[galaxy-dev] GCC2015: Early Reg closes 22 May; Call for Birds-of-a-feather; and more

[Dave Clements]

Hello all,

A couple of GCC2015 related items:

*Early Registration closes 22 May*

Just a reminder that early registration
 for the 2015 Galaxy Community
Conference (GCC2015, http://gcc2015.tsl.ac.uk/) closes Friday, 22 May.
Registering after that costs an average of 40% more.  Space is limited at
several events, and when that space is gone, it's gone for good.  Register
now  and attend the events you want
to, and save 40%.  GCC2015 includes several new events and features even
more training than before.


*Call for Birds of a Feather (BoFs) Meetups*

*Birds of a feather* meetups are informal gatherings of GCC attendees with
a shared interest.  They are an essential part of GCCs.  If you have an
idea then for a BoF then you are strongly encouraged to propose one:

   https://wiki.galaxyproject.org/Events/GCC2015/BoFs


*Oral Presentation Abstracts are Online*

*Most* of the abstracts for accepted talks at GCC2015 are now online.  We
expect to put a few more up in the coming week.

  http://gcc2015.tsl.ac.uk/abstracts/

They aren't (yet) listed in any particular order.


Again, please do remember to register by 22 May, and we hope to see you in
Norwich!

Cheers,

Dave C


-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/
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[galaxy-dev] custom builds

[Shrum, Donald C]

Hi all,

I have a public galaxy server here at FSU that is running behind an apache 
proxy and on our cluster file system so that jobs can be submitted to our hpc 
cluster.

I have a user that receives an 'Internal Server Error' when going to 'Custom 
Builds'  This error seems to only occur for the one user and from what I can 
see it may be the case that there is a single mapper is causing the problem.  
(Sys-admin here, not a bioinformatics person :)

The errors I pulled from the logs are below.  Is it possible there is some 
mapper causing the problem?  If so is there a way I can remove it?

Any help would be appreciated and thanks,
Don Shrum
FSU Research Computing Center

InvalidRequestError: One or more mappers failed to initialize - can't proceed 
with initialization of other mappers.  Original exception was: Class 
'kombu.transport.sqlalchemy.Message' is not mapped
galaxy.jobs.handler ERROR 2015-05-13 13:44:25,150 Exception in monitor_step


WSGI Variables
--
  application: 
  is_api_request: False
  original_wsgi.url_scheme: 'http'
  paste.cookies: (,
 '__utma=51326654.2116930099.1431360039.1431360039.1431360039.1; 
__utmz=51326654.1431360039.1.1.utmcsr=directory.fsu.edu|utmccn=(referral)|utmcmd=referral|utmcct=/;
 _ga=GA1.2.2116930099.1431360039; 
galaxysession=c6ca0ddb55be603abe1a0bf853fb54302d17fe1509e1ff998221f8b85399eb4a8bcf9d852c6fb740')
  paste.expected_exceptions: []
  paste.httpexceptions: 
  paste.httpserver.thread_pool: 
  paste.recursive.forward: 
  paste.recursive.include: 
  paste.recursive.include_app_iter: 
  paste.recursive.script_name: ''
  paste.throw_errors: True
  request_id: '57170782f99611e4af7a00219ba29ca2'
  webob._parsed_query_vars: (MultiDict([]), '')
  wsgi process: 'Multithreaded'
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Re: [galaxy-dev] Tool failure due to PYTHONPATH in job environment after upgrade to 15.03

[Nate Coraor]

Hi Brian,

$PYTHONPATH was previously only modified when a tool's command line started
with `python`. This somewhat arbitrary change was modified in ee1a2b8 to
allow the external set_metadata process to run without requiring an
absolute path to a script on disk.

However, the job script template should only prepend to $PYTHONPATH if it
already exists, it should not fully overwrite it. That said, it looks like
the problem may be with a conflict between Galaxy's packaged pkg_resources
and the one in your virtualenv.

This may be fixed by appending Galaxy's lib directory rather than
prepending it. We're working on removing the need for passing Galaxy's lib
directory to tools entirely.

