July 2014 - 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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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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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 21 Jul '15

21 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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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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datatype dependencies
by Eric Rasche 28 Nov '14

28 Nov '14

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Let's pretend for a second that I'm rather lazy (oh...wait), and I have ZERO interest in writing datatype parsers to sniff and validate whether or not a specific file is a specific datatype. I'm a sysadmin and bioinformatician, and I've worked with dozens of libraries that exist to parse file formats, and they all die in flames when I feed them bad data. Would it be possible to somehow define requirements for datatypes? I don't want to take on the burden of code I write saying "yes, I've sniffed+validated this and it is absolutely a genbank file". That's a lot of responsibility, especially if people have malformed genbank files and their tools fail as a result. I would like to do this with BioPython and turf the validation to another library that exists to parse genbank files, that will raise and exception if they're invalid. > def sniff(self, filename): > from Bio import SeqIO > try: > self.records = list(SeqIO.parse( filename, "genbank" )) > return True > except: > self.records = None > return False > > def validate(self, dataset): > from Bio import SeqIO > errors = list() > try: > self.records = list(SeqIO.parse( dataset.file_name, "genbank" )) > except Exception, e: > errors.append(e) > return errors > > def set_meta(self, dataset, **kwd): > if self.records is not None: > dataset.metadata.number_of_sequences = len(self.records) so much easier! And I can shift the burden of validation and sniffing to upstream, rather than any failures being my fault and requiring maintenance of a complex sniffer. Cheers, Eric - -- Eric Rasche Programmer II Center for Phage Technology Texas A&M University College Station, TX 77843 404-692-2048 esr(a)tamu.edu rasche.eric(a)yandex.ru -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (GNU/Linux) iQIcBAEBAgAGBQJTyBmyAAoJEMqDXdrsMcpVQa0P/jj0edAKM6QsodhRWHglR92W tej1tJjtPgtJ15wsFzq6wVfhbL5J39ytsWjjtk//jhVNXh4FEE/OFZe6Nx9uTFKP ybazyTrLSCrxsST+w+Rx8Q9vfzShr87vjP+fC1k5i2EZOgogPOcQml1ouOHHjC6z pArrwPOvL3ZxWJG7oEcZjUjrPD8+ffhfQ/x096YYIMw7Hg74d50ARwtawJRoslZD JnYWa+aUOcsvC3QMrLKkDm4qBaTHa5x7x7P07Lcx7X65iMPDcuMZNtImiLztNscF QwbbdJdcs8oeSRRnmKgAllRAKf4dMeiyaSI+muVzNlpvLlSMZBNawD0bO1OXmIQH vAaV0eU+rYmDJSGo330o+RydvlDJENTXOkDt0TxmvfYAPtg2TlJCiWUdL7V1LqqF n8J5Z7Cu/sqRGSr5ww6KY27QHq6TU1WZDsVZiyEWJeKg3HGzp0MUmzMdr7iSZawK gnZxv6qg3+FlSqA30niyAuxEq588vS8uEFjjOfhnNLsUM7FAuFANF5z9bPOhG2qM Xjc3/NY7NsERd9nsIwfRuz0DWni8upvZ39vfeRZ3OAW9NwjRzqXrQiQp08XHa934 z4EBnpcWc9rNSV/3APF/imecBTOoiKtZfzIfILLtOPGE407Bmd8cE8hWyW7ipvrT QU6DIimj3eoMn+elXDfX =M+s5 -----END PGP SIGNATURE-----

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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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