galaxy-dev February 2016

galaxy-dev@lists.galaxyproject.org

49 participants
82 discussions

Running jobs as real user and extra_file_path
by Louise-Amélie Schmitt 28 Apr '17

28 Apr '17

Hi everyone, I just wanted to ask how the extra_file_path is handled in case of job running as the real user since the file_path is only writable by the galaxy user. Any clue? Thanks, L-A

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Python ValueError: too many values to unpack
by Matthias De Smet 18 Oct '16

18 Oct '16

Hi all, I’m trying to develop a tool that lets you select a file on the server. I’m using the dynamic_options setting to let Galaxy render a dropdown list of available file. However, when I try to test the tool in its current form, I get the following error: <pre> galaxy.web.framework.decorators ERROR 2016-01-26 13:08:35,649 Uncaught exception in exposed API method: Traceback (most recent call last): File "lib/galaxy/web/framework/decorators.py", line 260, in decorator rval = func( self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/api/tools.py", line 98, in build return tool.to_json(trans, kwd.get('inputs', kwd)) File "lib/galaxy/tools/__init__.py", line 2602, in to_json populate_state(trans, self.inputs, state_inputs, state_errors, params.__dict__) File "lib/galaxy/tools/__init__.py", line 2471, in populate_state state[input.name] = input.get_initial_value(trans, context, history=history) File "lib/galaxy/tools/parameters/basic.py", line 984, in get_initial_value value = [ optval for _, optval, selected in options if selected ] ValueError: too many values to unpack </pre> My tool xml looks like this: <pre> <tool id="archivetolibrary" name="Copy files" version="0.1.0"> <description>from the archive to a data library</description> <code file="list_files.py"/> <command interpreter="bash"> test.sh > $log </command> <inputs> <param name="archive_source" type="select" display="radio" label="Choose source archive"> <options from_file="archives.loc"> <column name="name" index="0"/> <column name="value" index="1"/> </options> </param> <param name="query" type="text" label="Search for files"/> <param name="selected_file" type="select" label="Choose your file" dynamic_options="list_files(archive_source,query)"/> </inputs> <outputs> <data name="log" format="txt" label="${tool.name} on ${on_string}"></data> </outputs> <tests> <test> </test> </tests> <help> This tool copies data from and archive folder to your history. Keep in mind this folder MUST be readable by Galaxy in order for this tool to work. </help> </tool> </pre> and the script called in the “code” tag looks like this <pre> def list_files(dir,query): listing=[] for fname in listdir(dir): fullpath = path.join(dir, fname) #only select datafiles, not md5 checksums if path.isfile(fullpath) and not fullpath.endswith(".md5"): listing.append( fname ) return listing </pre> This script should return a list with filenames that should be displayed in the dropdown list. I’m tracking Galaxy release 15.10, running on a Ubuntu 14.04.3 server Thanks for your help! Matthias

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Re: [galaxy-dev] how to create users through Galaxy API?
by Martin Čech 03 Sep '16

03 Sep '16

Hi, you specify username, password and email in the body (payload) of the POST as Key:Value pairs. Code from the API method: ( https://galaxy-central.readthedocs.org/en/latest/_modules/galaxy/webapps/ga…) username = payload[ 'username' ] email = payload[ 'email' ] password = payload[ 'password' ] There are also other conditions that need to be fulfilled (e.g. user creation has to be turned on in the configuration) - you will find these when you look at the source code of the method (because the documentation is not perfect yet, sorry). M. On Sun, Dec 29, 2013 at 11:22 PM, xlwang <xlwang_0903(a)163.com> wrote: > hi, > I still have some confusion. > post /api/users , when i use postman, it seems like this: > > > No other parameters? How to confirm the new user's information?Such as > user name, password. > Can you give me a example please?Thank you! > > At 2013-12-30 06:04:15,"Martin Čech" <marten(a)bx.psu.edu> wrote: > > Hello, > > to create a user through API you send a POST request to /api/users > > More information about User API here: > > > https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.… > > Martin > > > On Fri, Dec 27, 2013 at 5:11 AM, xlwang <xlwang_0903(a)163.com> wrote: > >> hello, >> I want to create users through Galaxy API.For example, I can get users >> information through url like this(use postman): >> http://localhost:8080/api/users?key=my_key >> But how to create a user? >> >> >> >> ___________________________________________________________ >> 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: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > > > >

