
>>
>> I'm working on a tool that will have svg as an output file. Is this data
>> type already established? If not how do I start?
>>
>> Cheers Jochen
>> ___
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-- 
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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Re: [galaxy-dev] Create a new datatype svg

[Björn Grüning]

Hi Jochen,

svg is supported, see here:

https://github.com/galaxyproject/galaxy/blob/dev/config/datatypes_conf.xml.sample#L282

Cheers,
Bjoern

Am 07.02.2017 um 12:45 schrieb Jochen Bick:
> Hi all,
> 
> I'm working on a tool that will have svg as an output file. Is this data
> type already established? If not how do I start?
> 
> Cheers Jochen
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[galaxy-dev] Create a new datatype svg

[Jochen Bick]

Hi all,

I'm working on a tool that will have svg as an output file. Is this data
type already established? If not how do I start?

Cheers Jochen
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