- galaxy-dev - lists.galaxyproject.org

pop up on click
by Mohamed Kassam 08 Aug '16

08 Aug '16

Dear all, I have create a tool on javascript and html. I tried to use the xml tool from ucsc and flymine. I would like to know if it is possible to replace <inputs action="http://www.flymine.org" check_values="false" method="get"> <display>go to Flymine server $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" /> </inputs> By something like onclick it will display a pop up windows instead of opening the html adress on the same window. Best regards, Mohamed

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Re: [galaxy-dev] conversion issue
by Rathert, Philipp, Dr. 08 Aug '16

08 Aug '16

I tried to reinstall some tools, but I still get an error message: Fatal error: Exit code 1 () bedtools: /galaxy-central/tool_deps/ucsc_tools/312/iuc/package_ucsc_tools_312/2d6bafd63401/lib/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by bedtools) needLargeMem: trying to allocate 0 bytes (limit: 100000000000) Traceback (most recent call last): File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py", line 122, in <module> main(*args, **kwargs) File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py", line 57, in main convert_to_bigwig(temp_file, sizes, config, outfile) File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py", line 104, in convert_to_bigwig subprocess.check_call(cl) File "/galaxy-central/tool_deps/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/subprocess.py", line 540, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['bedGraphToBigWig', '/tmp/tmpkiKe2V', '/export/galaxy-central/database/files/003/dataset_3153-sizes.txt', '/export/galaxy-central/database/files/003/dataset_3153.dat']' returned non-zero exit status 255 It seems Bedrolls requires GLIBCXX_3.4.15 Since I am using Galaxy-docker I am not sure how to get this installed... Always grateful for help. Cheers, Philipp -----Original message----- From: Rathert, Philipp, Dr. <philipp.rathert(a)ibc.uni-stuttgart.de> Sent: Friday 5th August 2016 16:26 To: Peter Cock <p.j.a.cock(a)googlemail.com> Cc: Brad Chapman <chapmanb(a)50mail.com>; galaxy-dev(a)lists.galaxyproject.org Subject: Re: [galaxy-dev] conversion issue Hi Peter, it looks like samtools is not functional.... ==> /home/galaxy/logs/uwsgi.log <== galaxy.tools DEBUG 2016-08-05 14:25:25,686 Validated and populated state for tool request (52.679 ms) galaxy.tools.actions INFO 2016-08-05 14:25:25,754 Handled output named out for tool toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.2.0 (26.340 ms) galaxy.tools.actions INFO 2016-08-05 14:25:25,767 Added output datasets to history (13.170 ms) galaxy.tools.actions INFO 2016-08-05 14:25:25,793 Verified access to datasets for Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigw… (11.785 ms) galaxy.tools.actions INFO 2016-08-05 14:25:25,794 Setup for job Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigw… complete, ready to flush (26.847 ms) galaxy.tools.actions INFO 2016-08-05 14:25:25,841 Flushed transaction for job Job[id=2438,tool_id=toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig… (47.380 ms) galaxy.tools.execute DEBUG 2016-08-05 14:25:25,842 Tool [toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.2.0] created job [2438] (130.941 ms) galaxy.tools.execute DEBUG 2016-08-05 14:25:25,851 Executed 1 job(s) for tool toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.2.0 request: (164.591 ms) 172.17.0.1 - - [05/Aug/2016:14:25:25 +0000] "POST /api/tools HTTP/1.1" 200 - "http://129.69.102.30:8080/root <http://129.69.102.30:8080/root> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 381|app: 0|req: 53/85] 172.17.0.1 () {52 vars in 973 bytes} [Fri Aug 5 14:25:25 2016] POST /api/tools => generated 983 bytes in 256 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 0) 172.17.0.1 - - [05/Aug/2016:14:25:25 +0000] "GET /api/histories/b701da857886499b/contents?v=dev HTTP/1.1" 200 - "http://129.69.102.30:8080/root <http://129.69.102.30:8080/root> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 382|app: 0|req: 33/86] 172.17.0.1 () {46 vars in 921 bytes} [Fri Aug 5 14:25:25 2016] GET /api/histories/b701da857886499b/contents?v=dev => generated 125847 bytes in 127 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 2) ==> /home/galaxy/logs/handler0.log <== galaxy.jobs DEBUG 2016-08-05 14:25:26,391 (2438) Working directory for job is: /export/galaxy-central/database/job_working_directory/002/2438 galaxy.jobs.handler DEBUG 2016-08-05 14:25:26,401 (2438) Dispatching to slurm runner galaxy.jobs DEBUG 2016-08-05 14:25:26,436 (2438) Persisting job destination (destination id: slurm_cluster) galaxy.jobs.runners DEBUG 2016-08-05 14:25:26,450 Job [2438] queued (48.081 ms) galaxy.jobs.handler INFO 2016-08-05 14:25:26,457 (2438) Job dispatched galaxy.tools.deps DEBUG 2016-08-05 14:25:26,693 Building dependency shell command for dependency 'pysam' galaxy.tools.deps DEBUG 2016-08-05 14:25:26,693 Find dependency pysam version 0.8.3 galaxy.tools.deps DEBUG 2016-08-05 14:25:26,700 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x7fb0dd3b7f50> (isnull? False) galaxy.tools.deps DEBUG 2016-08-05 14:25:26,700 Building dependency shell command for dependency 'bedtools' galaxy.tools.deps DEBUG 2016-08-05 14:25:26,700 Find dependency bedtools version 2.24 galaxy.tools.deps DEBUG 2016-08-05 14:25:26,702 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x7fb0dc496ed0> (isnull? False) galaxy.tools.deps DEBUG 2016-08-05 14:25:26,702 Building dependency shell command for dependency 'ucsc_tools' galaxy.tools.deps DEBUG 2016-08-05 14:25:26,702 Find dependency ucsc_tools version 312 galaxy.tools.deps DEBUG 2016-08-05 14:25:26,705 