galaxy-dev April 2016

galaxy-dev@lists.galaxyproject.org

47 participants
55 discussions

Re: [galaxy-dev] [galaxy-bugs] Galaxy tool error report from etiennewalex@yahoo.fr (megablast_wrapper)
by Jennifer Hillman-Jackson 02 Apr '16

02 Apr '16

Hi Etienne, Sorry, I didn't notice that the job was run on the test server. The root of the problem could be that the job output exceeds quota. Running the job there will not get around quota, even if the tool has other issues on test that are triggering the failure (is possible - we do test on that server). If the tool did run, and the output hits your account, if it is over quota (10 GB) no more jobs will be permitted to run. It might be best to consider using a local or cloud Galaxy. I do not know when the Fetch Taxonomy tool will be restored to Main (or if yet). Thanks, Jen -- Jennifer Hillman-Jackson Galaxy Application Support http://usegalaxy.org http://galaxyproject.org http://biostar.usegalaxy.org On Thu, Mar 31, 2016 at 9:08 PM, etienne waleckx <etiennewalex(a)yahoo.fr> wrote: > Gracias Jenifer, > > I re-ran the tool but the same happens. It is strange as when running the > same tool with the same file in usegalaxy it is working well but I can't in > testgalaxy. > I want to run it in testgalaxy so I can use the fetch taxonomic > representation tool after. I already have the Megablast file but I can't > upload it directly to testgalazxy as it semms too big, so I would like to > run the megablast in testgalaxy, then fetch taxonomic representtion. > > Thanks for your help! > > Etienne > > > > > ------------------------------ > *De :* Jennifer Hillman-Jackson <jen(a)galaxyproject.org> > *À :* "galaxy-bugs(a)bx.psu.edu" <galaxy-bugs(a)bx.psu.edu> > *Cc :* etiennewalex(a)yahoo.fr > *Envoyé le :* Jeudi 31 mars 2016 18h03 > *Objet :* Re: [galaxy-bugs] Galaxy tool error report from > etiennewalex(a)yahoo.fr (megablast_wrapper) > > Hello, > > Please re-run the tool as this was most likely a transient cluster failure. > > Our apologies for any confusion, > > Jen > > -- > Jennifer Hillman-Jackson > Galaxy Application Support > http://usegalaxy.org > http://galaxyproject.org > http://biostar.usegalaxy.org > > > On Wed, Mar 30, 2016 at 11:09 PM, <galaxy-bugs(a)bx.psu.edu> wrote: > > > GALAXY TOOL ERROR REPORT > ------------------------ > > This error report was sent from the Galaxy instance hosted on the server > "https://test.galaxyproject.org/" > > ----------------------------------------------------------------------------- > This is in reference to dataset id 763833 (c5a49985053f8bd3) from history > id 328501 (aa1b4cb871c5e196) > > ----------------------------------------------------------------------------- > You should be able to view the history containing the related history item > (83ca2a7d5534e19e) > > 2: Megablast on data 1 > > by logging in as a Galaxy admin user to the Galaxy instance referenced > above > and pointing your browser to the following link. > > https://test.galaxyproject.org/history?id=aa1b4cb871c5e196 > > ----------------------------------------------------------------------------- > The user 'etiennewalex(a)yahoo.fr' provided the following information: > > Hi, > > Can you help me? I don't find why the tool is not running with this > dataset, > > Thanks! > > Etienne > > ----------------------------------------------------------------------------- > info url: > https://test.galaxyproject.org/datasets/83ca2a7d5534e19e/show_params > job id: 529174 (5c8c4452f3c278b5) > tool id: > toolshed.g2.bx.psu.edu/repos/devteam/megablast_wrapper/megablast_wrapper/1.… > tool version: 1.2.0 > job pid or drm id: 529174 > job tool version: None > > ----------------------------------------------------------------------------- > job command line: > None > > ----------------------------------------------------------------------------- > job stderr: > > > ----------------------------------------------------------------------------- > job stdout: > > > ----------------------------------------------------------------------------- > job info: > Remote job server indicated a problem running or monitoring this job. > > ----------------------------------------------------------------------------- > job traceback: > None > > ----------------------------------------------------------------------------- > (This is an automated message). > > > > >

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About Local Galaxy Tool Problem
by Ferhat Güzel 02 Apr '16

