September 2012 - galaxy-dev - lists.galaxyproject.org

Toolsheds and job runners
by Paul-Michael Agapow 07 Sep '12

07 Sep '12

I've "inherited" a galaxy setup from someone (details: a contractor set it up but left it unfinished so I'm completing the job while discovering and documenting what was done). The catch: it's setup as a twin galaxy instance with one as a front-end web-server and the other as the job runner. Admittedly the documentation is lighter on this sort of setup, but I've been able to puzzle it out until getting to the issue of toolsheds. We have a large number of custom tools we want to install from our own toolshed and the main Galaxy one. The problem: I'm not clear on how this supposed to work. Once I started installing tools, of course they all appeared in the front-end toolshed and are running on the front-end. Understandable - but not what I wanted. Does this mean that for every custom tool I install, I have to go to every Galaxy instance (frontend and job-runners) and install the tools into their toolshed? It would seem so, but this seems ... awkward. tl;dr: Toolsheds and job-ruuners - how is that supposed to work? Is there a convenient way to handle this? Any pointers to documentation or experience? -- Paul Agapow (pma(a)agapow.net)

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Adding tool to Galaxy
by kauerbach＠comcast.net 07 Sep '12

07 Sep '12

Hello, Can anyone tell me how to add a tool to Galaxy, to be shown on the panel on the left? In particular, I'd like to add the 'cuffmerge' tool to the cufflinks (RNA seq) group under NGS:RNA Analysis. Other cufflinks tools are there (cufflinks,cuffcompare,cuffdiff), but not cuffmerge. Thank you. '

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Temporary directories
by Joachim Jacob 07 Sep '12

07 Sep '12

Hi all, Just to share some experiences about temporary directories. - System /tmp is best put on a separate partition, with nosuid and noexec set. In /etc/fstab for example UUID=e35e1...d3 /tmp ext4 noexec,nosuid,noatime,nodiratime 0 0 - /tmp needs to be big, because it is used as temporarily storage for FTP upload to your galaxy (and copying from data libraries) - If you set the /tmp as described above, installation of R packages might be not working. /tmp is being used here by default, and no execution is allowed (noexec). If you encounter this, set env variable TMPDIR to some directory with exec perms: export TMPDIR='/var/tmp' before trying installation of R packages. - Of course, Galaxy has it's own temporary directory, set in universe_wsgi.ini as new_file_path (e.g. new_file_path = /mnt/galaxytemp). This is mainly used for tools needing temporary space. However, note that not all tools use this temporary directory, and use the system default. If designing tools however, it is best to pass ${__new_file_path__} in the cheetah template of your tool's xml to the tool, to allow using the Galaxy temporary directory. My 2 cents... if somebody want to add something, please do. Joachim

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How to add cuffmerge?
by kauerbach＠comcast.net 06 Sep '12

06 Sep '12

Hello, Our local installation of Galaxy doesn't have the 'cuffmerge' tool under "NGS:RNA RNA-Seq". It has 'cufflinks', 'cuffcompare', and 'cuffdiff', but no 'cuffmerge', which is essential for the workflow. Could anyone tell me how I could add "cuffmerge" to the list of tools? Thank you very much. Ken.

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get wsgi headers
by Mutlu Dogruel 06 Sep '12

06 Sep '12

Hi folk, Do you know any method for reading (the extended) WSGI HTTP headers from a custom tool? If I put some debugging lines in $galaxy/lib/galaxy/web/framework/middleware/xforwardedhost.py, I can read the HTTP headers I want. But I need to access them under tools/my_script.py. Is there a way to reach the "webapp"s http headers from there? Thanks. Mutlu

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Re: [galaxy-dev] Tools won't go away even after deleting it from tool_conf.xml
by Hans-Rudolf Hotz 06 Sep '12

06 Sep '12

moving to galaxy-dev.... this is probably related to this issue: http://dev.list.galaxyproject.org/problems-with-labels-in-the-tool-box-and-… Hence, try deleting "integrated_tool_panel.xml" first before you do a restart. Regards, Hans On 09/06/2012 01:29 PM, Makis Ladoukakis wrote: > Dear Galaxy users, > > Has anyone experienced this problem before? In my local instance of > Galaxy on a server I've deleted the path of almost all sections with > their corresponding tools from tool_conf.xml (wanting to leave my own > customized section) but after a restart and a new run of the run.sh > there are still two of them (SNP/WGA: Data; Filters andPhenotype > Association) left in the tool list with their first tool also appearing. > Is there a special setting for those two? Can anyone help me? > > Thank you, > Efthymios Ladoukakis > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ >

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Tooshed: latest repository revision on update
by Brad Chapman 06 Sep '12

06 Sep '12

Hi all; I've been working on updating the bam_to_bigwig tool in the Toolshed with an improved wrapper from Peter and Lance: http://toolshed.g2.bx.psu.edu/repository/view_repository?id=2498224736779bdb I pushed updates to the mercurial repository and now the latest revision is at 3:294e9dae5a9b. However, the pull down menu under 'Repository revision' doesn't provide the option to get the more recent revisions. The most recent version is the older 1:0ff100a057ef. Do I need to make any other changes to get the toolshed to recognize the updated revision? Apologies if I'm missing something obvious or have gotten out of sync. I'm trying to catch up on all the great toolshed improvements. Thanks much, Brad

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Re: [galaxy-dev] [galaxy-user] git mirror
by Shantanu Pavgi 05 Sep '12

05 Sep '12

On Sep 5, 2012, at 4:55 AM, Luca Pireddu wrote: > On 09/05/2012 01:30 AM, Peter Cock wrote: >> On Tue, Sep 4, 2012 at 5:57 PM, Luca Pireddu <pireddu(a)crs4.it> wrote: >>> Hello list. >>> >>> A simple question: is there a git mirror of the Galaxy repositories? If >>> not, what do git users here do to work with the Galaxy code base? >>> >>> Thanks, >> >> I don't think there is an official git mirror, but even if there was it >> wouldn't help for pushing changes or suggestion into Galaxy. >> >> Speaking as a git user who only has to use hg for Galaxy, I just >> learnt enough hg to get the basics done, and frequently consult >> resources like this: >> http://mercurial.selenic.com/wiki/GitConcepts#Command_equivalence_table >> >> Peter > > Similarly, I'm also a git user who's faced with the prospect of using Mercurial only for Galaxy. Sure, the two tools work in similar ways, but it's still something I'd rather avoid for a number of reasons. > > I noticed that BitBucket is now offering both mercurial and git access. Maybe there's an easy way projects can offer access to their repositories through both tools? > > A solution I'm trying at the moment is git-hg (https://github.com/cosmin/git-hg) Seems to work...I've managed to clone the galaxy-dist repository as a local git repository. > I have been using git to track all local changes for more than a year now. I had looked into possible git-hg integration tools, but I hadn't found this git-hg tool back then. So I started using following workaround, but it doesn't track/convert upstream commit database in the git repo. A pristine copy of upstream galaxy-dist code is maintained in a branch called upstream-tracker. The mercurial database is not tracked by git, but it's present in my development env's working directory. When I want to get latest changes from upstream galaxy-dist I perform following steps: * checkout git controlled upstream-tracker branch and perform 'hg pull -u' to get latest code * commit updated code in git and record hg revision number in git-commit for reference And then to merge upstream code in our git repo: * create a new branch for merge operation starting from latest git master/develop branch * merge updated upstream-tracker branch with the merge operation branch * resolve conflicts, test the code and then merge with the master/develop branch I am going to try out this git-hg tool as well, but I am not sure how would I get my local git repository changes in this new git-hg cloned repo now. Thank you Luca for pointing out this git-hg tool. -- Shantanu

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Would like to Post to Galaxy List
by Gloria 05 Sep '12

05 Sep '12

I would like to be able to post questions to the galaxy-dev and/or galaxy-user lists. I am using Galaxy with Amazon Cloud EC2. Could I have my name added to the list? Gloria I tried registering myself under my university's email: gkreitinger(a)wisc.edu

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fetch sequences
by Deepthi Theresa 05 Sep '12

05 Sep '12

Hi all, I want to fetch sequences from a file(in interval format) using custom genome build(using built-in index). How can I do that? I tried "fetch sequences" in the menu. But I could not find option for a custom genome. Thanks, Deeps

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