Re: [galaxy-dev] Galaxy and ENCODE

It's an excellent idea . Does anybody have a document around the work package ? I'm sure that many people will be happy to participate. Victoria On Mon, Nov 19, 2012 at 8:03 PM, Scooter Willis hwil...@scripps.edu wrote: Thank you for the clarification. Would be an interesting project for a

[galaxy-dev] Unable to run jobs in Galaxy: runners/local.py # stdout_file.close() # python2.7/tempfile.py # self.unlink(self.name) # OSError: [Errno 2] No such file or directory

Hi all Since updating to the latest Galaxy-dist version, I'm unable to run any jobs. galaxy.jobs.handler INFO 2012-11-20 12:22:09,018 (6403) Job dispatched galaxy.objectstore CRITICAL 2012-11-20 12:22:15,362 /home/galaxy/galaxy-dist/database/job_working_directory/006/6403 delete error [Errno 2]

[galaxy-dev] format sensitive tools not working properly after upgrade

I performed an upgrade over the weekend. Since then, I've observed an odd behavior - bowtie2 will not list the new fastqsanger files in my history. It will work with files that had already been groomed before the upgrade. I also see that the groomer is not recognizing fastq files. The format

Re: [galaxy-dev] First questions from a new developer

Thanks James - I had figured out that I needed to restart the server after changing config files, and the debug info you sent was helpful. Thanks for taking the time to respond. Joshua On Mon, Nov 19, 2012 at 10:38 AM, James Taylor ja...@jamestaylor.orgwrote: On Fri, Nov 16, 2012 at 2:35

Re: [galaxy-dev] DRMAA job will now be errored - Segmentation fault

On Thu, Nov 15, 2012 at 11:21 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Nov 15, 2012 at 10:12 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Nov 15, 2012 at 10:06 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, Something has changed in the job handling, and

[galaxy-dev] Where is the eye icon for datasets in error state?

Hey devs!   It seems that many things related to history datasets has changed since I have updated my local Galaxy instance and the current version.   Unfortunately it seems that one cannot Display data in browser (eye icon) if the dataset is in error state. Where can I get that feature

Re: [galaxy-dev] Where is the eye icon for datasets in error state?

Let me echo Sascha. I've been thinking about this problem. I suggest that we need an Error Document dataset type that contains two kinds information: 1. which will help the end user correct the problem (E.g. Please be sure to use MAF files not BAM files etc). 2. which will help tool developers

[galaxy-dev] Direct access the fastq files stored in galaxy server local storage

We have a local galaxy server. I know I can get data by ftp, upload directly from browser, or by a URL. If I have some fastq files in the Galaxy server local storage, is it possible to let Galaxy use it directly? Thanks, Fenglou ___ Please

[galaxy-dev] Move files between histories?

Hello Is it possible to move a file from one history to another? I have generated BAM files in separate histories that now must be merged. How can I do this without downloading and then uploading the files? Thanks, Gregory Thyssen, PhD Molecular Biologist Cotton Fiber Bioscience USDA-ARS-Southern

[galaxy-dev] NGS assembly?

Hello I would like to assemble my Illimuna reads along with some Sanger reads. Is Velvet or ABySS hidden somewhere in the menu? Please advise. Thanks, Gregory Thyssen, PhD Molecular Biologist Cotton Fiber Bioscience USDA-ARS-Southern Regional Research Center 1100 Robert E Lee Blvd New Orleans, LA

Re: [galaxy-dev] Direct access the fastq files stored in galaxy server local storage

I don't think this is possible. Galaxy is designed to import data files and track their relationships and disk usage internally. You can import lots of files at once though.. see: http://wiki.galaxyproject.org/Admin/Data%20Libraries/Uploading%20Library%20Files Brad On Nov 20, 2012, at 3:49

Re: [galaxy-dev] Move files between histories?

Yes. If you click on the little sprocket icon in your history panel and go to Copy Datasets, you'll be able to do this. -Dannon On Nov 20, 2012, at 2:52 PM, Thyssen, Gregory - ARS gregory.thys...@ars.usda.gov wrote: Hello Is it possible to move a file from one history to another? I have

Re: [galaxy-dev] NGS assembly?

Hello Gregory, The Tool Shed has some assembly tools that you would be able to use with a local or cloud instance. Please see: http://toolshed.g2.bx.psu.edu/ Under Category name: Assembly Help with the tool shed and local/cloud Galaxy instances is in our wiki:

Re: [galaxy-dev] Direct access the fastq files stored in galaxy server local storage

This is actually possible using data libraries. What you'd want to do is upload by filepath (described in the wiki page Brad linked, heading Upload files from filesystem paths) and check the No box under Copy data into Galaxy. -Dannon On Nov 20, 2012, at 4:13 PM, Langhorst, Brad

Re: [galaxy-dev] Multiple language in one tool

Hi Philippe: You can just wrap a bash script if you want to to that… or even write a simple pipeline in the xml wrapper with interpreter='bash' or no interpreter at all. I've done that sort of thing before with good results. brad On Nov 20, 2012, at 10:03 PM, Philipe Moncuquet

Re: [galaxy-dev] Multiple language in one tool

Hi Brad, Thanks a lot for that tip, will try that. Cheers, Philippe 2012/11/21 Langhorst, Brad langho...@neb.com Hi Philippe: You can just wrap a bash script if you want to to that… or even write a simple pipeline in the xml wrapper with interpreter='bash' or no interpreter at all.