galaxy-dev May 2015

galaxy-dev@lists.galaxyproject.org

44 participants
62 discussions

GCC2015: Early Reg closes 22 May; Call for Birds-of-a-feather; and more
by Dave Clements 14 May '15

14 May '15

Hello all, A couple of GCC2015 related items: *Early Registration closes 22 May* Just a reminder that early registration <http://gcc2015.tsl.ac.uk/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 <http://gcc2015.tsl.ac.uk/registration/> 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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Tool failure due to PYTHONPATH in job environment after upgrade to 15.03
by Brian Claywell 13 May '15

13 May '15

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 <module> from pkg_resources import load_entry_point File "/mnt/scdata/scdata_03/galaxy/containers/galaxy-qa/stable/lib/pkg_resources.py", line 2603, in <module> 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 <http://matsen.fhcrc.org/> Fred Hutchinson Cancer Research Center

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file_path passed directly to wrappers
by Sabrina rodriguez 13 May '15

13 May '15

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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13 May '15

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/bf0806da5b28c6d… ", "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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Re: [galaxy-dev] reference in builds.txt
by Hans-Rudolf Hotz 13 May '15

13 May '15

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_genome ensembl_sus_scrofa_genome ensembl sus > scrofa genome /bank/bowtie2db/ensembl_sus_scrofa_genome > > In STAR.loc, I have: > STAR-ensembl_sus_scrofa_genome STAR-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_genome STAR-ensembl_sus_scrofa_genome > (ensembl_sus_scrofa) > I would just add an extra line, similar to the existing one for 'susScr2', eg: susScrLX local 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 >>> ___________________________________________________________ >>> 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/mailinglists/ >

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reference in builds.txt
by Sabrina rodriguez 13 May '15

13 May '15

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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trinity tool form not allowing "None" input for strand-specificity
by Christian Schudoma (TSL) 11 May '15

11 May '15

Hi all, I have encountered a problem when trying to run trinityrnaseq (Galaxy Tool Version 0.0.1) from Galaxy. Leaving the strand-specificity input parameter as "None" will prevent the form from being submitted. Instead, the strand-specificity input box will be highlighted in red and I'm asked to "Please verify this parameter." Before the last update we were running a very very old instance of Galaxy (I think the update before the last was in 2013) from which we could submit trinity-jobs just fine. I found a commit from Aysam from late 2014 which does something in the immediate vicinity of the "Please verify this parameter" - message. (https://bitbucket.org/galaxy/galaxy-central/commits/bda732e549b7/), which I am guessing could have something to do with it. Anyone got any ideas regarding this? Any help would be appreciated. Thanks Christian -- Dr. Christian Schudoma Bioinformatics Support Officer Bioinformatics Group The Sainsbury Laboratory Norwich Research Park Norwich NR4 7UH United Kingdom ****************************** +44 (0) 1603 450 601 christian.schudoma(a)tsl.ac.uk<mailto:christian.schudoma@tsl.ac.uk> twitter: @cpt_bwt

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'Boolean' parameter type misbehaves in tool tests if truevalue starts with hyphen?
by Peter Briggs 08 May '15

08 May '15

Hello I'm currently writing tests for a tool and think I've found a situation where the behaviour of the boolean parameter type does not seem correct within the test environment. The tool defines the following boolean parameter: <param name="spmr" type="boolean" truevalue="--SPMR" falsevalue="" checked="False" ... /> and accesses its value in the <command> tag using: -B $spmr i.e. if the boolean is true then this should output "-B --SPMR", if not then it should output "-B ". This appears to work as expected when the tool is installed and used interactively. But when running the tests the 'falsevalue' is always returned, even if the value is set to the 'truevalue' in the tests i.e.: <param name="spmr" value="--SPMR" /> and <param name="spmr" value="" /> both return "-B ". More generally: I've written a small tool to investigate the issue, and it appears that the errant behaviour only manifests when the 'truevalue' starts with a hyphen (e.g. using "-Yes" is broken, but "Yes" is okay). The demo tool is available via https://gist.github.com/pjbriggs/5bfbcf22f72e0266e61 and I've been using planemo v0.7.0 to run the tests ("planemo t --install_galaxy boolean_test_issue.xml"). Have I done something wrong here or is this a genuine bug? Thanks for your help, best wishes Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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Questions about deploying galaxy on Azure
by Marc 08 May '15

08 May '15

Dear developer, I’m trying to deploy the local galaxy on a VM on Azure cloud. But I have encountered a problem. When I set up the galaxy local on the cloud VM, I couldn’t find the right url to access the web interface. Can you help in any way? Regards, Marc

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sender address of galaxy tool report
by Rémy Dernat 07 May '15

07 May '15

Hi, We run a galaxy server locally. When a user want to send an error through galaxy GUI "Report this error to the Galaxy Team" . We do not have any anonymous/guest users (not allowed). So we are sure that the content of the email textbox is always effective. The problem is that we use a remote helpdesk program that is using email piping to retrieve the email and convert it to a ticket. When we want to process galaxy ticket "GALAXY TOOL ERROR REPORT" the sender address is always the address "error_email_to" from the configuration file galaxy.ini / universe.ini So we can not replay into our helpdesk program, because the answer would be send to the address "error_email_to" and not to the user. Is there a way to get the real email address from the user who reported the error instead of this address ? Or, if it is not possible, could it be plan in the future galaxy release ? Or, eventually, if this is easy to do, what python file should I modify ? Best regards, Remy

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