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x7fb0dd3b7f50> (isnull? False) galaxy.jobs.command_factory INFO 2016-08-05 14:25:26,737 Built script [/export/galaxy-central/database/job_working_directory/002/2438/tool_script.sh] for tool command[PACKAGE_BASE=/galaxy-central/tool_deps/pysam/0.8.3/brad-chapman/bam_to_bigwig/9163e1db4c16; export PACKAGE_BASE; . /galaxy-central/tool_deps/pysam/0.8.3/brad-chapman/bam_to_bigwig/9163e1db4c16/env.sh; PACKAGE_BASE=/galaxy-central/tool_deps/bedtools/2.24/brad-chapman/bam_to_bigwig/9163e1db4c16; export PACKAGE_BASE; . /galaxy-central/tool_deps/bedtools/2.24/brad-chapman/bam_to_bigwig/9163e1db4c16/env.sh; PACKAGE_BASE=/galaxy-central/tool_deps/ucsc_tools/312/brad-chapman/bam_to_bigwig/9163e1db4c16; export PACKAGE_BASE; . /galaxy-central/tool_deps/ucsc_tools/312/brad-chapman/bam_to_bigwig/9163e1db4c16/env.sh; python /shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py /export/galaxy-central/database/files/003/dataset_3088.dat --outfile=/export/galaxy-central/database/files/003/dataset_3117.dat --split] galaxy.tools.deps DEBUG 2016-08-05 14:25:26,884 Building dependency shell command for dependency 'samtools' galaxy.tools.deps DEBUG 2016-08-05 14:25:26,884 Find dependency samtools version None galaxy.tools.deps DEBUG 2016-08-05 14:25:26,885 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7fb0ea2c3dd0> (isnull? True) galaxy.tools.deps DEBUG 2016-08-05 14:25:26,885 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7fb0ea2c3dd0> (isnull? True) galaxy.tools.deps DEBUG 2016-08-05 14:25:26,886 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7fb0ea2c3dd0> (isnull? True) galaxy.tools.deps DEBUG 2016-08-05 14:25:26,886 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7fb0ea2c3dd0> (isnull? True) galaxy.tools.deps DEBUG 2016-08-05 14:25:26,887 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7fb0ea2c3dd0> (isnull? True) galaxy.tools.deps WARNING 2016-08-05 14:25:26,887 Failed to resolve dependency on 'samtools', ignoring galaxy.jobs.runners DEBUG 2016-08-05 14:25:26,907 (2438) command is: mkdir -p working; cd working; /export/galaxy-central/database/job_working_directory/002/2438/tool_script.sh; return_code=$?; cd '/export/galaxy-central/database/job_working_directory/002/2438'; python "/export/galaxy-central/database/job_working_directory/002/2438/set_metadata_hmqtZc.py" "/export/galaxy-central/database/files/tmpBPe1aw" "/export/galaxy-central/database/job_working_directory/002/2438/working/galaxy.json" "/export/galaxy-central/database/job_working_directory/002/2438/metadata_in_HistoryDatasetAssociation_3277_AUIB9T,/export/galaxy-central/database/job_working_directory/002/2438/metadata_kwds_HistoryDatasetAssociation_3277_5_v2O7,/export/galaxy-central/database/job_working_directory/002/2438/metadata_out_HistoryDatasetAssociation_3277_96qP8H,/export/galaxy-central/database/job_working_directory/002/2438/metadata_results_HistoryDatasetAssociation_3277_mCFIaX,/export/galaxy-central/database/files/003/dataset_3117.dat,/export/galaxy-central/database/job_working_directory/002/2438/metadata_override_HistoryDatasetAssociation_3277_Fi9GIQ" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.drmaa DEBUG 2016-08-05 14:25:26,936 (2438) submitting file /export/galaxy-central/database/job_working_directory/002/2438/galaxy_2438.sh galaxy.jobs.runners.drmaa DEBUG 2016-08-05 14:25:26,937 (2438) native specification is: --ntasks=1 --share galaxy.jobs.runners.drmaa INFO 2016-08-05 14:25:26,938 (2438) queued as 7 galaxy.jobs DEBUG 2016-08-05 14:25:26,938 (2438) Persisting job destination (destination id: slurm_cluster) ==> /home/galaxy/logs/slurmctld.log <== [2016-08-05T14:25:26.938] _slurm_rpc_submit_batch_job JobId=7 usec=251 [2016-08-05T14:25:26.941] sched: Allocate JobId=7 NodeList=5e2648045373 #CPUs=1 ==> /home/galaxy/logs/slurmd.log <== [2016-08-05T14:25:26.955] Launching batch job 7 for UID 1450 ==> /home/galaxy/logs/handler0.log <== galaxy.jobs.runners.drmaa DEBUG 2016-08-05 14:25:27,244 (2438/7) state change: job is running ==> /var/log/nginx/access.log <== 172.17.0.1 - admin [05/Aug/2016:14:25:30 +0000] "GET /api/histories/b701da857886499b/contents?v=dev&q=update_time-ge&qv=2016-08-05T14%3A25%3A26.000Z HTTP/1.1" 200 33 "http://129.69.102.30:8080/root <http://129.69.102.30:8080/root> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" ==> /home/galaxy/logs/slurmctld.log <== [2016-08-05T14:25:30.946] completing job 7 [2016-08-05T14:25:30.947] sched: job_complete for JobId=7 successful, exit code=0 ==> /home/galaxy/logs/slurmd.log <== [2016-08-05T14:25:30.945] [7] sending REQUEST_COMPLETE_BATCH_SCRIPT, error:0 [2016-08-05T14:25:30.947] [7] done with job I will check if anything is wrong on that side... -----Original message----- From: Peter Cock <p.j.a.cock(a)googlemail.com> Sent: Friday 5th August 2016 16:15 To: Rathert, Philipp, Dr. <philipp.rathert(a)ibc.uni-stuttgart.de> Cc: galaxy-dev(a)lists.galaxyproject.org; Brad Chapman <chapmanb(a)50mail.com> Subject: Re: [galaxy-dev] conversion issue I think you will need to look at the Galaxy logs for some clues about if the dependencies are being found or not. The simple "hack" is to install them on the $PATH manually, which would be the practical solution if this is urgent. Peter On Fri, Aug 5, 2016 at 3:09 PM, Rathert, Philipp, Dr. <philipp.rathert(a)ibc.uni-stuttgart.de> wrote: > Yes I did. > All tools are installed and I see no error message. > > Philipp ___________________________________________________________ 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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uploading multi-file archives and creation of potentially large collections
by Stephan Oepen 08 Aug '16