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tabular file displayed without tabs
by Ryan G 22 Jun '16

22 Jun '16

Hi - I have a tools that generates a tab-delimited text file as output. when I click the eye icon to view the data, all the fields are compressed as if there were no tabs. If I expand the history view, the little preview window shows the contents as tabbed. I've verified that the spaces are indeed '\t' tab characters. Why would Galaxy not display this file as a tab-delimited file?

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not sure what I can do about this...
by Fernandez Edgar 08 Jun '16

08 Jun '16

Hello Gents, So someone asked me to install the package Prokka on Galaxy. I did and everything went well! However, the following error comes up, when they try to work with Prokka: Fatal error: Exit code 2 () [tbl2asn] This copy of tbl2asn is more than a year old. Please download the current version. [20:20:53] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.10 from http://www.vicbioinformatics.com' -Z outdir\/prokka\.err -i outdir\/prokka\.fsa 2> /dev/null According to a google search, there is very little on this error. And it has been around for a while but I didn't find a posted solution. Any suggestions? Cordialement / Regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication * Bur. : 1-514-343-6111 poste 16568 Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218

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How to replace 'BioMart Central server' in the "Get Data" tools ?
by Hans-Rudolf Hotz 08 Jun '16

08 Jun '16

Hi As you probably know, the central BioMart server is currently unavailable (see: http://www.biomart.org/notice.html). Hence, the "Get Data -> BioMart Central server" tool in our local Galaxy installation does not work anymore - well, this is also the case on usegalaxy.org. We can easily switch the tool to point to a different Mart server, i.e.: Change: <inputs action="http://www.biomart.org/biomart/martview" .... to: <inputs action="http://www.ebi.ac.uk/uniprot/biomart/martview" .... However, we would like to switch to the ensembl Mart server: http://www.ensembl.org/biomart/martview It looks like the ensembl Mart server is nowadays embedded in the ensembl web site, and the requests are not send to Galaxy, but end up on the ensembl web page, where they cause a "Error 404 - Page not found". Unfortunately, I am not that savvy about the inner works of the ensembl web site anymore ;) Has anyone else looked into this problem and found already a solution? Thank you very much for any help Hans-Rudolf

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atlas 3.10 IUC error
by Olivier CLAUDE 03 Jun '16

03 Jun '16

Hello again, I am truly sorry to bother everyone again but i still experience problems: This time with atlas 3.10 owned by iuc At the beginning without modifying anything, the error log was saying " mkdir : cannot create directory ATLAS/build : No such file or directory" After that I tried to modify the tool_dependencies.xml : L48 : "mkdir ATLAS/build &&" changed to "mkdir build &&" The error is "/bin/sh: 4 : cannot open /host/static_full_blas_lapack.diff: No such file" I can see it, if I go with a web browser, but I cannot download it manually nor click on it without crashing the web browser. Any idea? Thanks again, M Olivier CLAUDE- PhD Student INSERM/UPMC UMRS ICAN 1166 – Equipe 2 Faculté de médecine Pitié-Salpêtrière 91, bld de l'Hôpital - 3ème étage - Porte 305 75013 Paris - FRANCE

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Data removal after ftp import.
by Zuzanna K. Filutowska 15 Apr '16

15 Apr '16

Dear All, is there any option to not remove files that has been imported to Galaxy from FTP directory and to not remove files that haven't been imported since 3 days? -- Regards, -- Zuzanna K. Filutowska, HPC Systems Administrator Poznan Supercomputing and Networking Center Institute of Bioorganic Chemistry Polish Academy of Sciences Seize the day boys! Make your lifes extraordinary! --John Keating

