[galaxy-dev] HMMER wrappers
Hello all, Has anyone done a wrapper for HMMER2 or HMMER3? http://hmmer.janelia.org/software I can't find anything in the Tool Shed http://toolshed.g2.bx.psu.edu/ so we are likely to look into doing this ourselves - starting with hmmerscan. Thanks, Peter ___ 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/
[galaxy-dev] NFS, Cluster and working directories questions
Hello, We're currently trying to switch to a big cluster but we have a lot of doubts and questions, especially since the I/O is a serious issue for our NFS. - We saw the outputs_to_working_directory option in the .ini file, but it only concerns output files, is there a way to make a local copy of all the input files in the job working directory? (including indices) - Can we set the job working directory as an absolute path so it's local to the nodes, like /tmp ? - If it's possible, will the job working directories created for each job be cleaned properly at the end? Thanks, L-A ___ 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/
[galaxy-dev] Galaxy-Development site error
Good Morning, I have been attempting to go to the the Galaxy-Dev site this morning at http://gmod.827538.n3.nabble.com/Galaxy-Development-f815885.html and Get a Content Encoding Error message. The error says that The page you are trying to view cannot be shown because it uses an invalid or unsupported form of compression. This happens with Firefox 3.6.27, but not with Crome or Safari. By default I use Firefox 3.6.x due to performance issues with the later versions. Thanks, Iry Witham Scientific Applications Administrator Scientific Computing Group Computational Sciences Dept. The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6744 email: iry.wit...@jax.org ___ 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/
[galaxy-dev] [API] allow_user_impersonation
Hello everyone! I just wanted to know if the user impersonation will be available through the API someday :) It could be veeery useful for triggering automatic QA on the data without having to share the resulting histories afterwards. Best regards, L-A ___ 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/
Re: [galaxy-dev] [API] allow_user_impersonation
Hi L-A, This exists. See your universe_wsgi for the following lines: # Optional list of email addresses of API users who can make calls on behalf of # other users #api_allow_run_as = None And then with any api call from a user in the allow list above you can add an extra parameter to the request, 'run_as' with the value being the encoded user ID you wish to impersonate. Good luck! Dannon On Feb 28, 2012, at 10:18 AM, Louise-Amélie Schmitt wrote: Hello everyone! I just wanted to know if the user impersonation will be available through the API someday :) It could be veeery useful for triggering automatic QA on the data without having to share the resulting histories afterwards. Best regards, L-A ___ 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/ ___ 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/
Re: [galaxy-dev] Problem previewing a tool in the Toolshed
Hi Carlos, I've uploaded a fix for the problem you saw when attempting to reset all metadata on your cummerbund tool. Thanks for reporting this issue. Looking at your change sets, it seems that you are attempting to use the public tool shed hosted by Penn State as a source code repository for your tool development efforts. If so, this is not the intent the public tool shed - it's intent is rather to share fully functional tools with others in the Galaxy community (fully functional implies that the tools was developed in an environment that included a Galaxy instance, and the tool proved to be functional within the Galaxy instance before it was uploaded to the tool shed). The tool shed inspects every change set and performs certain functions based on the content of the change set. For example, if a change set includes a tool, an attempt to load the tool will be made to generate information about the tool. Data types included in a change set are processed as well. Because of this, it is best to upload changes to the tool shed that contain development efforts that are in a finished state. See my additional inline comments and questions in your message. Thanks! Greg Von Kuster On Feb 15, 2012, at 2:24 PM, Carlos Borroto wrote: Hi Greg, Thanks for your answer. Would be great to get the tool to preview correctly but is not a big deal. I'm having a few more problems. I'm getting this error from time to time when I do hg push or even when I delete all files from the toolshed and upload new ones: Version information for the tools included in the cummerbund repository is missing. Reset all of this repository's metadata in the tool shed, then set the installed tool versions from the installed repository's Repository Actions menu. The fix that I've pushed to the tool shed should hopefully resolve this issue. Doing a Reset metadata in the toolshed doesn't solve this issue. I can't find how to do then set the installed tool versions from the installed repository's Repository Actions menu. I'm also having problem including a datatype with the tool. One of the outputs of the tool is a sqlite database. I have this datatypes_conf.xml: ?xml version=1.0? datatypes registration datatype extension=sqlite type=galaxy.datatypes.binary:Binary mimetype=application/octet-stream