- galaxy-dev - lists.galaxyproject.org

Thread nucleotides onto a protein alignment (back-translation)
by Peter Cock 06 Mar '14

06 Mar '14

Hi all, If anyone is interested, I've just wrapped a little Python script I'd prepared early for use in Galaxy for a fairly common need - "back translating" a protein alignment into a nucleotide alignment by threading the unaligned sequence. We're testing this locally, and barring any major issues I would expect to release this to the main Tool Shed in a week or so - but if any of you want to have a play with it now, and pass on feedback, please do so: Development repository: https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans Test Tool Shed release: http://testtoolshed.g2.bx.psu.edu/view/peterjc/align_back_trans Planned Tool Shed release: http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans (pending) This uses Biopython's AlignIO [*] module and so can handle a range of alignment file formats - for now I have restricted this to "fasta", "clustal" and "phylip" which I believe are all already in use on the tool shed - there is probably scope here for a more coordinated effort to define Galaxy datatypes in this area, including things like the PFAM/Stockholm format and strict/relaxed variants of PHYLIP. Regards, Peter [*] http://biopython.org/wiki/AlignIO

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Uploaded files not previewing at random
by Sanka, Ravi 06 Mar '14

06 Mar '14

Greetings, Since yesterday, I have been experiencing an unusual problem with Uploading files. Seemingly at random, an uploaded will finish successfully (history item in green) but no preview is available. Under the title of the item, the keyword "empty" is found and preview box says "no peek". Such an item cannot be previewed or downloaded; attempts to do so result in this error displayed in the browser: """"""""""""""" OK The requested URL /datasets/{API ID}/display/ was not found on this server. ________________________________ Apache/2.2.25 (Unix) mod_ssl/2.2.25 OpenSSL/1.0.0-fips DAV/2 Server at <our galaxy URL> Port 80 """"""""""""""" However, the Full Path of the item is still valid and, when viewed in command line, shows all the data. Furthermore, the item can still be used in tools and so forth. I and other users have tried multiple attempts at uploading the exact, same file (a small FASTA) and the results are the same: sometimes this issue is present, other times it is not. There seems to be no pattern nor are there any errors in the paster.log. ---------------------------------------------- Ravi Sanka ICS – Sr. Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 ----------------------------------------------

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Cluster jobs running as real user
by Shane Sturrock 06 Mar '14

06 Mar '14

Has anyone had any success in getting cluster jobs running as the real user? I've got our server happily working with LSF via drmaa but all jobs run as the galaxy user and I would like to be able to separate out the jobs on a per user basis. I've followed the instructions at https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#Submitting_… but I'm having no luck with it so was wondering if someone would know how I might debug it, like where could I find the script it is trying to execute? All I'm getting is code 18: invalid LSF job id although it does seem to be creating files in my databases/tmp directory owned by the user. Shane -- Dr Shane Sturrock shane.sturrock(a)biomatters.com Senior Scientist Tel: +64 (0) 9 379 5064 76 Anzac Ave Auckland New Zealand

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Unable to share data
by Sanka, Ravi 06 Mar '14

06 Mar '14

Greetings, I and another individual are attempting to test Galaxy's ability to share data. We have attempted to share histories and workflows, selecting only each other's user email address for people to allow sharing with. All cases have failed, we go to the Shared Data section in both accounts, but nothing appears. Is there some kind of parameter in a config file that must be set to enable sharing? ---------------------------------------------- Ravi Sanka ICS – Sr. Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 ----------------------------------------------

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System developer position available at the University of Oslo, Norway (Galaxy/HyperBrowser work)
by Sveinung Gundersen 05 Mar '14

