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HOWTO share tool parameter settings?
by Lukasse, Pieter 18 Dec '14

18 Dec '14

Hi, Do we have a way (or plans) for sharing tool parameter settings in Galaxy? I know the following workarounds : * Share a history with all users: so users can import your step and do "rerun" to run on their own file with your settings * Wrap the step in a workflow with all parameters set and publish this workflow: users can run this "workflow" * Have a dummy tool to produce a settings file and allow the users to choose this file when running the real tool * Use a conditional and many macros that are basically a copy of each other, only differing in the parameter values But what I would like to have is a way to define bindings between a settings file and the parameters in the tool form. Any plans, ideas? Thanks, Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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Stop autoselecting in drop-down menus
by Aleksey Jironkin 18 Dec '14

18 Dec '14

Hi, I was wondering if there is a way to prevent auto-selecting an option for Running a workflow? Quiet often users (especially novices) would re-run workflows without checking much the data that goes in thinking it will be the same as before. But because the options in drop down menus are auto-populated it seems the top option is always selected by default. For example, previously we had a single fasta file as reference and in the process of a workflow few other fasta files get generated. they appear above the previous fasta in the selection, so without paying attention people skip the input without really checking it. Can we manually add a "blank" selection at the top to force users to select something? Alex -- Dr Aleksey Jironkin Bioinformatician Bioinformatics Unit Infectious Disease Informatics Microbiologicy Services, Colindale Public Health England 61 Colindale Avenue London NW9 5EQ Aleksey.Jironkin(a)phe.gov.uk Tel: 020 83 276610 www.gov.uk/phe Follow us on Twitter @PHE_uk Protecting and improving the nation’s health

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Error when opening bowtie2 tool page
by Anna Terry 18 Dec '14

18 Dec '14

Hi, I am getting an error page when I try to open the bowtie2 tool page (after selecting older version 0.2 a54de7e658f7 from drop down on version 0.3 c1ec08cb34f9 page). URL: http://....../tool_runner/index File '/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 107 in __call__ return self.app( environ, start_response ) File '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py', line 90 in index template, vars = tool.handle_input( trans, params.__dict__ ) File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in handle_input errors, params = self.__check_param_values( trans, expanded_incoming, expanded_state, old_errors, process_state, history=history, source=source ) File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in __check_param_values errors = self.update_state( trans, inputs, state.inputs, incoming, old_errors=old_errors or {}, source=source ) File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in update_state group_state = state[input.name] KeyError: 'params' I can't see anything that gives me a clue where to investigate further, hopefully someone here knows? I have tried updating to latest changeset, and have restarted a few times, but still the same error. Thanks in advance for help Anna

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[Spam:*****] Re: How galaxy workflow work ?
by Bruijn, Freek de 18 Dec '14

