galaxy-dev April 2016

galaxy-dev@lists.galaxyproject.org

47 participants
55 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 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 19 Oct '16

19 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 23 Jun '16

23 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 09 Jun '16

09 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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Refresh of screens in Galaxy Docker environment
by George Weingart 23 May '16

23 May '16

Hello, We are installing Galaxy in a Docker environment and we are encountering an issue where we need to refresh the screen (For Example, using F5) in order to see the status of the job. We see that using chrome as browser. If we don't refresh the screen, it stays (The job might have completed long ago but it still shows executing in yellow) Any suggestions how to resolve the problem? Thanks! George Weingart

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Re: [galaxy-dev] iRODS
by Dan Bedard 13 May '16

13 May '16

The iRODS dev team is certainly interested in how people are using and want to use iRODS with Galaxy. Mikael, we would be happy to host the PDF and/or a guest blog post about making it work. And we can provide some assistance if there are difficulties on the iRODS side of this. Cheers, Dan Bedard — Dan Bedard Executive Director iRODS Consortium mobile: 1-919-346-3262 email: danb(a)renci.org twitter: @DataDanB iRODS User Group Meeting 2016 June 7-9 -- Chapel Hill, NC -- https://irods.org/ugm2016 > Message: 2 > Date: Wed, 9 Mar 2016 01:24:24 +0000 > From: "Kandalaft, Iyad" <Iyad.Kandalaft(a)AGR.GC.CA> > To: James Taylor <james(a)bx.psu.edu>, Mohamed Kassam > <k.mamoud(a)gmail.com> > Cc: "galaxy-dev(a)lists.galaxyproject.org" > <galaxy-dev(a)lists.galaxyproject.org> > Subject: Re: [galaxy-dev] iRODS > Message-ID: > <CA1994D763C7444CB37EFC823D43C3824933F672(a)ONOTTAXES1.AGR.GC.CA> > Content-Type: text/plain; charset="us-ascii" > > We were considering implementing data pull/push tools for Galaxy-iRODS integration but we haven't started work on that. > I recall that the Galaxy team looked at backing Galaxy with iRODS but moved away from the idea. There was a trello card with that information. > > > Iyad Kandalaft > Bioinformatics Systems Developer > Microbial Biodiversity Bioinformatics > Science & Technology Branch > Agriculture & Agri-Food Canada > Iyad.Kandalaft(a)agr.gc.ca | (613) 759-1228 > > ________________________________________ > From: galaxy-dev [galaxy-dev-bounces(a)lists.galaxyproject.org] on behalf of James Taylor [james(a)bx.psu.edu] > Sent: March 8, 2016 10:09 AM > To: Mohamed Kassam > Cc: galaxy-dev(a)lists.galaxyproject.org > Subject: Re: [galaxy-dev] iRODS > > Mohamed, > > We implemented but never deployed the iRODS object store, so I suspect > it has not been tested much. If anyone out there is using it please > let us know. > > On Mon, Mar 7, 2016 at 10:30 AM, Mohamed Kassam <k.mamoud(a)gmail.com> wrote: >> Dear all, >> I would like to use our interlan iRODs to pull data. >> I searched and i find that there is an object store for that. >> How it works ? DO I need to configure something else ? >> >> Thanks in advance, >> >> >> Mohamed >> >> ___________________________________________________________ >> 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: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > > ------------------------------ > > Message: 3 > Date: Wed, 9 Mar 2016 12:01:38 +0100 > From: Mikael Loaec <mikael.loaec(a)versailles.inra.fr> > To: galaxy-dev(a)lists.galaxyproject.org > Cc: Olivier Inizan <Olivier.Inizan(a)versailles.inra.fr> > Subject: [galaxy-dev] iRODS > Message-ID: <56E00292.5070604(a)versailles.inra.fr> > Content-Type: text/plain; charset=utf-8 > > Hi, > > @URGI, we have sucessfully tested connexion of galaxy instance with an > iRODS. > We have a pdf doc 67ko) explaining how we implement it if you want, but > don't know if i can send attachement on this mailinglist ? > > We (URGI) are also very interresting in data pull/push tools for > Galaxy-iRODS integration. Let us know when you will begin working on it. > > Regards, > > Mikael LOAEC > Systems and Networks Administrator > URGI INRA > > > ------------------------------ > > Message: 4 > Date: Wed, 9 Mar 2016 12:43:36 +0100 > From: Mohamed Kassam <k.mamoud(a)gmail.com> > To: Mikael Loaec <mikael.loaec(a)versailles.inra.fr> > Cc: galaxy-dev(a)lists.galaxyproject.org, Olivier Inizan > <Olivier.Inizan(a)versailles.inra.fr> > Subject: Re: [galaxy-dev] iRODS > Message-ID: > <CAJrYSO8e2dfb2JjdAqCB9CFkg=NELV8vrBCrwnQQ-FpKjU6Pkw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Thank you for your message, > > I sent to you Mikael an email if you can semd your pdf. > > It is a good idea to see if in The galaxy dev team they can integrate iRODS > for the next release. > > Best regards, > > Mohamed > > 2016-03-09 12:01 GMT+01:00 Mikael Loaec <mikael.loaec(a)versailles.inra.fr>: > >> Hi, >> >> @URGI, we have sucessfully tested connexion of galaxy instance with an >> iRODS. >> We have a pdf doc 67ko) explaining how we implement it if you want, but >> don't know if i can send attachement on this mailinglist ? >> >> We (URGI) are also very interresting in data pull/push tools for >> Galaxy-iRODS integration. Let us know when you will begin working on it. >> >> Regards, >> >> Mikael LOAEC >> Systems and Networks Administrator >> URGI INRA >> ___________________________________________________________ >> 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: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > -------------- next part --------------

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galaxy-dev April 2016