08 Aug '16

colleagues, in our adaptation of galaxy for large-scale natural language processing, a fairly common use pattern is to invoke a workflow on a potentially large number of text files. hence, i am wondering about facilities for uploading an archive (in ‘.zip’ or ‘.tgz’ format, say) containing several files, where i would like the upload tool to extract the files from the archive, import each individually into my history, and (maybe optionally) create a list collection for the set of files. in my current galaxy instance (running version 2015.03), when i upload a multi-file ‘.zip’ file, part of the above actually happens: however, the upload tool only imports the first file extracted from the archive (and helpfully shows a warning message on the corresponding history entry). have there been relevant changes in this neighborhood in more recent galaxy releases? related to the above, we have started to experiment with potentially large collections and are beginning to worry about the scalability of the collection mechanism. in principle, we would like to operate on collections comprised of tens or hundreds of thousands of individual datasets. what are common collection sizes (in the number of components, not so much in the aggregate file size) used in other galaxy instances to date? what kind of gut reaction do galaxy developers have to the idea of a collection containing, say, a hundred thousand entries? with thanks in advance,

4 3

provide a field to upload a file as part of tool input
by Ryan G 06 Aug '16

06 Aug '16

Hi all - I have a custom tool that can optionally take a file as input. Right now, users have to upload the file into their history, then select the file when running the tool. Is there a way to let the user select a file local on their computer as input to the tool, then when run, the file is uploaded? And (second question), how can I make this field optional, such that the user does not need to provide a file at all when running the tool? Right now, my input field is: <param name="factorSheet" type="data" label="Factor Sheet" help="Select a factor sheet (if any)." />

2 2

Parameter Storing in Database
by Katherine Beaulieu 05 Aug '16

05 Aug '16

Would anyone be able to tell me in what file the storing of tool parameters into the database occurs? Thanks! Katherine