--nate

On Tue, May 12, 2015 at 11:57 PM, Brian Claywell 
wrote:

> After upgrading from the October 2014 release to 15.03 we started
> experiencing job failures for one of our custom tools, which I eventually
> tracked down to PYTHONPATH now being set in the job environment to
> $GALAXY_HOME/lib. The dependencies for this tool are installed in a
> virtualenv that is activated by the tool dependency package's env.sh. It
> looks like one of the scripts in this virtualenv attempts to use setuptools
> to find its dependencies, but because of the PYTHONPATH setting ends up in
> Galaxy's $GALAXY_HOME/lib/pkg_resources.py:
>
> ```
> Traceback (most recent call last):
>   File
> "/mnt/scdata/scdata_03/galaxy/containers/galaxy-qa/export/tool_deps/yapp_env/new/venv/bin/sequencing_quality_report.py",
> line 8, in 
> from pkg_resources import load_entry_point
>   File
> "/mnt/scdata/scdata_03/galaxy/containers/galaxy-qa/stable/lib/pkg_resources.py",
> line 2603, in 
> working_set.require(__requires__)
>   File
> "/mnt/scdata/scdata_03/galaxy/containers/galaxy-qa/stable/lib/pkg_resources.py",
> line 666, in require
> needed = self.resolve(parse_requirements(requirements))
>   File
> "/mnt/scdata/scdata_03/galaxy/containers/galaxy-qa/stable/lib/pkg_resources.py",
> line 565, in resolve
> raise DistributionNotFound(req)  # XXX put more info here
> pkg_resources.DistributionNotFound: pytz>=2011k
> ```
>
> I worked around this issue by prepending the virtualenv's
> lib/python2.7/site-packages directory to PYTHONPATH in the tool dependency
> package's env.sh, but I'm a bit confused why this is now necessary. Can
> anyone shed some light on what changed?
>
>
> Cheers,
>
> Brian
>
> --
> Brian Claywell | programmer/analyst
> Matsen Group   | http://matsen.fredhutch.org 
> Fred Hutchinson Cancer Research Center
>
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Re: [galaxy-dev] file_path passed directly to wrappers

[Nate Coraor]

On Wed, May 13, 2015 at 7:23 AM, Sabrina rodriguez <
sabrina.rodrig...@toulouse.inra.fr> wrote:

> Dear all,
>
> I am integrating some tools into galaxy and I would like to use some of
> the paths from the file "universe_wsgi.ini" (ex:file_path) directly into my
> perl wrappers in order for my per script to work in this directory.
> For now, I am providing the path in each perl script, manually, which is
> not maintainable when we change that path.
>
> Could you please tell me how to pass the file_path variable directly from
> the .xml to the .pl script?
>
>
Hi Sabrina,

Galaxy tools are strongly encouraged to run as self-contained units.
Objects that you need to to access (such as other datasets) should be
passed to your tool as parameters. If you provide some additional details
on what you're trying to accomplish in the file_path directory, we can
probably help with some alternative options to directly accessing file_path.

That said, it is possible to access that config value - all of Galaxy's
config options are exposed in the tool template using ${__app__.config}, so
you'd want to look at ${__app__.config.file_path}.

--nate


> Thanks in advance.
>
> Best regards,
>
> SAbrina
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Re: [galaxy-dev] Login problems with Galaxy on Chrome, Firefox is running fine, where should I look?

[Martin Čech]

Hello Melissa,

I created a user on your instance (https://galaxyxena.soe.ucsc.edu), logged
in and successfully uploaded a file all using Chrome.
Please try wiping out Chrome's cache and/or running it in the incognito
mode.

Thank you for using Galaxy.

Martin, Galaxy Team

On Tue, May 12, 2015 at 10:41 PM Melissa Cline  wrote:

