Re: [galaxy-dev] suggestion for multithreading

2011-08-08 Thread Andrew Warren
So would the current correct method for setting up multi-threaded jobs on a cluster be to specify custom runners in the [galaxy:tool_runners] section of the universe config file for EVERY tool that uses a multiple threads (assuming the default is set to one)? For example, for the bowtie program

Re: [galaxy-dev] galaxy-dev Digest, Vol 63, Issue 8

2011-09-08 Thread Andrew Warren
I would also like to voice my support for this feature. I wrote a wrapper for bowtie that converts the SAM output to BAM after bowtie is finished just to avoid the hassle of letting galaxy know that the SAM file existed (didn't want to run Tophat). After thinking about how I would go about

[galaxy-dev] an attempt on multiple multiple inputs

2011-11-07 Thread Andrew Warren
8cf8d25557b2 Hope this helps somebody. Andrew Warren ___ 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

[galaxy-dev] bug? workflow controller item slug for shared workflows

2011-11-10 Thread Andrew Warren
. There is a loop there for slug creation and the following check OUTSIDE the loop: if slug_set: trans.sa_session.flush() Should that be in the loop? Otherwise its just flushing the session if the last workflow gets a slug created. -Andrew Warren

[galaxy-dev] software installs: PATH vs env.sh

2012-01-21 Thread Andrew Warren
with our galaxy setup? I think we recently pulled updates for some major tool_shed release but I haven't been able to determine if any of the tools listed above were affected by that. Wish I were in Český Krumlov asking this question. Missed the registration deadline...doh. Thanks, Andrew Warren

Re: [galaxy-dev] software installs: PATH vs env.sh

2012-01-24 Thread Andrew Warren
the registration deadline...doh. Thanks, Andrew Warren __**_ 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

Re: [galaxy-dev] software installs: PATH vs env.sh

2012-01-25 Thread Andrew Warren
-V -cwd works for me. On Wed, Jan 25, 2012 at 12:12 PM, Andrew Warren anwar...@vbi.vt.edu wrote: Thanks for the replies. One extra element I failed to properly describe is that we are running on a cluster with a similar setup to CloudMan. This means we have a galaxyTools/tools

[galaxy-dev] advanced parameters: all or nothing?

2012-02-09 Thread Andrew Warren
without using all of them. Cheers, Andrew Warren ___ 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] advanced parameters: all or nothing?

2012-02-20 Thread Andrew Warren
, Peter Cock p.j.a.c...@googlemail.comwrote: On Fri, Feb 10, 2012 at 4:18 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote: On Thu, Feb 9, 2012 at 11:27 PM, Andrew Warren anwar...@vbi.vt.edu wrote: Hello, I was recently adjusting advanced parameters when running Tophat in Galaxy and noticed

[galaxy-dev] potential bug in DefaultToolAction collecting chrom info

2012-03-20 Thread Andrew Warren
Hello, In the file lib/galaxy/tools/actions/__init__.py for the execute function of the DefaultToolAction class line 198 has the following code: if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in trans.user.preferences[ 'dbkeys' ] ): In this case

[galaxy-dev] Unable to read builds file: publicbuilds.txt

2012-08-21 Thread Andrew Warren
. Is the best way to deal with this just to create these files (even though I am not using them)? Are these files being read every time a web transaction goes down due to the property in lib/galaxy/web/framework/__init__.py ? @property def ucsc_builds( self ): Thanks, Andrew Warren

[galaxy-dev] ENA galaxy import link broken?

2013-08-13 Thread Andrew Warren
? Thanks for any help, Andrew Warren ___ 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-dev] SLURM and hidden success

2013-11-08 Thread Andrew Warren
Hello all, We are in the process of switching from SGE to SLURM for our galaxy setup. We are currently experiencing a problem where jobs that are completely successful (no text in their stderr file and the proper exit code) are being hidden after the job completes. Any job that fails or has some

Re: [galaxy-dev] SLURM and hidden success

2013-11-11 Thread Andrew Warren
the corresponding dataset via the history API or in the database and determine if they indeed are having visible set to False - this I guess is what should cause a dataset to become hidden? -John On Fri, Nov 8, 2013 at 11:40 AM, Andrew Warren anwar...@vbi.vt.edu wrote: Hello all, We

[galaxy-dev] large drill down selection UI component?

2014-11-12 Thread Andrew Warren
Hi all, I was wondering if there were any existing implementations of, or any plans for, a drill down selection component that supports thousands of items? For example a taxonomy based drill down. Thanks, Andrew ___ Please keep all replies