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
On Tue, Apr 5, 2011 at 10:58 AM, Peter Cock p.j.a.c...@googlemail.com 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
On Mon, Apr 4, 2011 at 6:07 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Apr 4, 2011 at 5:55 PM, Kanwei Li kan...@gmail.com 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
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
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 error
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:
command
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 p.j.a.c...@googlemail.comwrote:
Use qrsh instead of qsub to submit the job should help, I believe.
On Tue, Apr 5, 2011 at 10:27 AM, andrew stewart
andrew.c.stew...@gmail.comwrote:
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
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
On Tue, Apr 5, 2011 at 12:27 PM, andrew stewart
andrew.c.stew...@gmail.com 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:
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
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
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
13 matches
Mail list logo
