Hi andrew
What you need to do is to add the qsub parameter '-sync y'. This puts a
hold on the qsub command and makes it wait until the SGE job is finished.
regards
Bram
On 05/04/2011 18:27, andrew stewart wrote:
I'm aware of how to configure Galaxy to use SGE in universe_wsgi.ini,
however wh
Hi Peter,
I get the same error here.
Florent
On 06/04/11 01:50, Peter Cock wrote:
Hi all,
I had wondered why none of the tools on the Galaxy Tool Shed had a
rating, and had assumed it was just that so far no-one had bothered. I
have a new theory, it doesn't work?
I just viewed Brad's "BAM to
I've performed an alignment using BWA on a file of paired-end illumina
reads. The SAM file looks fine, and contains header information. I'm
converting it to BAM using the sam to bam converter, however it
consistently errors out after running for a while. The error is:
"Error extracting alig
I just tried via command line and re-did the steps that Galaxy attempted on the
same files. I got through the samtools sorting of the bam file without a
problem, but then soon saw the same error when I tried executing freebayes
itself:
[perin@variome 000]$ freebayes --fasta-reference
/share/a
I just noticed a lot of files in my galaxy tmp directory. Since this
isn't a system tmp directory, the system cron scripts don't clean it up.
Is there a galaxy cron script that can be used to clean up this directory?
--
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con
Hi Gordon - It looks like on the samtools mailing lists there is an
active discussion on speeding up sorting:
http://sourceforge.net/mailarchive/message.php?msg_id=27247076
http://sourceforge.net/mailarchive/message.php?msg_id=26990598
Interestingly enough there is a recommendation on using Pic
Hello Ryan,
I'm in the exact same situation with my bowtie/tophat tools,
going back and forth between outputing a SAM, sorted SAM, BAM or sorted BAM,
and I'm still not sure what's the best method.
Storage wise - you're correct, just saving the sorted BAM is the best (even
more with the fact the
Hi all - I find it redundant to hold on to SAM output from NGS Mapping
tools such when I end up converting the SAM files to BAM files anyway.
The cleanup scripts require the history items to be deleted, but I don't
want to delete them yet as I want the entire workflow to be kept until
we are do
On Tue, Apr 5, 2011 at 12:27 PM, andrew stewart
wrote:
> I'm aware of how to configure Galaxy to use SGE in universe_wsgi.ini,
> however what I want to do is a little different.
Hi, Andrew. Take a look at this page:
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster
In particular,
andrew stewart wrote:
> I'm aware of how to configure Galaxy to use SGE in universe_wsgi.ini,
> however what I want to do is a little different. Because I only want
> certain processes to be submitted to the queue, I'd rather control this at
> the tool configuration level (the xml wrapper). For e
Use qrsh instead of qsub to submit the job should help, I believe.
On Tue, Apr 5, 2011 at 10:27 AM, andrew stewart
wrote:
> I'm aware of how to configure Galaxy to use SGE in universe_wsgi.ini,
> however what I want to do is a little different. Because I only want
> certain processes to be submi
Ah, I should have added that this is for a strictly in-house Galaxy
implementation with absolutely no intention of publishing these specific
tools (just these ones! I promise I'll publish other tools in the future
:)
On Tue, Apr 5, 2011 at 12:38 PM, Peter Cock wrote:
> On Tue, Apr 5, 2011 at 5:
On Tue, Apr 5, 2011 at 5:27 PM, andrew stewart
wrote:
> I'm aware of how to configure Galaxy to use SGE in universe_wsgi.ini,
> however what I want to do is a little different. Because I only want
> certain processes to be submitted to the queue, I'd rather control this at
> the tool configuratio
I'm aware of how to configure Galaxy to use SGE in universe_wsgi.ini,
however what I want to do is a little different. Because I only want
certain processes to be submitted to the queue, I'd rather control this at
the tool configuration level (the xml wrapper). For example:
qsub myscript.sh
Hi all,
I had wondered why none of the tools on the Galaxy Tool Shed had a
rating, and had assumed it was just that so far no-one had bothered. I
have a new theory, it doesn't work?
I just viewed Brad's "BAM to BigWig" tool, clicked on "Tool Actions"
then "Rate Tool", and got:
Server Error
An er
Great. I will check out, thanks!
On Thu, Mar 17, 2011 at 2:46 PM, Jeremy Goecks wrote:
> > However, when I tried to use the Edit Pages function, there is no "Embed
>> Galaxy Object" and "Insert Link to Galaxy Object" in the "Page Editor". I
>> have set the "enable_pages = True" in "universe_wsgi.
Hello,
I've encountered a strange combination of factors that results in file access
problems.
Perhaps I'm doing something wrong - any advice will be appreciated.
I'm using Apache + XSendFile.
when viewing a strict BED file, everything works, because the actual dataset
filename is passed on to
On Mon, Apr 4, 2011 at 6:07 PM, Peter Cock wrote:
> On Mon, Apr 4, 2011 at 5:55 PM, Kanwei Li wrote:
>> Done the manual way
>>
>
> Thanks.
>
> I was hoping to have finished this today, but it turns out there are
> some subtle but annoying changes to how BLAST records the hit
> id/name/description
On Tue, Apr 5, 2011 at 10:58 AM, Peter Cock wrote:
> Hi all,
>
> I'd like to write a tool test where the sample output and the
> generated output are the same except for white space.
> i.e. running diff with the -w switch reports no differences.
>
> Is this possible at the moment with the Galaxy t
Juan,
I'm not sure of a likely cause of this error off the top of my head. Have you
tried running Freebayes from the command line on the same data input? That
might be an easy way to explore what particular options with the newer version
of Freebayes that you have are causing issues, or perha
Hi all,
I'd like to write a tool test where the sample output and the
generated output are the same except for white space.
i.e. running diff with the -w switch reports no differences.
Is this possible at the moment with the Galaxy test framework?
I'm hoping for a attribute. I don't see anythin
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