galaxy-dev April 2014

galaxy-dev@lists.galaxyproject.org

91 participants
161 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 02 Sep '16

02 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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Strange issue with datatypes in Galaxy version of last week
by Lukasse, Pieter 12 Dec '14

12 Dec '14

Hi, Apparently a new datatypes bug has been introduced in the Galaxy version of last week: I have a tool that generates a csv file. Tool configuration is like this: <outputs> <data name="simOut" format="msclust.csv" label="${tool.name} on ${on_string} - SIM file"/> The datatypes has this entry: <datatype extension="msclust.csv" type="galaxy.datatypes.tabular:Tabular" mimetype="text/csv" display_in_upload="true" subclass="true"/> At first Galaxy output seems fine: [cid:image001.png@01CF4847.DE4A1A70] But when I download the file, the downloaded file name will be : Galaxy40-[MsClust_on_data_1_-_SIM_file]- When I go to "edit attributes" and just click "save", then upon downloading again, the file name is correct... Galaxy40-[MsClust_on_data_1_-_SIM_file].msclust.csv . Anyone faced this issue? Thanks and regards, Pieter. Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317481122; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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Re: [galaxy-dev] Some plugin for digital normalization
by Michael R. Crusoe 24 Nov '14

24 Nov '14

> From: Cristian Alejandro Rojas <alejandro.0317(a)gmail.com> > Date: December 26, 2013 2:37 AM > To: galaxy-dev(a)lists.bx.psu.edu > Subject: [galaxy-dev] Some plugin for digital normalization > Hello all, > > I've been searching in tool sheds(main and test) for a plugin to do digital normalization of reads, for example Trinity has one script to do this (./util/normalize_by_kmer_coverage.pl), diginorm is another alternative (http://ged.msu.edu/papers/2012-diginorm/). > > Do you know if there is a galaxy tool ready for this work or should I develop my own? Hello Cristian, I am actively working on a wrapper for normalize-by-median.py and the other tools in the khmer suite. https://github.com/ged-lab/khmer/blob/galaxy-integration/scripts/normalize-… It requires some changes on our end which you can track here: https://github.com/ged-lab/khmer/pull/237 You can install this branch of khmer via pip pip install -e git+git@github.com:ged-lab/khmer.git@output_naming1#egg=khmer or if you don't have a github account: pip install -e git+ https://github.com/ged-lab/khmer.git@output_naming1#egg=khmer (Instructions on installing using a virtualenv or on OS X are at: https://khmer.readthedocs.org/en/latest/install.html just substitute in the pertinent pip line from above) I haven't tested it much; doing so is the top of my to-do list for the rest of this week. If you or anyone else is feeling adventurous I would be happy to have the feedback. Cheers! -- Michael R. Crusoe: Software Engineer and Bioinformatician mcrusoe(a)msu.edu @ the Genomics, Evolution, and Development lab; Michigan State University http://ged.msu.edu/ http://orcid.org/0000-0002-2961-9670 @biocrusoe

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filtering a <param> of type 'data' so only one type is available
by Dan Tenenbaum 24 Oct '14

24 Oct '14

Hi, I have a tool wrapper with a <param> of type="data". Currently, this renders as a text box with a drop down list that has 52 items in it (the number of things I have in my history, I guess). I'd like to filter this list so that only some items in the history (in my case any item whose name ends with '.rda') are shown in this dropdown. It seems like maybe the 'format' parameter to the 'param' tag is what I want, but: 1) I tried format="rda" and that didn't seem to change anything. 2) "rda" is not in the datatypes.conf file which the documentation suggests is required? (.rda is an extension used for serialized R objects.) The tool I'm working on only accepts rda files as input and the reason I'm asking for this is that it is all too easy to accidentally feed it a file of some other type. If the dropdown could be filtered so that only items which will work with the tool are shown, that would be great. Is there a way to do that? Thanks, Dan

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Workflow param error leads to template error
by Paul-Michael Agapow 19 Sep '14

19 Sep '14

Looking for pointers on what might be causing this problem: A user had a moderately complicated workflow that when run under certain parameter values results in a traceback that ends: Module workflow_run_mako:232 in render_body >> for ic in oc.input_step.module.get_data_inputs(): AttributeError: 'WorkflowStep' object has no attribute 'module' After some puzzling, I realized one of the parameters was outside the allowed range (a max on an integer param) and that Galaxy was trying to render "run.mako" flagging up the error but erroring out. Why Galaxy tries to call this non-existent member is unclear to me. Any insight or places I should start exploring? Galaxy version: various (started with an 6-month old one, upgraded to latest production to see if it would fix error, it didn't) Hosting OS: CentOS 6 ------ Paul Agapow (paul-michael.agapow(a)hpa.org.uk) Bioinformatics, Health Protection Agency (UK) ************************************************************************** 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 the HPA, 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.HPA.org.uk **************************************************************************

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Packaging pycurl on toolshed
by Saket Choudhary 14 Aug '14

14 Aug '14

My attempt to 'package' pycurl on testtoolshed fails with the following error: src/pycurl.c: In function ‘do_multi_info_read’: src/pycurl.c:3549:15: warning: call to ‘_curl_easy_getinfo_err_string’ declared with attribute warning: curl_easy_getinfo expects a pointer to char * for this info [enabled by default] src/pycurl.c: In function ‘do_curl_getinfo’: src/pycurl.c:2888:19: warning: call to ‘_curl_easy_getinfo_err_curl_slist’ declared with attribute warning: curl_easy_getinfo expects a pointer to struct curl_slist * for this info [enabled by default] error: could not create '/usr/local/share/doc': Permission denied A local install worked fine. Is this because of libcurl-devel missing on toolshed instance?

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bioblend problem trying to use run_tool function
by Olivia Doppelt 24 Jul '14

24 Jul '14

Dear Developers, I would like to use bioblend to export the result of a galaxy workflow. To do that, we want to use an implemented tool called export_data; which enables the copy of a result file from galaxy arborescence to a local directory which belong to the user making the analysis and the export. We tried to launch this tool using the run_tool function but it doesn't work. giOlivia.tools.run_tool(history_id='xxxxxxxxxxx',tool_id='yyyyyyyy/export_data/export/2.2',tool_inputs={'input':'id_data','name':"data"}) I get an error message which is very long and attached to this email. Please help me on that it is the final step of several ones using bioblend. Have a nice day, -- Olivia Doppelt-Azeroual, PhD Tel: 92 15 CIB - Institut Pasteur

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galaxy-dev April 2014