subclass=True display_in_upload=true/ /registration /datatypes Still sqlite doesn't appear as an option when I try to upload a file to Galaxy. The new datatype does appear if I choose the edit a dataset attributes. I'm not quite sure what your intentions are here, but attempting to make a Galaxy datatypes be a sqlite database sounds like it will be complex and fragile, Lastly, when I try to upload a sqlite database I get this error: An error occurred running this job: The uploaded binary file contains inappropriate content Uploading a sqlite database to the tool shed will certainly result in this behavior as our code inspectors will not handle this types o content. $ file -i cummerbund.sqlite cummerbund.sqlite: application/octet-stream; charset=binary I was hoping by including a sqlite datatype this would be resolved. Thanks, Carlos On Tue, Feb 14, 2012 at 3:10 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Carlos, Not every tool form parameter will properly display when previewing the tool in the tool shed because the tool shed doesn't have access to some Galaxy components (e.g., a Galaxy history ) that are required for some tool parameter types. When I get a chance, I'll take a closer look, but if your tool is functional when installed from the tool shed to a local Galaxy instance, all should be ok. Thanks for your contribution! Greg Von Kuster On Feb 14, 2012, at 1:49 PM, Carlos Borroto wrote: Hi, I'm currently developing my first Galaxy tool. I'm working on a wrapper for R's library cummeRbund[1]. I got to the point where the tool although incomplete on functionality, I think is ready to be uploaded to the Toolshed. I was able to do so. I also made sure I could then install it on my local instance using the toolshed repository. Everything is working as expected, except, the tool preview is not working correctly. There is no error, but the inputs, most of them conditional inputs, aren't being displayed correctly. This is the direct link to the tool in the test toolshed: http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?operation=view_or_manage_repositoryid=575665a9f01c6d41 [1]http://compbio.mit.edu/cummeRbund/ Kind regards, Carlos ___ 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/ ___ Please keep all replies on the list by using
Re: [galaxy-dev] Timeout and Galaxy - Cluster could not complete job
i believe the latest stable update of galaxy included changes to drmaa.py which allows a job to be rechecked indefinitely with regard to scheduler communication errors, so perhaps your cluster could not complete job errors are due to a filesystem race condition, whereby the cluster node completes the job but the inode metadata table updates haven't propagated completely so the files appear to be missing to the job runner, on a different server. in this case, the config variable you want to increase is the new retry_job_output_collection, also part of the last update to stable. On Wed, Feb 22, 2012 at 5:52 AM, Aurélien Bernard aurelien.bern...@univ-montp2.fr wrote: Hello everybody :) Today, I have a question related to timeout management in Galaxy. More particularly, I'm searching for a way to set (in a configuration file if possible) all timeouts related to DRMAA and timeouts related to communication between Galaxy and SGE. My goal is to increase current timeouts to avoid the Cluster could not complete job error on successful jobs when there is a temporary problem of job status checking (due to heavy write load on the hard drive or whatever). Is this possible ? Thank you in advance, Have a nice day A. Bernard -- Aurélien Bernard IE Bioprogrammeur - CNRS Université des sciences Montpellier II Institut des Sciences de l'Evolution France __**_ 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/ ___ 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/
Re: [galaxy-dev] Tutorials for SICER
H.K., Are your questions related to Galaxy, or SICER? Galaxy doc is available at http://wiki.g2.bx.psu.edu/Learn. SICER doc is at http://home.gwu.edu/~wpeng/Software.htm. I don't think there is any particular doc on running SICER under Galaxy. Dave C. On Tue, Feb 28, 2012 at 1:14 AM, Vidya .H.K hvi...@ibab.ac.in wrote: Hi, I am exploring SICER peak calling tool for ChIP seq data analysis. Can anyone suggest me tutorial site for galaxy SICER tool?? Regards H.K.VIDYA ___ 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/ -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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/
Re: [galaxy-dev] HMMER wrappers
Hi Peter, I think hmmerscan has been wrapped, but there is a missing e in the repository name. Look for hmmscan in the toolshed. The description for it is: hmmscan, for searching pfam with AA seqs. also included is hmm datatypes although hmmbuild, etc. isnt included yetX ill try to finish the rest of the hmmer suite soon Does that help? Dave C. On Tue, Feb 28, 2012 at 2:31 AM, Peter Cock p.j.a.c...@googlemail.comwrote: Hello all, Has anyone done a wrapper for HMMER2 or HMMER3? http://hmmer.janelia.org/software I can't find anything in the Tool Shed http://toolshed.g2.bx.psu.edu/ so we are likely to look into doing this ourselves - starting with hmmerscan. Thanks, Peter ___ 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/ -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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/