05 Mar '14

Dear Galaxy developers, The University of Oslo is in the process of hiring a system developer that will partly work on Galaxy-based infrastructure in the context of the ELIXIR infrastructure project, and partly as a developer of the Genomic HyperBrowser and related Galaxy-based analysis software. Please see attached information. The application deadline is very soon: Sunday the 9th of March. Please apply or contact us if you are interested! Regards, Sveinung Gundersen, PhD --- Head Engineer: System developer - ELIXIR infrastructure project/ Bioinformatics core Facility --- Position as Head Engineer, SKO (1087) available for a systems developer as part of the national Elixir project, at the Oslo node, having office at Department of Informatics, University of Oslo. It is a full time position for one year, with possibilities for prolongation. Starting date as soon as possible. The position will be located at the University of Oslo, with possible visits at local Oslo user sites as per arrangement. Languages: Norwegian or English. The ELIXIR project is a part of the recently established European bioinformatics Research infrastructure project (http://www.bioinfo.no/elixir, http://bit.ly/nfr_elixir) The position will also be an integral element of The joint Helse Sør-Øst/UiO bioinformatics core facility, consisting of a group of service personnel with a broad combined bioinformatics competence. We provide services to users in the Oslo region, with an emphasis on the biomedical community. For further description of the range of services provided, please consult the Core Facility web page: http://core.rr-research.no/index.php?section=3. Job Description: The successful candidate will be expected to be part of the service team, as well as to undertake development tasks within the Elixir.no/Bioinformatics core facility infrastructure. An important such task will be to participate in further developmental team effort of the Genomic HyperBrowser (http://hyperbrowser.uio.no) a software system catering to statistical analyses of massive genomic datasets. The aim is to find statistically and biologically significant relations between experimental genomic datasets, typically stemming from high-throughput genome sequencing. This system has been developed in Python (> 90.000 code lines), using NumPy for efficient vector calculations and Rpy2 for connecting to the R statistical platform. The HyperBrowser system has been used in a range of bioinformatics and biomedical research projects, both nationally and internationally, and is also the basis for a growing number of master projects in the Department of Informatics. The initial ELIXIR.NO infrastructure, as well as the HyperBrowser system, is based upon the Galaxy framework (http://usegalaxy.org) which is a leading framework for accessible, reproducible and transparent biomedical research. Setup, tool development and some maintenance of Galaxy installations will preferably also be a part of the position. Qualifications: We are seeking a candidate with a Baceholor level degree (or higher) within computer science and with an interest to work in bioinformatics. Competence within biology or bioinformatics is a bonus, but not a requirement for the position. Prior learning relevant for the particular tasks can compensate education requirement. We are a looking for a candidate with solid experience in Python or other high-level programming languages, furthermore competence/experience in the following areas is desirable: • Algorithms • System architecture/design patterns • Agile/extreme programming • Statistics • Linux Salary: Pay grade 52 – 60 (NOK 435 100 – 499 200 per year) (depending on competence) Application should contain: • Application letter • CV (complete overview of education, work experience and academic work • Copies of educational certificates, transcript of records and letters of recommendation • Names and contact details of 2-3 references (name, relation to candidate and telephone number) Foreign applicants are advised to attach an explanation of their University's grading system. Please remember that all documents should be in English or a Scandinavian language. In accordance with the University of Oslo's equal opportunities policy, we invite applications from all interested individuals regardless of gender or ethnicity. UiO has an agreement for all employees, aiming to secure rights to research results a.o Region: Oslo Job type: Contract Working hours: Full-time Working days: Day Application deadline: March 9, 2014 Location: Blindern Reference number: 2014/1036 Home page: http://www.ifi.uio.no Contacts: • Head Engineer Sveinung Gundersen, E-mail: sveinung.gundersen (at) medisin.uio.no, Telephone: +47 22840862 • Professor II Eivind Hovig, E-mail: ehovig (at) ifi.uio.no --- More information about the position and application form: http://uio.easycruit.com/vacancy/1139753/64290?iso=no

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BOSC 2014 Call for Abstracts
by Dave Clements 05 Mar '14