18 Dec '14

I am also having problems using the Galaxy API, with a similar error message to the one reported by Bongsoo Park a few weeks ago (Uncaught exception in exposed API method). We noticed it a few days ago and have not found the cause yet. What we do know: - the problem occurs on several Galaxy servers, including the main instance at https://usegalaxy.org/; - the problem seems to occur whilte using BioBlend, blend4j, and api Python scripts; - even some of the blend4j unit tests are failing. One of my colleagues noticed a lot of changes in for example workflows.py (in lib/galaxy/webapps/galaxy/api): https://bitbucket.org/galaxy/galaxy-dist/annotate/579d211c2b0fa8ef4195930cb… Did something change in the Galaxy API? Should we adjust the libraries and the programs that use them? Cheers, Freek ________________________________________ From: galaxy-dev [galaxy-dev-bounces(a)lists.galaxyproject.org] on behalf of galaxy-dev-request(a)lists.galaxyproject.org [galaxy-dev-request(a)lists.galaxyproject.org] Sent: Tuesday, December 16, 2014 18:00 To: galaxy-dev(a)lists.galaxyproject.org Subject: galaxy-dev Digest, Vol 102, Issue 17 Send galaxy-dev mailing list submissions to galaxy-dev(a)lists.galaxyproject.org To subscribe or unsubscribe via the World Wide Web, visit https://lists.galaxyproject.org/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-request(a)lists.galaxyproject.org You can reach the person managing the list at galaxy-dev-owner(a)lists.galaxyproject.org When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..." HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. Re: How galaxy workflow work ? (John Chilton) 2. Re: Metadata error in uploading files to data libraries (John Chilton) 3. Re: package_numpy_1_7 can't be installed (Wang, Yu) 4. Re: "join" produces an import error (Wang, Yu) 5. Re: package_numpy_1_7 can't be installed (Björn Grüning) ---------------------------------------------------------------------- Message: 1 Date: Mon, 15 Dec 2014 14:24:13 -0500 From: John Chilton <jmchilton(a)gmail.com> To: Bongsoo Park <bxp12(a)psu.edu> Cc: galaxy-dev <galaxy-dev(a)lists.bx.psu.edu> Subject: Re: [galaxy-dev] How galaxy workflow work ? Message-ID: <CANwbokcggD3W7Tkyd5fy-9d6qedLT+ta1gzzmkfE1Apa2R8w1A(a)mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Somehow your user object is not being set. Are you sure you have initialized bioblend with the correct API key? Do other operations work with that key? -John On Wed, Dec 3, 2014 at 11:00 AM, Bongsoo Park <bxp12(a)psu.edu> wrote: > Hi All, > > I faced a problem after I tested the Bio-Blend API. I cannot access the > history anymore with the below error messages. Although, I tried > installation from the scratch, but I got the same error message. Please let > me know how to fix this problem. Thanks! > > (GALAXY User Interface) > > ======================================================= > > "xhr": { > > "readyState": 4, > > "responseText": "{\"err_msg\": \"Uncaught exception in exposed API > method:\", \"err_code\": 0}", > > "responseJSON": { > > "err_msg": "Uncaught exception in exposed API method:", > > "err_code": 0 > > }, > > "status": 500, > > "statusText": "Internal Server Error", > > "responseHeaders": { > > "Date": "Wed, 03 Dec 2014 15:50:02 GMT\r", > > "cache-control": "max-age=0,no-cache,no-store\r", > > "Server": "PasteWSGIServer/0.5 Python/2.7.8\r", > > "Connection": "close\r", > > "content-type": "application/json\r" > > } > > ======================================================= > > I found the error message in the Galaxy instance shell interface. > > ======================================================= > > galaxy.web.framework.decorators ERROR 2014-12-03 10:50:02,279 Uncaught > exception in exposed API method: > > Traceback (most recent call last): > > File "/home/bxp12/galaxy-dist/lib/galaxy/web/framework/decorators.py", > line 244, in decorator > > rval = func( self, trans, *args, **kwargs) > > File > "/home/bxp12/galaxy-ist/lib/galaxy/webapps/galaxy/api/history_contents.py", > line 76, in index > > and ( history_id == trans.security.encode_id( trans.history.id ) ) ): > > AttributeError: 'NoneType' object has no attribute 'id' > > ======================================================= > > Best, > > Bongsoo > > > ___________________________________________________________ > 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/ ------------------------------ Message: 2 Date: Mon, 15 Dec 2014 14:31:20 -0500 