> Hi Folks,
>
> I'm working on setting up a Galaxy production server, following the
> instructions on
> https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer.
> I'm using postgresql and an Apache proxy server.  It's not going well, and
> I could use some guidance.
>
> When I access the galaxy server on Google Chrome, I can't log in.  I can
> go to the login prompt and enter my credentials, but after I do that, I
> continue to see the login prompt as if I hadn't logged in.
>
> Then when I try to do a simple file upload, I see this message in pink in
> the history panel:
>
> "An error occurred while getting updates from the server.  Please contact
> a Galaxy admninistrator if the problem persists"
>
> and when I click on the little bug icon, here's what I see in the Galaxy
> pane:
>
> {
>   "agent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_3)
> AppleWebKit/537.36 (KHTML, like Gecko) Chrome/42.0.2311.90 Safari/537.36",
>   "url": "
> https://galaxyxena.soe.ucsc.edu/galaxy/galaxy/api/histories/bf0806da5b28c6d9/contents
> ",
>   "data": "",
>   "options": {
> "data": {},
> "parse": true,
> "emulateHTTP": false,
> "emulateJSON": false
>   },
>   "xhr": {
> "readyState": 4,
> "responseText": "{\"err_msg\": \"History is not accessible by user\",
> \"err_code\": 403002}",
> "responseJSON": {
>   "err_msg": "History is not accessible by user",
>   "err_code": 403002
> },
> "status": 403,
> "statusText": "Forbidden",
> "responseHeaders": {
>   "Date": "Wed, 13 May 2015 02:23:16 GMT\r",
>   "cache-control": "max-age=0,no-cache,no-store\r",
>   "Transfer-Encoding": "chunked\r",
>   "Server": "PasteWSGIServer/0.5 Python/2.7.1\r",
>   "Connection": "close\r",
>   "x-frame-options": "SAMEORIGIN\r",
>   "content-type": "application/json\r"
> }
>
>   },
>   "source": [],
>   "user": {
> "quota_percent": null,
> "nice_total_disk_usage": "0 bytes",
> "total_disk_usage": 0,
> "id": null,
> "username": "(anonymous user)",
> "email": "",
> "is_admin": false
>   }
> }
>
> Meanwhile, paster.log shows the following error messages:
>
> galaxy.tools ERROR 2015-05-12 19:23:16,766 Exception caught while
> attempting to\
>
> ol execution:
>
> Traceback (most recent call last):
>
>   File "/scratch/home/galaxy/galaxy/lib/galaxy/tools/__init__.py", line
> 1303, in handle_single_execution
> job, out_data = self.execute( trans, incoming=params, history=history,
> rerun_remap_job_id=rerun_remap_job_id,mapping_over_collection=mapping_over_collection
> )
>
>   File "/scratch/home/galaxy/galaxy/lib/galaxy/tools/__init__.py", line
> 1867, in execute
> return self.tool_action.execute( self, trans, incoming=incoming,
> set_output_hid=set_output_hid, history=history, **kwargs )
>   File "/scratch/home/galaxy/galaxy/lib/galaxy/tools/actions/upload.py",
> line 21, in execute
> uploaded_datasets = upload_common.get_uploaded_datasets( trans, '',
> incoming, precreated_datasets, dataset_upload_inputs, history=history )
>   File
> "/scratch/home/galaxy/galaxy/lib/galaxy/tools/actions/upload_common.py", line
> 242, in get_uploaded_datasets
> data = new_upload( trans, cntrller, uploaded_dataset,
> library_bunch=library_bunch, history=history )
>   File
> "/scratch/home/galaxy/galaxy/lib/galaxy/tools/actions/upload_common.py", line
> 232, in new_upload
> return __new_history_upload( trans, uploaded_dataset, history=history,
> state=state )
>   File
> "/scratch/home/galaxy/galaxy/lib/galaxy/tools/actions/upload_common.py",line
> 135, in __new_history_upload
> hda.state = hda.states.QUEUED
>   File "/scratch/home/galaxy/galaxy/lib/galaxy/model/__init__.py", line
> 1546, in set_dataset_state
> object_session( self ).add( self.dataset )
> AttributeError: 'NoneType' object has no attribute 'add'
>
> Meanwhile, if I'm working on Firefox, I can log in and upload files with
> no trouble.
>
> Any ideas?
>
> Thanks!
>
> Melissa
>
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To search Gal

[galaxy-dev] file_path passed directly to wrappers

[Sabrina rodriguez]

Dear all,

I am integrating some tools into galaxy and I would like to use some of 
the paths from the file "universe_wsgi.ini" (ex:file_path) directly into 
my perl wrappers in order for my per script to work in this directory.
For now, I am providing the path in each perl script, manually, which is 
not maintainable when we change that path.


Could you please tell me how to pass the file_path variable directly 
from the .xml to the .pl script?