2 1

Re: [galaxy-dev] Command line building
by Katherine Beaulieu 05 Aug '16

05 Aug '16

On Fri, Aug 5, 2016 at 11:20 AM, Katherine Beaulieu < katherine.beaulieu014(a)gmail.com> wrote: > Thats perfect thanks so much!:) > > On Fri, Aug 5, 2016 at 11:18 AM, Dannon Baker <dannon.baker(a)gmail.com> > wrote: > >> Got it, misunderstood your interest. You want this, see the >> fill_template usage in this method: >> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tools/evaluatio… >> >> On Fri, Aug 5, 2016 at 11:10 AM Katherine Beaulieu < >> katherine.beaulieu014(a)gmail.com> wrote: >> >>> Hi Dannon, >>> This is sort of what I'm looking for. I'm looking for the place where >>> cheetah variables get replaced with input parameter values. I think this >>> may be in another file? >>> >>> On Fri, Aug 5, 2016 at 10:57 AM, Dannon Baker <dannon.baker(a)gmail.com> >>> wrote: >>> >>>> Check out >>>> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/command_fa… >>>> >>>> Let me know if this wasn't what you were looking for. >>>> >>>> -Dannon >>>> >>>> On Fri, Aug 5, 2016 at 10:49 AM Katherine Beaulieu < >>>> katherine.beaulieu014(a)gmail.com> wrote: >>>> >>>>> Within the galaxy app itself, does anyone know where the command line >>>>> is being built? >>>>> Thanks! >>>>> Katherine >>>>> ___________________________________________________________ >>>>> 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/ >>>> >>>> >>> >

1 0

Command line building
by Katherine Beaulieu 05 Aug '16

05 Aug '16

Within the galaxy app itself, does anyone know where the command line is being built? Thanks! Katherine

2 1

conversion issue
by Rathert, Philipp, Dr. 05 Aug '16

05 Aug '16

Dear All, I get the following errors when I try to Convert BAM to BigWig Traceback (most recent call last): File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py", line 103, in <module> main(*args, **kwargs) File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py", line 48, in main convert_to_graph(bam_file, split, config, temp_handle) File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py", line 76, in convert_to_graph subprocess.check_call(cl, stdout=out_handle) File "/usr/lib/python2.7/subprocess.py", line 535, in check_call retcode = call(*popenargs, **kwargs) File "/usr/lib/python2.7/subprocess.py", line 522, in call return Popen(*popenargs, **kwargs).wait() File "/usr/lib/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory The tool produced the following additional output: Have 93 references Calculating coverage... or Fatal error: Exit code 1 () bedtools: /galaxy-central/tool_deps/ucsc_tools/312/iuc/package_ucsc_tools_312/2d6bafd63401/lib/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by bedtools) needLargeMem: trying to allocate 0 bytes (limit: 100000000000) Traceback (most recent call last): File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py", line 122, in <module> main(*args, **kwargs) File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py", line 57, in main convert_to_bigwig(temp_file, sizes, config, outfile) File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py", line 104, in convert_to_bigwig subprocess.check_call(cl) File "/galaxy-central/tool_deps/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/subprocess.py", line 540, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['bedGraphToBigWig', '/tmp/tmp2F67r6', '/export/galaxy-central/database/files/003/dataset_3116-sizes.txt', '/export/galaxy-central/database/files/003/dataset_3116.dat']' returned non-zero exit status 255 The tool produced the following additional output: Have 93 references Calculating coverage... Converting 0 MB graph file to bigwig.. depending what version of the tool i am using. Any idea what this can be? I am using the latest Docker-galaxy-stable version (16.04) but I think this is not related to docker. All tools are updated. Thank you very much for your help, Philipp

2 4

Retrieving bam index file for visualization outside of Galaxy
by Ouellette, Scott 05 Aug '16

05 Aug '16

Hi all, I have a use case where I need to programmatically download both the .bam and it's index file to run IGV outside of Galaxy, but have not found a straightforward way to do so. It seems that Galaxy always generates this .bai file under the hood, and I can download it manually by clicking the "save" icon on the dataset in my history. Although, the application I am coding for relies on the bioblend Python library. --- In bioblend I see a field returned upon a `DatasetClient(<galaxy_instance>).show_dataset(<dataset_id>)` but that is as far as I've got: "meta_files": [ { "file_type": "bam_index" } ], Any help is appreciated! Thanks, Scott O.

2 1

Removing job in error state
by Ryan G 04 Aug '16

04 Aug '16

Hi - In the Manage Jobs admin job, I have a job from a user that never ran successfully. It shows: Job ID User Last Update Tool State Inputs Command Line Job Runner PID/Cluster ID 12772 user(a)company.com 654 hours ago cshl_fastx_collapser new 13653 error None None None How do I remove this job? I can't find a way to delete it.

2 2