galaxy-dev October 2014

galaxy-dev@lists.galaxyproject.org

64 participants
99 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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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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error loading files into galaxy
by Hakeem Almabrazi 04 Mar '16

04 Mar '16

Hi, I started getting the following error whenever I try to load a file into Galaxy local. Traceback (most recent call last): File "/usr/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 8, in <module> from galaxy import eggs ImportError: cannot import name eggs I will appreciate if someone can tell me what could happen to cause such issue and how to resolve it. Regards,

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Upload issue in local installation
by Batsal Devkota 05 Feb '16

05 Feb '16

I installed galaxy locally in a linux server. However, I cannot upload the files (no matter how small, I have tried few kb size fasta files). When I try to upload, the link to the file shows up in the History and gets a new number (purple box). When I click on the link I get 'Dataset is uploading' forever. In the terminal window where I start galaxy, I get the following error report: 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /root/tool_menu HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /history HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:33 -0400] "POST /root/user_get_usage HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:40 -0400] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://redhat:8080/root/tool_menu" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /tool_runner/upload_async_create HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /tool_runner/upload_async_message HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /history HTTP/1.1" 200 - "http://redhat:8080/tool_runner/upload_async_message" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /root/user_get_usage HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:34:04 -0400] "POST /root/history_item_updates HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:34:08 -0400] "POST /root/history_item_updates HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" The last line keeps going for ever... writes new line every 4 secs. I am stuck and don't know where to look. Please help. Batsal.

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Rename output from a repeat
by Ulf Schaefer 27 Aug '15

27 Aug '15

Hi all We frequently use the syntax below to rename outputs of workflows that we run in batch. It is convenient to have sample names from fastqs carried over to sams, bams, vcfs, etc. #{input1 | basename}.bam This does not seem to be working for inputs that are in repeats, e.g. the VelvetOptimiser. Does anybody know if there is a syntax to make this work, maybe #{repeatname[0].input1 | basename}.bam ? Thanks a lot for your help Ulf ************************************************************************** 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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Object-Store, setting filetypes crashes Galaxy
by bjoern.gruening＠googlemail.com 22 Jul '15

22 Jul '15

Hi, I have configured to use the hierarchical object store but as soon as I try to reset the filetpye of a dataset Galaxy is crashing with: galaxy.objectstore DEBUG 2014-06-12 14:39:21,180 Using preferred backend 'files3' for creation of MetadataFile 5963 132.230.153.57 - - [12/Jun/2014:14:39:20 +0200] "POST /datasets/966f24627ef70c12/edit HTTP/1.1" 500 - " http://galaxy.uni-freiburg.de/datasets/966f24627ef70c12/edit" "Mozilla/5.0 (X11; Linux x86_64; rv:29.0) Gecko/20100101 Fire fox/29.0" Error - <type 'exceptions.OSError'>: [Errno 2] No such file or directory: 'database/tmp/metadata_temp_file_1xnGcE' URL: http://galaxy.uni-freiburg.de/datasets/966f24627ef70c12/edit File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py', line 295 in edit trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming = { 'input1':data }, overwrite = False ) #overwrite is False as per existi ng behavior File '/usr/local/galaxy/galaxy-dist/lib/galaxy/tools/actions/metadata.py', line 18 in execute overwrite, history, job_params ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/tools/actions/metadata.py', line 79 in execute_via_app kwds = { 'overwrite' : overwrite } ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py', line 717 in setup_external_metadata shutil.copy( dataset.metadata.get( meta_key, None ).file_name, metadata_temp.file_name ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py', line 575 in file_name self._filename = abspath( tempfile.NamedTemporaryFile( dir = self.tmp_dir, prefix = "metadata_temp_file_" ).name ) File '/usr/local/python/2.7/lib/python2.7/tempfile.py', line 454 in NamedTemporaryFile (fd, name) = _mkstemp_inner(dir, prefix, suffix, flags) File '/usr/local/python/2.7/lib/python2.7/tempfile.py', line 235 in _mkstemp_inner fd = _os.open(file, flags, 0600) OSError: [Errno 2] No such file or directory: 'database/tmp/metadata_temp_file_1xnGcE' I have attached my object_store_conf.xml file. Thanks, Bjoern

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problems installing tool dependency
by Sajdak, Doris 27 Feb '15

27 Feb '15

Hi all, I am trying to install the Genome Diversity tools from the Miller Lab that are in the Galaxy toolshed. I've been able to get all dependencies installed except Quicktree. Whenever I try to install it, I get the error: Error downloading from URL ftp://ftp.sanger.ac.uk/pub4/resources/software/quicktree/quicktree.tar.gz: <urlopen error ftp error: 550 pub4: No such file or directory> This is the tool_dependencies.xml file for installing quicktree: <?xml version="1.0"?> <tool_dependency> <package name="quicktree" version="1.1"> <install version="1.0"> <actions>  <action type="download_by_url" target_filename="quicktree_1.1.tar.gz">ftp://ftp.sanger.ac.uk/pub4/resources/software/quicktree/quicktree.tar.gz</action>  <action type="shell_command">make quicktree</action>  <action type="shell_command">cp -R bin $INSTALL_DIR</action>  <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> </package> </tool_dependency> I know this is not their file I'm downloading but the thing is, if I copy and paste the URL, I can download it with no problem. I'm not sure why it's reporting that it can't be found but the xml looks right to me. I've tried contacting the Miller Lab about this but haven't heard from anyone so I'm hoping someone here can tell me how to move past this problem. Is there a way to install this tool manually and have the main Genome Diversity tools recognize it on the Galaxy server? Also, I noticed when looking at the Tool Dependency Definitions at https://toolshed.g2.bx.psu.edu/ there are errors going back many versions for this tool (see Test runs - Installation errors - Tool dependencies). Thank you for any help you can provide. Dori ********************************** Dori Sajdak Senior Systems Administrator State University of NY at Buffalo Center for Computational Research 701 Ellicott St Buffalo, NY 14203 Phone: (716) 881-8934 Fax: (716) 849-6656 Web: http://ccr.buffalo.edu **********************************

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Galaxy Bioblend option for importing dataset into a library?
by Dooley, Damion 09 Jan '15

09 Jan '15

I see Galaxy API has a feature to import a history dataset into the library (in copy_hda_to_ldda() fn from GCC2013 training day course). Is this available as well via Bioblend? Latest docs don't seem to include this feature. It would be the opposite of Bioblend's upload_dataset_from_library(history_id, lib_dataset_id) ) Objective is to get customized blast indexes into library that way for shared use. Or have them actually exist outside galaxy, and linked in. Regards, Damion Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada

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Job wrapper object
by Alexandre Defelicibus 18 Dec '14

18 Dec '14

Hi all, I'm developing some tools on my Galaxy instance and I need to get some information about the job that a tool creates. The question is, how can I have a job_wrapper object in my tool wrapper? I tried to use the reserved variable $__app__, but I got errors. I couldn't import and use the galaxy lib in order to get the job information. Could someone show me the correct way to do that, with some examples? I appreciate all the help. Best regards, -- Alexandre Defelicibus Mestrando em Bioengenharia Programa de Pós-Graduação em Bioengenharia Universidade de São Paulo - USP

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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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galaxy-dev October 2014