June 2016 - galaxy-dev - lists.galaxyproject.org

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 script can't can't import BioPython modules in Galaxy 16.01
by Makis Ladoukakis 17 Jan '17

17 Jan '17

Hello everyone, I've recently upgraded to Galaxy 16.01 and i have some issues with a python wrapper from a tool. When I run it via Galaxy I get the following error: Traceback (most recent call last): File "/home/galaxy_user/galaxy/tools/myTools/know_parser/know_parser.py", line 12, in <module> from Bio import SeqIO ImportError: No module named Bio However when I click on the "view details" icon to copy the command from the tool and run it on my command line the tool works perfectly. In addition this issue occurs while I already have installed BioPython. When I type Python and write "from Bio import SeqIO" I get no error. Can this be an issue related to the virtual environment that is initialized each time Galaxy starts? Thank you in advance, Makis Ladoukakis

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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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workflow import error
by Tony Schreiner 30 Sep '16

30 Sep '16

We have 2 galaxy instances running one is v15.05-74-gf6b894a the other is v15.10-30-g6a47d2d a user is trying to import a workflow file, it works on the older one, but raises an error on the newer one. URL: http://redacted.edu:8080/workflow/import_workflow <http://prince.bc.edu:8080/workflow/import_workflow> File '/cluster/home/galaxy/galaxy/lib/galaxy/web/framework/middleware/error.py', line 151 in __call__ app_iter = self.application(environ, sr_checker) File '/cluster/home/galaxy/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/cluster/home/galaxy/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/cluster/home/galaxy/galaxy/lib/galaxy/web/framework/base.py', line 133 in __call__ return self.handle_request( environ, start_response ) File '/cluster/home/galaxy/galaxy/lib/galaxy/web/framework/base.py', line 191 in handle_request body = method( trans, **kwargs ) File '/cluster/home/galaxy/galaxy/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 921 in import_workflow workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source=src, add_to_menu=add_to_menu ) File '/cluster/home/galaxy/galaxy/lib/galaxy/web/base/controller.py', line 1111 in _workflow_from_dict publish=publish File '/cluster/home/galaxy/galaxy/lib/galaxy/managers/workflows.py', line 159 in build_workflow_from_dict module, step = self.__module_from_dict( trans, step_dict, secure=False ) File '/cluster/home/galaxy/galaxy/lib/galaxy/managers/workflows.py', line 605 in __module_from_dict module.save_to_step( step ) File '/cluster/home/galaxy/galaxy/lib/galaxy/workflow/modules.py', line 592 in save_to_step step.tool_inputs = self.tool.params_to_strings( self.state.inputs, self.trans.app ) File '/cluster/home/galaxy/galaxy/lib/galaxy/tools/__init__.py', line 1980 in params_to_strings return params_to_strings( self.inputs, params, app ) File '/cluster/home/galaxy/galaxy/lib/galaxy/tools/parameters/__init__.py', line 92 in params_to_strings value = params[ key ].value_to_basic( value, app ) File '/cluster/home/galaxy/galaxy/lib/galaxy/tools/parameters/grouping.py', line 574 in value_to_basic rval[ self.test_param.name ] = self.test_param.value_to_basic( value[ self.test_param.name ], app ) KeyError: 'uncol' i'm not able conclude much from this dump. Can anyone suggest some steps to debug this. Cheers Tony Schreiner

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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 running JBrowse
by Raymond Wan 17 Aug '16

17 Aug '16

Dear all, I'm trying to run the JBrowse tool within Galaxy. The installation was fine (I think), but when I run the tool, I get this error: Fatal error: Exit code 1 () Traceback (most recent call last): File "/d15/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/d022577ff9cf/jbrowse/jbrowse.py", line 11, in <module> from Bio.Data import CodonTable ImportError: No module named Does this mean I'm missing something? In the history, if I click the "(i)" icon for the incomplete job (in red), everything looks fine, except that it says: Tool Version: python: can't open file 'jbrowse.py': [Errno 2] No such file or directory However, "jbrowse.py" does exist in the path above. Any idea what could be wrong? Thank you! Ray

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Amazon Instance Types for Galaxy
by Lapointe, David 14 Jul '16

14 Jul '16

Are there instance types which will not work for Galaxy/Cloudman on AWS? EBS volumes for example. Thanks, David -- David Lapointe Ph.D. Sr. Bioinformatics Specialist Research Technology (RT) Tufts Technology Services (TTS) 16 Dearborn Road Somerville MA 02144 Phone: 617-627-5319 Fax: 617-627-3667 http://it.tufts.edu

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Python tool wrapper with multiple input and output files
by Marco Tangaro 08 Jul '16

08 Jul '16

Dear experts, my name is Marco and I'm working to port our python tool to the Galaxy framework. The main script needs a rna.bam file as input, a reference fasta file, both mandatory. Finally, you can add a dna.bam file, but this is optional. Therefore an example command is: script.py -i rna.bam -f reference.fa -j dna.bam The outout is a tabular. Again the -j dna.bam option is completely optional. So quite soon it turned out that I had to use a python wrapper to parse our script. Now the wrapper works fine. The next step is to run the tool over multiple input file and we would like to avoid to use a workflow. The idea is that to each input file corresponds an output file. The reference is still the same. For instance, we have: rna_1.bam + dna_1.bam -> output_1.txt rna_2.bam + dna_2.bam -> output_2.txt rna_3.bam + dna_3.bam -> output_3.txt ... and so on. But I don't know the best strategy to give to my wrapper multiple input files. Moreover I have to be sure, when the dna_xyz.bam files are uploaded, that they correspond to the right rna_xyz.bam file. I would like to have as output a page which is showing as results the link to the single output files as suggested here. https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files planning to integrate a javascript interface. I've browsed a lot, but on multiple input file the posts are old. I'm using the last galaxy release (16_04). I'm quite new to the galaxy world... Thanks a lot for your suggestions, Marco

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Auto detection of output format Galaxy custom tool
by Katherine Beaulieu 08 Jul '16

08 Jul '16

Hi everyone, I am looking to auto-detect the file format of a file outputted by a python tool I have written. Does anyone have any idea how to do this? I have tried setting the format attribute to "auto" with no luck. Let me know if you would like to see my tool config file. Cheers, Katherine

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Implementing iRODS with Galaxy
by Yip, Miu ki 01 Jul '16

01 Jul '16

Hello Galaxy Team, We're from the Bioinformatics Shared Resources (BSR) at Cold Spring Harbor Labs and we're looking to implement irods on a newly installed version of Galaxy. We want to incorporate iRODS (http://irods.org/) Is there a recommended way to do this, or no? Thanks in advance for the advice. Best, Miuki Yip

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