From: John Chilton <jmchilton(a)gmail.com> To: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Cc: galaxy-dev <galaxy-dev(a)lists.bx.psu.edu> Subject: Re: [galaxy-dev] Metadata error in uploading files to data libraries Message-ID: <CANwbokdzjumt4abseN3b6rxOkaXH+9fB23+_OhqmUtFqnxbxWw(a)mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Hello, Sorry we haven't made progress on this - and thanks for creating a Trello card (https://trello.com/c/tw75nq1U) It looks like samtools is not on your path, can you use it from the command-line? If not you should probably install it - I would suggest install samtools 0.1.19 with homebrew (looks like you are a on Mac). If you can run samtools from the command-line - can you do a which `samtools` from your command-line and see where it is coming from and then add that directory explicitly to your Galaxy PATH - say at the top of run.sh in your Galaxy root (let me know if you need more details on that). -John On Tue, Dec 9, 2014 at 3:02 AM, Jelle Scholtalbers <j.scholtalbers(a)gmail.com> wrote: > Hi all, > > after an update to the following changeset(14859:7ba05957588a, stable, > 05.12.14), our bam files that are uploaded(linked) to a data library, are no > longer indexed. The metadata_xxx.dat is created, but it stays empty. > The following error message appears in the log, although the state of the > dataset is 'ok': > > galaxy.jobs WARNING 2014-12-05 12:47:02,218 Error accessing /g/K/K27.bam, > will retry: [Errno 1] Operation not permitted: '/g/K/K27.bam' > galaxy.jobs WARNING 2014-12-08 13:38:57,045 Error accessing /g/K/K2.bam, > will retry: [Errno 1] Operation not permitted: '/g/K/K2.bam' > > All file permissions are correct (i.e. galaxy owns them). Furthermore, > executing samtools index, just works on those files: > samtools index /g/K/K2.bam > /g/galaxy/galaxy_data/files/_metadata_files/006/metadata_6598.dat > > When uploading the file - "copy files into galaxy" - the samtools index just > works. > > ============== > > Now, on a clean local install(14874:885f940bff64, stable, 05.12.14) and > samtools installed globally and with the bam file sorted, I get the > following situation: > When I try to upload this bam to a data library by linking the following > error is shown on the dataset (note: here the dataset is set in error state, > which does not happen on our server) > > Uploaded by: scholtal(a)embl.de > Date uploaded: Mon Dec 8 17:42:39 2014 (UTC) > File size: 2.6 GB > UUID: d23cf11a-0372-41cb-939a-7c8761d78b73 > Data type: auto > Build: ? > Miscellaneous information: Traceback (most recent call last): File > "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", > line 407, in __main__() File > "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", > line 396, in _ > Job Standard Error > > Traceback (most recent call last): > File > "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", > line 407, in > __main__() > File > "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", > line 396, in __main__ > add_file( dataset, registry, json_file, output_path ) > File > "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", > line 294, in add_file > if datatype.dataset_content_needs_grooming( dataset.path ): > File > "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py", > line 147, in dataset_content_needs_grooming > version = self._get_samtools_version() > File > "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py", > line 129, in _get_samtools_version > output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, > stdout=subprocess.PIPE ).communicate()[1] > File > "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", > line 711, in __init__ > errread, errwrite) > File > "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", > line 1308, in _execute_child > raise child_exception > OSError: [Errno 2] No such file or directory > > error > Database/Build: ? > Number of data lines: None > Disk file: /Users/scholtalbers/workspace/idr_data/WT1.sort.bam > > =============================== > When uploading the bam without linking, I see the following processes: > Upload->set meta->samtools index->'error state' > > Miscellaneous information: uploaded bam file Traceback (most recent call > last): File > "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", > line 407, in __main__() File > "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.p > Job Standard Error > > Traceback (most recent call last): > File > "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", > line 407, in > __main__() > File > "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", > line 396, in __main__ > add_file( dataset, registry, json_file, output_path ) > File > "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", > line 324, in add_file > if link_data_only == 'copy_files' and > datatype.dataset_content_needs_grooming( output_path ): > File > "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py", > line 147, in dataset_content_needs_grooming > version = self._get_samtools_version() > File > "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py", > line 129, in _get_samtools_version > output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, > stdout=subprocess.PIPE ).communicate()[1] > File > "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", > line 711, in __init__ > errread, errwrite) > File > "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", > line 1308, in _execute_child > raise child_exception > OSError: [Errno 2] No such file or directory > > error > Database/Build: ? > Number of data lines: None > Disk file: > /Users/scholtalbers/workspace/galaxy-dist-new/database/files/000/dataset_6.dat > > ================================= > > Although the error messages are different, it might be related? > > Cheers, > > Jelle > > ___________________________________________________________ > 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/ ------------------------------ Message: 3 Date: Mon, 15 Dec 2014 17:16:41 +0000 From: "Wang, Yu" <Yu.Wang(a)lrz.de> To: John Chilton <jmchilton(a)gmail.com> Cc: "Wang, Yu" <Yu.Wang(a)lrz.de>, "galaxy-dev(a)lists.galaxyproject.org" <galaxy-dev(a)lists.galaxyproject.org> Subject: Re: [galaxy-dev] package_numpy_1_7 can't be installed Message-ID: <f4c6170a-5f28-4871-971b-2881fc739510(a)BADWLRZ-SW13MB1.ads.mwn.de> Content-Type: text/plain; charset="utf-8" Hi, John,thanks for your answer. I installed svnversion, and compiled/installed ATLAS/Blas/ LAPACK. I still got error messages like ATLAS/Blas/ LAPACK are not found. I could install package_numpy_1_9 by using galaxy main tool shed. There is something wrong with package_numpy_1_7 on my environment. Cheers, Yu di29her wang(a)lrz.de<mailto:wang@lrz.de> On 15 Dec 2014, at 16:12, John Chilton <jmchilton(a)gmail.com<mailto:jmchilton@gmail.com>> wrote: Looks like this - https://github.com/clarete/curdling/issues/19 I think you somehow need to install the package svn on your machine - if you have root on that machine the command might be something like "sudo zypper install svn" or may it is "sudo zypper install subversion". If you don't have root on the machine I would ask the operating system maintainer or try to compile and install svn locally and make it available to Galaxy. Hope this helps, -John On Fri, Dec 12, 2014 at 7:14 AM, Wang, Yu <Yu.Wang(a)lrz.de<mailto:Yu.Wang@lrz.de>> wrote: Hi, I am running galaxy on SLSE11, when I tried to install bumpy 1.7.1, I got the following error. Can anyone point what goes wrong here? Error Running from numpy source directory. /bin/sh: svnversion: command not found /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1494: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1503: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. warnings.warn(BlasNotFoundError.__doc__) /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1506: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. warnings.warn(BlasSrcNotFoundError.__doc__) /bin/sh: svnversion: command not found /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1408: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1419: UserWarning: Lapack (http://www.netlib.org/lapack/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [lapack]) or by setting the LAPACK environment variable. warnings.warn(LapackNotFoundError.__doc__) /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1422: UserWarning: Lapack (http://www.netlib.org/lapack/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [lapack_src]) or by setting the LAPACK_SRC environment variable. warnings.warn(LapackSrcNotFoundError.__doc__) error: must supply either home or prefix/exec-prefix -- not both Cheers, Yu di29her wang(a)lrz.de<mailto:wang@lrz.de> ___________________________________________________________ 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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visualization in anonymous mode ?
by Loraine Guéguen 18 Dec '14