05 Mar '14

Hello all The call for abstracts for BOSC 2014 is out. See below for details. If you have questions I'm sure that Peter, Brad, Chris, and Hans-Rudolf, all frequent contributors to this list, would be answer them. And glad to see that GigaScience, a GCC sponsor, is also sponsoring BOSC this year. Cheers, Dave C. Call for Abstracts for the 15th Annual Bioinformatics Open Source Conference (BOSC 2014) A Special Interest Group (SIG) of ISMB 2014 Dates: July 11-12, 2014 Location: Boston, MA, USA Web site: http://www.open-bio.org/wiki/BOSC_2014 Email: bosc(a)open-bio.org BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce Important Dates: March 24, 2014: Registration opens for ISMB and BOSC (https://www.iscb.org/ismb2014-registration) April 4, 2014: Deadline for submitting BOSC abstracts (http://www.open-bio.org/wiki/BOSC_Abstract_Submission) May 1, 204: Notification of accepted talk abstracts emailed to authors July 9-10, 2014: Codefest 2014, Boston (http://www.open-bio.org/wiki/Codefest_2014) July 11-12, 2014: BOSC 2014, Boston (http://www.open-bio.org/wiki/BOSC_2014) July 11-15, 2014: ISMB 2014, Boston The Bioinformatics Open Source Conference (BOSC) covers the wide range of open source bioinformatics software being developed, and encompasses the growing movement of Open Science, with its focus on transparency, reproducibility, and data provenance. We welcome submissions relating to all aspects of bioinformatics and open science software, including new computational methods, reusable software components, visualization, interoperability, and other approaches that help to advance research in the biomolecular sciences. Two full days of talks, posters, panel discussions, and informal discussion groups will enable BOSC attendees to interact with other developers and share ideas and code, as well as learning about some of the latest developments in the field of open source bioinformatics. BOSC is sponsored by the Open Bioinformatics Foundation, a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Scien! ce within the biological research community. We invite you to submit one-page abstracts for talks and posters. This year's session topics are: Open Science and Reproducible Research Software Interoperability Genome-scale Data and Beyond Visualization Translational Bioinformatics Bioinformatics Open Source Libraries and Projects Once again we thank Eagle Genomics for sponsoring the BOSC Student Travel Awards, and welcome the open access journal GigaScience as a new sponsor for BOSC 2014. BOSC 2014 Organizing Committee: Nomi Harris and Peter Cock (co-chairs), Raoul Jean Pierre Bonnal, Brad Chapman, Robert Davey, Christopher Fields, Hans-Rudolf Hotz, Hilmar Lapp _______________________________________________ Members mailing list Members(a)lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/members _______________________________________________ Biopython mailing list - Biopython(a)lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biopython -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Graph Datatypes
by Björn Grüning 04 Mar '14

04 Mar '14

Hi, we are currently working on a few graph based tools and we would like to add some new graph-datatypes, namely: gspan, gml, gexf, graphml, pajek. I saw that xgmml and sif are already integrated into core-galaxy and I'm wondering if a PR with these new datatypes would be appropriate or a new toolshed repository? Also, are there any plans to enhance graphview in the near future? Thanks, Bjoern

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Exporting & Importing Tool Shed repository is just great!
by Björn Grüning 04 Mar '14

04 Mar '14

Hi Tool Shed Team! I know I'm always finding bugs and keeping you busy, but this mail is different! The Tool Shed exporting and importing feature is just great, its save so much time and is a pleasure to use. Everyone should try it! So thanks for the hard work you all put into the Tool Shed over the last month. I really enjoy to put my tools into it! Thanks, Bjoern

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Re: [galaxy-dev] Torque.py Bug
by John Chilton 04 Mar '14

