- galaxy-dev - lists.galaxyproject.org

URGENT HELP!
by Ali Al-Shahib 29 Oct '15

29 Oct '15

Hi all I am due to give galaxy training tomorrow and the Galaxy server has gone down. Our galaxy admin is travelling and not responding and I appreciate a quick response to this issue. When I run galaxy_restart.sh I get the following error in web0.pid: migrate.versioning.repository DEBUG 2015-10-28 23:07:47,285 Config: {'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]', 'version_table': 'migrate_version', 'repository_id': 'Galaxy'}} lib/galaxy/model/migrate galaxy.model.migrate.check DEBUG 2015-10-28 23:07:47,296 psycopg2 egg successfully loaded for postgresql dialect Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 52, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self ) File "/home/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 104, in create_or_verify_database % ( db_schema.version, migrate_repository.versions.latest, config_arg ) ) Exception: Your database has version '124' but this code expects version '115'. Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'. ------ I did then try to do sh manage_db.sh downgrade 115 but I got this error: Traceback (most recent call last): File "./scripts/manage_db.py", line 62, in <module> main( repository=repo, url=db_url ) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/shell.py", line 207, in main ret = command_func(**kwargs) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py", line 202, in downgrade return _migrate(url, repository, version, upgrade=False, err=err, **opts) File "<string>", line 2, in _migrate File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/util/__init__.py", line 159, in with_engine return f(*a, **kw) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py", line 345, in _migrate changeset = schema.changeset(version) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/schema.py", line 80, in changeset changeset = self.repository.changeset(database, start_ver, version) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py", line 225, in changeset changes = [self.version(v).script(database, op) for v in versions] File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py", line 189, in version return self.versions.version(*p, **k) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/version.py", line 140, in version return self.versions[VerNum(vernum)] KeyError: <VerNum(124)> Any help asap will be greatly appreciated. Ali ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************

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Bismark installation dependencies error
by Jose Juan Almagro Armenteros 28 Oct '15

28 Oct '15

Hello, I have tried to install the last version of Bismark from the toolshed and I got an error while installing. Basically it can't install bowtie and bowtie2 because the folder name is written twice in the download directory. Here is the error: File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 142, in install_and_build_package_via_fabric tool_dependency = self.install_and_build_package( tool_shed_repository, tool_dependency, actions_dict ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 100, in install_and_build_package initial_download=True ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step initial_download=initial_download ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 685, in execute_step dir = self.url_download( work_dir, downloaded_filename, url, extract=True, checksums=checksums ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 223, in url_download extraction_path = archive.extract( install_dir ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 89, in extract os.chmod( absolute_filepath, unix_permissions ) [Errno 2] No such file or directory: './database/tmp/tmp-toolshed-mtdM4XBx_/bowtie-0.12.8/bowtie-0.12.8/' As you see "bowtie-0.12.8" is twice in the path and when I check the directory, the last "bowtie-0.12.8" folder doesn't exists. Do you know what could go wrong or an alternative way of specifying the correct path? Best regards, Jose

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Opening Galaxy with a specified History Name -- how to convert the clear text history id to an encrypted id?
by rbrown Brown 28 Oct '15

28 Oct '15

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Re: [galaxy-dev] Hey, I got some problem using galaxy, If you have a time, I hope your help..!!
by Greg Von Kuster 28 Oct '15

28 Oct '15

Hello Yoong, The best place to ask questions like this is the Galaxy Dev mailing list (galaxy-dev(a)lists.galaxyproject.org) There are many developers that support this mailing list, so you will undoutedly receive optimal answers to any of your questions. I’ve forwarded your current questions to the mailing list. Regards, Greg Von Kuster > On Oct 28, 2015, at 12:56 AM, 홍윤지 <yoong0525(a)gmail.com> wrote: > > hey, my name is yoong in korean student . > i'd like to run the program name Mapsplice2, so i made a xml file, and submit that > > this is my xml file.. > > > <tool id="mapsplice" name="Mapsplice" version="2.2.0"> > > <description>MapSplice2 Description</description> > > <command interpreter="python"> > /home/yoong/galaxy/tools/MapSplice-v2.1.9/mapsplice.py -o $alignments.files_path -p 20 --qual-scale phred33 --bam --fusion -c /home/yoong/1_reference/hg19 -x /home/yoong/1_reference/BowtieIndex -1 $input_reads_1 -2 $input_reads_2 > </command> > > <inputs> > <param format="fastq" name="input_reads_1" type="data" label="Source file1"/> > <param format="fastq" name="input_reads_2" type="data" label="Source file2"/> > </inputs> > <outputs> > <data format="bam" name="alignments" label="alignments.bam"/> > <data format="txt" name="deletions" label="deletions.txt"/> > <data format="txt" name="fusions_candidates" label="fusions_candidates.txt"/> > <data format="txt" name="fusions_raw" label="fusions_raw"/> > <data format="txt" name="insertions" label="insertions.txt"/> > <data format="txt" name="junctions" label="junctions.txt"/> > <data format="txt" name="stats" label="stats.txt"/> > </outputs> > <help> > Help > </help> > </tool> > > and, look at the report error, there is no special error... what's was the problom..? Do I something wrong ?... > plz help me...!! Thank you ...