18 Dec '14

Hi, I'd like to use the visualization in anonymous mode, but the visualize icon on the dataset is not available in anonymous mode (although it works fine when connected). Is it possible to activate the dataset visualization in anonymous mode ? Thanks, Loraine -- Loraine Guéguen Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences) Service Informatique et Bioinformatique Station Biologique de Roscoff FR 2424 CNRS UPMC Place Georges Teissier CS 90074 29688 Roscoff cedex tel: ++33 (0)2 98 29 56 46 (interne : 415) http://abims.sb-roscoff.fr/ http://www.sb-roscoff.fr/

1 0

"join" produces an import error
by Wang, Yu 17 Dec '14

17 Dec '14

Hi, I am testing Basic Protocol 1 on my local galaxy instance. But Join didn't work. What did I do wrong? I installed join from galaxy main tool shed, bx_python_0_7 was installed but with installation Status "missing tool dependencies". Thanks. ----------------------------------------------------------------------------- job id: 49 tool id: toolshed.g2.bx.psu.edu/repos/devteam/join/gops_join_1/1.0.0<http://toolshed.g2.bx.psu.edu/repos/devteam/join/gops_join_1/1.0.0> tool version: 1.0.0 job pid or drm id: 46018 job tool version: ----------------------------------------------------------------------------- job command line: python /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/join/de21bdbb8d28/join/gops_join.py<http://toolshed.g2.bx.psu.edu/repos/devteam/join/de21bdbb8d28/join/gops_joi…>/local/galaxy/database/files/000/dataset_45.dat /local/galaxy/database/files/000/dataset_46.dat /local/galaxy/database/files/000/dataset_50.dat -1 1,2,3,6 -2 1,2,3,6 -m 1 -f none ----------------------------------------------------------------------------- job stderr: Traceback (most recent call last): File "/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/join/de21bdbb8d28/join/gops_join.py<http://toolshed.g2.bx.psu.edu/repos/devteam/join/de21bdbb8d28/join/gops_joi…>", line 13, in <module> from bx.intervals import * ImportError: No module named bx.intervals Cheers, Yu di29her wang(a)lrz.de<mailto:wang@lrz.de>

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Re: [galaxy-dev] disk space does not add up...
by Dooley, Damion 17 Dec '14

17 Dec '14

Just a small question about this - you have purge_datasets.sh, and then delete_datasets.sh . Shouldn't it be the other way around, since purging only works on the deleted datasets? (I realise this doesn't address your main issue, since running it twice should have maximized free space.) Damion On 12/17/2014 01:05 PM, Langhorst, Brad wrote: > My glaaxy user data area is using 40T > > But the repots server only show usage of about 16T… > > Im nearly out of space and I’m not sure how to resolve the disparity. > I have run the clearnup_datasets.py and other > > > > I’m running mainenance scripts like this: > > #!/bin/sh > > echo 'running galaxy maintenace scripts' > #runs galaxy maintenance scripts > GALAXY_PATH=/mnt/galaxy/data/galaxy/galaxy-dist > SCRIPT_PATH=${GALAXY_PATH}/scripts/cleanup_datasets > sh ${SCRIPT_PATH}/delete_userless_histories.sh > sh ${SCRIPT_PATH}/purge_histories.sh > sh ${SCRIPT_PATH}/purge_libraries.sh > sh ${SCRIPT_PATH}/purge_folders.sh > sh ${SCRIPT_PATH}/purge_datasets.sh > sh ${SCRIPT_PATH}/delete_datasets.sh > > > -- > Brad Langhorst, Ph.D. > Applications and Product Development Scientist >

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Functional tests using gzipped inputs have broken
by Peter Cock 17 Dec '14