02 Apr '16

Hi, I want to convert .bcl file (data from illumina NextSeq500) to fastq. Firstly, i tried Galaxy on public server and it became success. But i have large dataset and i couldnt wait for weeks to solve. Then, i set up Galaxy locally. But most of tools dissappared in menu. I tried to upload published workflows but i had too many errors. I couldnt do any analysis on local host. What can i do now? Regards, Ferhat GÜZEL

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IUC Hackathon - Conda dependencies
by Rémi MARENCO 02 Apr '16

02 Apr '16

Hi! On monday 04/04, @bgruening <https://github.com/bgruening> and some members of Galaxy team (me and @nitesh1989 <https://github.com/nitesh1989> at least) would want to get a Hackathon on adding IUC / Devteam tools Conda dependencies. Hackathon begins at: 2pm (UTC-4) / 8pm (UTC+2). It will be as following: - @bgruening <https://github.com/bgruening> will give a small introduction how to create a recipe and the scripts involved in it] - Introduce everyone to conda and bioconda - Then we pick a simple tool and create it - @bgruening <https://github.com/bgruening> will provide a list with bugs that needs to be fixed on the framework level Aims: - get familiar with conda packaging the conda-Galaxy integration - remove tools from the testing blacklists: 1 <https://github.com/galaxyproject/tools-iuc/blob/master/.tt_blacklist> 2 <https://github.com/galaxyproject/tools-devteam/blob/master/.tt_blacklist> 3 <https://github.com/bgruening/galaxytools/blob/master/.tt_blacklist> - Integrate Travis-conda testing in GalaxyP - Integrate Travis-conda testing in galaxy_blast (@peterjc <https://github.com/peterjc>?) Infrastructure work: - galaxyproject/galaxy#2047 <https://github.com/galaxyproject/galaxy/issues/2047> - condarc is update if you add new channels, but you can not remove channels - conda is not working in the Galaxy Docker image - bioconda needs to archive all tarballs to depot.galaxyproject.org - Galaxy Admin support to remove environments Let us know <https://github.com/galaxyproject/tools-iuc/issues/700> if you are interested :). Regards, Bjorn, Remi and the Galaxy Team

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Sandbox repository item says "This revision can be installed: False
by rbrown1422＠comcast.net 02 Apr '16

02 Apr '16

Good afternoon, I loaded a tool into the Galaxy https://testtoolshed.g2.bx.psu.edu/ toolshed. It is an xml and python module. It accepted the file fine but with the following output Sharable link to this repository:https://testtoolshed.g2.bx.psu.edu/view/insilico-bob/mean_center… Clone this repository:hg clone https://insilico-bob@testtoolshed.g2.bx.psu.edu/repos/insilico-bob/mean_cen… Repository type:Unrestricted This repository's type cannot be changed because its contents are valid only for its current type or it has been cloned. Revision:4:ac64a6acfdaf This revision can be installed: False Times cloned / installed: 0 =========================== I cannot see the tool when I search on it from my Galaxy instance or from the test shed itself. FYI, I did not add a test scenario to the load. What am I missing? How do I correct this. thanks, Bob

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Problem on postgress database
by jarod_v6＠libero.it 01 Apr '16

01 Apr '16

Hi! I have centos 6.7 and I have install galaxy. I setup galaxy.ini with: database_connection = postgresql://user:password@localhost/galaxydb # TYPE DATABASE USER CIDR-ADDRESS METHOD # "local" is for Unix domain socket connections only local all all trust # IPv4 local connections: host all all 127.0.0.1/32 trust # IPv6 local connections: host all all ::1/128 trust host all all 0.0.0.0/0 trust host all all 127.0.0.1/32 trust host galaxydb galaxy 127.0.0.1/32 md5 and I have the database postgres=# \l List of databases Name | Owner | Encoding | Collation | Ctype | Access privileges -------------+----------+----------+-------------+-------------+----------------------- galaxy_prod | postgres | UTF8 | en_US.UTF-8 | en_US.UTF-8 | =Tc/postgres : postgres=CTc/postgres : galaxy=CTc/postgres galaxydb | postgres | UTF8 | en_US.UTF-8 | en_US.UTF-8 | =Tc/postgres : postgres=CTc/postgres : galaxy=CTc/postgres what can I do?

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galaxy-dev April 2016