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Error in tool parameters when histories are exported/imported
by Simon Gladman 28 Oct '15

28 Oct '15

Hi all, I've noticed that when I export a history with complex parameter settings for the tool Freebayes, when I re-import it, all of the parameter settings disappear. Does anyone know what is going on? Cheers, Simon. -- Simon Gladman | Bioinformatician Victorian Life Sciences Computation Initiative - LSCC 700 Swanston Street, The University of Melbourne | Victoria 3010 Australia T +61 3 9035 5822 | M 0418 421 077 Mail: simon.gladman(a)unimelb.edu.au Web: http://www.vlsci.org.au

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Re: [galaxy-dev] search paths for custom tools
by Peter Cock 26 Oct '15

26 Oct '15

On Mon, Oct 26, 2015 at 4:37 PM, Tony Schreiner <anthony.schreiner(a)bc.edu> wrote: > I take it the tool_dependencies.xml file goes in the same directory as the > custom tool xml files are. And as such applies to any of them in this > folder? > > Thanks > Tony They need to be in the same tar-ball when the tool is uploaded to the Tool Shed, by convention in the same folder as the tool XML file(s), yes. However, if you are not using the Tool Shed and simply install your tools manually into Galaxy then I'm not 100% sure if you can trigger the env.sh files via the requirement tag in the tool: <requirements> <requirement type="package" version="1.66">biopython</requirement> </requirements> Hopefully one of the Galaxy team can clarify... For local development and deployment outside the Tool Shed, I always installed the dependencies myself at system level, or at the Galaxy Linux user level. Peter

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GCC2016 Training Topic Voting is Open
by Dave Clements 26 Oct '15

26 Oct '15

Hello all, *Voting is now open <http://bit.ly/gcc2016vote>* on what training topics <https://wiki.galaxyproject.org/Events/GCC2016/Training> are offered at GCC2016 Training <https://wiki.galaxyproject.org/Events/GCC2016/Training>. There are nominated topics <https://wiki.galaxyproject.org/Events/GCC2016/Training> spanning from basic usage to advanced deployment. No matter what you do with Galaxy, there are topics for you to choose from. Your vote <http://bit.ly/gcc2016vote> will determine the topics that are offered, which topics should be offered more than once, and which ones should not be scheduled at the same time. Your vote matters. *Topic voting closes November 6.* The Training schedule, including instructors, will be published before early registration opens. *About GCC2016 Training <https://wiki.galaxyproject.org/Events/GCC2016/Training>:* The 2016 Galaxy Community Conference (GCC2016) <https://wiki.galaxyproject.org/Events/GCC2016> will be held June 25-29 at Indiana University <http://indiana.edu/> in Bloomington, Indiana, United States. GCC2016 features two full days of training on June 26-27 <https://wiki.galaxyproject.org/Events/GCC2016/Training>. Each day will have multiple tracks, with each track featuring several sessions throughout the day. Workshops will be hands-on and participants will be strongly encouraged to bring a laptop and follow along. If you work in data-intensive biomedical research, there is no better place than GCC2016 to present your work and to learn from others. As always, please let us know if you have any questions. Thanks, The GCC2016 Exec <https://wiki.galaxyproject.org/Events/GCC2016/Organizers> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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search paths for custom tools
by Tony Schreiner 26 Oct '15

26 Oct '15

Beginner question, I apologize. I recently set up a galaxy server for the first time. The users of this server are installing custom tools of their own creation. Some of these tools use binaries from fastx_toolkit, and python libs from biopython. Both of these have been added from tool_shed. I have not understood yet, how to set the search path for these dependencies in the custom tools. I see the env.sh files in the tool_shed directories, but am now wondering if there is way to specify in the custom tools' xml files how to invoke the needed env.sh. Or what is the more proper way to do do this. Tony Schreiner Boston College

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HTML and download links
by Sabrina Legoueix Rodriguez 23 Oct '15

23 Oct '15

Hi, I would like to generate an html output (in the .xml) in my wrapper with links to other outputs. The user wants to obtain only 1 html output file when the tool has finished to run ; and that html page should contain links to all other outputs to be downloaded (zip files). Could you please tell me if there s a way to do so in galaxy and could you please tell le how ? Thanks in advance, Best regards, -- Signature e-mail TWB Sabrina **Sabrina LEGOUEIX RODRIGUEZ** Responsable Plateau Bioinformatique Tél. : +33 (0) 5 61 28 57 92 sabrina.legoueix(a)toulouse.inra.fr <mailto:[MAIL]> www.toulouse-white-biotechnology.com <http://www.toulouse-white-biotechnology.com/> LinkedIn <https://www.linkedin.com/company/2757525h> Twitter <https://twitter.com/TWB_Biotech> TWB - Parc technologique du canal • Bâtiment NAPA CENTER B • 3, rue Ariane • 31520 Ramonville Saint-Agne Ce message et ses pièces jointes sont strictement personnels. Ils peuvent contenir des informations confidentielles. Si vous avez reçu ce message par erreur, merci d'en avertir l'expéditeur et de détruire le message et les documents joints. Toute utilisation des informations reçues par erreur est interdite. This message and the attachments are strictly personal. They may contain confidential information. If you have received this message in error, please notify the sender and delete the message and the attachments. Any use of this communication received in error is prohibited.

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Deleting / deprecating an empty Tool Shed repository?
by Peter Cock 22 Oct '15

22 Oct '15

Hi all, Following the Biopython 1.66 release, I will be creating: https://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_66/ https://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_66/ Due to user error and a planemo bug [1], I accidentally created the following on the Test Tool Shed: https://testtoolshed.g2.bx.psu.edu/view/peterjc/package_biopython_1_66/ https://testtoolshed.g2.bx.psu.edu/view/peterjc/package_biopython_1_66/0000… At this point nothing has been uploaded, so I would ideally like to delete it. Failing that, I would manually deprecate it - but I can't see any action to do so - only an upload file button. (From memory there is an automatic deprecation process for empty repositories which should take care of this.) Would offering deletion be reasonable in this situation? Thanks, Peter [1] https://github.com/galaxyproject/planemo/issues/246

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