17 Dec '14

Hi all, Using gzipped input files in tool functional tests (which would be decompressed by the upload tool) used to work, e.g. https://travis-ci.org/peterjc/pico_galaxy/builds/42395911 https://github.com/peterjc/pico_galaxy/blob/539260fa4348ed454ce464e48c9dbbc… But with more recent versions of Galaxy this has broken, e.g. https://travis-ci.org/peterjc/pico_galaxy/builds/44038046 https://github.com/peterjc/pico_galaxy/blob/e3064cc8f42253efd1f8eed56844d4c… According to the TravisCI failure, the command run was: python /home/travis/build/peterjc/pico_galaxy/galaxy-central-master/tools/seq_filter_by_mapping/seq_filter_by_mapping.py -i "None" -f "data" -m lax -p /tmp/tmpaCsMm5/tmpEpBIX1/database/files/000/dataset_50.dat /tmp/tmpaCsMm5/tmpEpBIX1/database/files/000/dataset_49.dat In this case the -i argument was $input_file, and -f was its extension/datatype. Somehow the gzipped FASTQ was not found, which is why the filename is just "None" and its datatype the default "data". My tool is sensibly returning error code 1, and: Missing input file: 'None' I have made some minor changes to this tool between those TravisCI tests, but the test is the same: <tests> <test> <param name="input_file" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" /> <param name="mapping_file" value="SRR639755_sample_by_coord.sam" ftype="sam" /> <param name="pair_mode" value="lax" /> <param name="output_choice" value="pos" /> <output name="output_pos" file="SRR639755_sample_lax.fastq" ftype="fastqsanger" /> </test> <test> <param name="input_file" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" /> <param name="mapping_file" value="SRR639755_sample_by_coord.sam" ftype="sam" /> <param name="pair_mode" value="strict" /> <param name="output_choice" value="pos" /> <output name="output_pos" file="SRR639755_sample_strict.fastq" ftype="fastqsanger" /> </test> </tests> -- I could reproduce this on my development machine running an older Galaxy: $ hg log | head changeset: 16732:212e1d5e9be5 branch: stable tag: tip parent: 16716:2db0fb9594d6 parent: 16731:7adac1842adf user: John Chilton <jmchilton(a)gmail.com> date: Wed Dec 10 12:20:55 2014 -0500 summary: Merged in dannon/galaxy-central/stable (pull request #602) And again updating to the current tip, $ hg log | head changeset: 16850:e614c7c1e0e9 tag: tip parent: 16848:1cf0af0a6324 parent: 16849:d13f2b265dbf user: Dannon Baker <dannon.baker(a)gmail.com> date: Tue Dec 16 15:48:44 2014 -0500 summary: Merged in nitesh1989/galaxy-central3 (pull request #615) I can "fix" it by swapping the gzipped test input_file SRR639755_mito_pairs.fastq.gz to the uncompressed SRR639755_mito_pairs.fastq instead, as in this commit: https://github.com/peterjc/pico_galaxy/commit/126e3e716965016808ec2ba3a4be3… https://travis-ci.org/peterjc/pico_galaxy/builds/44317785 I would like to revert this workaround since the uncompressed FASTQ file is a bit large to bundle as a test case - so I hope this is simply due to an accidental regression in Galaxy itself. Thanks, Peter

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disk space does not add up...
by Langhorst, Brad 17 Dec '14

17 Dec '14

My glaaxy user data area is using 40T But the repots server only show usage of about 16T… Im nearly out of space and I’m not sure how to resolve the disparity. I have run the clearnup_datasets.py and other I’m running mainenance scripts like this: #!/bin/sh echo 'running galaxy maintenace scripts' #runs galaxy maintenance scripts GALAXY_PATH=/mnt/galaxy/data/galaxy/galaxy-dist SCRIPT_PATH=${GALAXY_PATH}/scripts/cleanup_datasets sh ${SCRIPT_PATH}/delete_userless_histories.sh sh ${SCRIPT_PATH}/purge_histories.sh sh ${SCRIPT_PATH}/purge_libraries.sh sh ${SCRIPT_PATH}/purge_folders.sh sh ${SCRIPT_PATH}/purge_datasets.sh sh ${SCRIPT_PATH}/delete_datasets.sh -- Brad Langhorst, Ph.D. Applications and Product Development Scientist

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param name="type"
by Jorrit Boekel 17 Dec '14

17 Dec '14

Hi all, Just a heads-up, I had a tool.xml file in which a command line was called with a parameter called —type. I therefore set <param name=“type” type=“select > etc etc. to do: command —type $type Big mistake. This lead to errors as soon as the tool was modified in the workflow (set as runtime triggered an error for me), due to the fact that the workflow module type was not one of tool, data input, data collection, but was instead the value of the type param which was currently filled in. Now I know not to do this, hope you already did. cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden

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