04 Mar '14

Great, thanks for testing. This fix has been merged into stable and default branches of galaxy-central. -John On Mon, Mar 3, 2014 at 7:58 PM, ngsflow(a)hygenomics.com <ngsflow(a)hygenomics.com> wrote: > hi,John : > It's ok. > > ________________________________ > ngsflow(a)hygenomics.com > > From: John Chilton > Date: 2014-02-28 22:36 > To: ngsflow(a)hygenomics.com > CC: galaxy-dev > Subject: Re: [galaxy-dev] Torque.py Bug > Thanks for the bug report, that is indeed a problem - I am not sure > how the torque runner here would ever reach a complete job state. I > prefer the following fix however, if you would be willing to verify it > fixes the problem you are encountering I would be happy to apply it to > Galaxy's stable branch. > > diff -r 6a633b37c4c4 lib/galaxy/jobs/runners/cli_job/torque.py > --- a/lib/galaxy/jobs/runners/cli_job/torque.py Fri Feb 28 08:52:52 2014 > -0500 > +++ b/lib/galaxy/jobs/runners/cli_job/torque.py Fri Feb 28 08:32:41 2014 > -0600 > @@ -131,4 +131,5 @@ > def __get_job_state(self, state): > return { 'E' : job_states.RUNNING, > 'R' : job_states.RUNNING, > - 'Q' : job_states.QUEUED }.get(state, state) > + 'Q' : job_states.QUEUED, > + 'C' : job_states.OK }.get(state, state) > > -John > > > On Fri, Feb 28, 2014 at 12:13 AM, ngsflow(a)hygenomics.com > <ngsflow(a)hygenomics.com> wrote: >> Hi, >> >> base: >> os:centos6.4 >> torque:4.2.7 >> >> I built a glaxy cluster today,and then I found the job completion status >> of >> torque queue is 'c',but the need state of galalxy is "ok".So I modified >> the >> torque.py file and solved this error. I do, right? >> >> >> diff -r 8411a9f30feb lib/galaxy/jobs/runners/cli_job/torque.py >> --- a/lib/galaxy/jobs/runners/cli_job/torque.py Thu Dec 19 14:38:03 2013 >> -0500 >> +++ b/lib/galaxy/jobs/runners/cli_job/torque.py Fri Feb 28 13:02:48 2014 >> +0800 >> @@ -117,6 +117,8 @@ >> if id in job_ids: >> state = job.find('job_state').text >> # map PBS job states to Galaxy job states. >> + if state == u'C' : >> + state = 'ok' >> rval[id] = self.__get_job_state(state) >> return rval >> >> ________________________________ >> ngsflow(a)hygenomics.com >> >> ___________________________________________________________ >> 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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reference genome
by Changyu Fan 04 Mar '14

04 Mar '14

Dear Sir or Madam, We have installed our local Galaxy server and everything looks fine. But there are some issues with reference genome index. The BWA and Mageblast is working. Here is how bwa_index.loc looks like: hg18full hg18 Human (Homo sapiens): hg18 Full /u03/galaxy/galaxy_data/hg18/seq/hg18full.fa But Bowtie2, Bowtie, Lastz do not work. When we choose "use a built-in index",nothing is listed in "Select a reference genome:" option. The bowtie2_indices.loc looks like hg18 hg18 Human(hg18) /u03/galaxy/galaxy_data/hg18/hg18full/bowtie2_index/hg18full Here is the directory of bowtie2_index. -rw-rw-r-- 1 galaxy galaxy 964771848 Jan 28 13:41 hg18full.1.bt2 -rw-rw-r-- 1 galaxy galaxy 720355432 Jan 28 13:41 hg18full.2.bt2 -rw-rw-r-- 1 galaxy galaxy 77255 Jan 28 12:49 hg18full.3.bt2 -rw-rw-r-- 1 galaxy galaxy 720355424 Jan 28 12:49 hg18full.4.bt2 lrwxrwxrwx 1 galaxy galaxy 21 Jan 28 12:47 hg18full.fa -> ../../seq/hg18full.fa -rw-rw-r-- 1 galaxy galaxy 964771848 Jan 28 14:38 hg18full.rev.1.bt2 -rw-rw-r-- 1 galaxy galaxy 720355432 Jan 28 14:38 hg18full.rev.2.bt2 We did double check that the tabs was not replaced by multiple spaces in the .loc files. And Galaxy server was restarted each time we changed .loc file. However, There is still no reference is available through the NGS: mapping Bowtie2. How should we debug this? We could not find any errors. Is there any log file we should look into? Anything we missed here? Thanks a lot. Changyu

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