Thanks in advance.

Best regards,

SAbrina
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Re: [galaxy-dev] reference in builds.txt

[Hans-Rudolf Hotz]

Hi Sabrina

Always include the mailing list, so others can help and/or learn as 
well. See my comments below


On 05/13/2015 09:40 AM, Sabrina rodriguez wrote:

Hi Hans-Rudolf,

Thanks for your answer.

I have made 2 .loc files for indexed genomes for 2 different tools (STAR
and tophat) on the same reference genome fasta file (ex: sus crofa).

In tophat.loc, I have:
ensembl_sus_scrofa_genomeensembl_sus_scrofa_genomeensembl sus
scrofa genome/bank/bowtie2db/ensembl_sus_scrofa_genome

In STAR.loc, I have:
STAR-ensembl_sus_scrofa_genomeSTAR-ensembl_sus_scrofa_genome
STAR-ensembl_sus_scrofa_genome /bank/STARdb/STAR-ensembl_sus_scrofa_genome



Since it is the same genome, I would use the same dbkey for both 
'*loc'files'. Short names for for dbkeys are recomended, eg: 'susScrLX'



In builds.txt, I have:
STAR-ensembl_sus_scrofa_genomeSTAR-ensembl_sus_scrofa_genome
(ensembl_sus_scrofa)



I would just add an extra line, similar to the existing one for 
'susScr2', eg:


susScrLXlocal Pig May 2015 (susScrLX) (susScrLX)



The 2 indexed come from the same reference genome.

Once the tools are processed, I need to precise the reference genome
using the "pencil" and so using the "builds.txt" information ; because
after that I am using a tool that needs the reference genome information
(sam-to-bam tool).


Make sure the input data (fastq files I assume) have already the right 
dbkey. This way, the results (sam files) will inherit the dbkey.





I think I read that the dbkey must be the same as the one from the .loc
file.

If the dbkey is unique in builds.txt file, does it mean that I need to
create 1 line per tool per reference genome in the builds.txt file?


no, just one per genome, which is then used in the different '*loc' files



How does galaxy know where to find the information from the builds.txt
file as in the builds.txt file, no path are indicated?


The information from the "builds.txt" is more like meta data associated 
with the individual history items, And hence independent of the tools used


Hans-Rudolf




Thanks in advance for your answers.

Best regards,

Sabrina




On 13/05/2015 09:17, Hans-Rudolf Hotz wrote:

Hi Sabrina

yes, you can add any genome to "builds.txt" (as an example, we have
several plasmids added as genomes in our Galaxy server). Just make
sure the dbkey (e.g. hg19) you gonna add is unique.

If you also intend to use the built in visualization tools, make sure
to add the corresponding files to "/tool-data/shared/ucsc/chrom/"


And don't forget to restart the server, to put the changes into effect


Hans-Rudolf

On 05/12/2015 05:29 PM, Sabrina rodriguez wrote:

Dear all,

I am working on integrating some bioinformatics tools into galaxy for a
research team in France.
I have a question with regard to the "/tool-data/shared/ucsc/builds.txt"
file. I would like to add a new reference genome that is not coming from
UCSC.
Could you please tell me if this is feasible and, in that case, how to
process?

Thank you very much in advance.

Best regards,

Sabrina
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Re: [galaxy-dev] reference in builds.txt

[Hans-Rudolf Hotz]

Hi Sabrina

yes, you can add any genome to "builds.txt" (as an example, we have 
several plasmids added as genomes in our Galaxy server). Just make sure 
the dbkey (e.g. hg19) you gonna add is unique.


If you also intend to use the built in visualization tools, make sure to 
add the corresponding files to "/tool-data/shared/ucsc/chrom/"



And don't forget to restart the server, to put the changes into effect


Hans-Rudolf

On 05/12/2015 05:29 PM, Sabrina rodriguez wrote:

Dear all,

I am working on integrating some bioinformatics tools into galaxy for a
research team in France.
I have a question with regard to the "/tool-data/shared/ucsc/builds.txt"
file. I would like to add a new reference genome that is not coming from
UCSC.
Could you please tell me if this is feasible and, in that case, how to
process?

Thank you very much in advance.

Best regards,

Sabrina
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