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Tool Visibility feature
by SAPET, Frederic 29 Mar '16

29 Mar '16

Hello I'm trying to set up this feature : https://wiki.galaxyproject.org/Admin/Config/Access%20Control it seems that some files have been moved from : lib/galaxy/tools/filters/ to lib/galaxy/tools/toolbox/filters/ by the way, when I uncomment " user_tool_filters = examples:restrict_upload_to_admins, examples:restrict_encode" in my galaxy.ini file, it does not work. When I click on "Manage your ToolBox filters" (/user/toolbox_filters?cntrller=user) in my User preferences panel, I'm facing this error : Internal Server Error Galaxy was unable to successfully complete your request URL: http://galaxy.biogemma.fr/user/toolbox_filters?cntrller=user sys.path: [ '/softs/bioinfo/galaxy-prod/eggs/Parsley-1.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/Fabric-1.7.0-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/ssh-1.7.14-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/paramiko-1.11.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/SVGFig-1.1.6-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/drmaa-0.7.6-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/Whoosh-2.4.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/Beaker-1.4-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/MySQL_python-1.2.3c1_5.1.41_static-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/sqlalchemy_migrate-0.9.6-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/Tempita-0.5.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/decorator-3.1.2-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/sqlparse-0.1.14-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/six-1.9.0-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/Babel-1.3-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/pytz-2013.9-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/mercurial-3.2.4-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/Mako-0.4.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/kombu-3.0.24-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/ordereddict-1.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/importlib-1.0.3-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/anyjson-0.3.3-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/PyYAML-3.10-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/WebHelpers-1.3-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/bx_python-0.7.2-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/SQLAlchemy-1.0.8-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/WebOb-0.8.5-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/Routes-2.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/repoze.lru-0.6-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/amqp-1.4.6-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/wchartype-0.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/docutils-0.7-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/PasteDeploy-1.5.0-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/lib', '/usr/lib/python2.6/site-packages/pip-7.1.2-py2.6.egg', '/usr/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg', '/usr/lib/python2.6/site-packages/bz2file-0.98-py2.6.egg', '/usr/lib64/python26.zip', '/usr/lib64/python2.6', '/usr/lib64/python2.6/plat-linux2', '/usr/lib64/python2.6/lib-tk', '/usr/lib64/python2.6/lib-old', '/usr/lib64/python2.6/lib-dynload', '/usr/lib64/python2.6/site-packages/gtk-2.0', '/usr/lib64/python2.6/site-packages', '/usr/lib/python2.6/site-packages'] Module galaxy.web.framework.middleware.error:151 in __call__ >> app_iter = self.application(environ, sr_checker) Module paste.recursive:84 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.middleware.remoteuser:143 in __call__ >> return self.app( environ, start_response ) Module paste.httpexceptions:633 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:133 in __call__ >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:191 in handle_request >> body = method( trans, **kwargs ) Module galaxy.web.framework.decorators:68 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.user:1331 in toolbox_filters >> tool_filters = get_filter_mapping( saved_user_tool_filters, trans.app.config.user_tool_filters ) Module galaxy.webapps.galaxy.controllers.user:1284 in get_filter_mapping >> module = __import__( module_name, globals(), fromlist=['temp_module'] ) ImportError: No module named examples Could you please provide me some help ? I have launched a git pull origin master before testing... Thank you. Fred

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Galaxy tools for docking protein-compounds.
by Léo Biscassi 15 Mar '16

15 Mar '16

Hi folks, I've been developing Galaxy tools for docking protein-compounds. My docking program is Autodock Vina. In [1] is my repository. I'm writing here for two purpose: 1) Is there someone working in this way? I've found the project [2]. 2) I would like to share these tools to Galaxy project. Are they welcome for Galaxy project? Let me know the best practices for developing tools to be shared in Galaxy project. [1] https://github.com/leobiscassi/galaxy_tools [2] https://toolshed.g2.bx.psu.edu/ Thanks for any help. Att. -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi

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galaxy-dev February 2016