On 01/10/2012 06:31 AM, Vidya .H.K wrote:
Hi,
I think macs is exceutable with galaxy user.
what happens if you execute macs_wrapper.py on the command line?
Regards, Hans
PS: Please send all follow-up with a cc to the mailing list (reply-all).
On 01/09/2012 05:04 AM, Vidya .H.K
On Jan 9, 2012, at 7:45 PM, Derrick LIN wrote:
Hi guys,
I am trying to configure our test galaxy to run on our SGE cluster
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster.
This is my first time to come across to drmaa, so a bit confused.
I installed teh galaxy on a NFS location
In case anyone is interested I posted a message to samtools-dev and got a
few responses about it. The thread is called 'Picard bait/target format
file for HsMetrics'. Now, for Galaxy, I think the wrapper should not
accept the BED file as input as that doesn't work. I like the idea of a
new file
Hi,
Happy New Year 2012!
Having read the public Galaxy server now has ENA/SRA data available I'm
wondering if EBI's dbfetch or wsdbfetch is an option to consider as
well. Dbfetch has a web interface and is also supported using Web Services:
Web: http://www.ebi.ac.uk/Tools/dbfetch/
and
WS:
On Jan 9, 2012, at 2:38 PM, Ryan Golhar wrote:
On Fri, Jan 6, 2012 at 12:55 PM, Ryan Golhar ngsbioinformat...@gmail.com
wrote:
This indicates that set_meta is running locally, in the runner process. Can
you make sure there's not a typo in your config? The other possibility is
that
I've been looking at this all day today, and here's what I've figured out.
The picard_wrapper.py simply puts the SAM header from the input BAM file
at the top of the BED file. However, the interval file actually has
different columns of the order:
Seq Name, Start Pos (1-based), End Pos, Strand,
Dear All,
I have a file path that I'd like to link into Galaxy using a RESTful WEB
API call with some additional metadata key-value pairs. How can I do
that? I know the /api/libraries/ call respects JSON keys like
folder_id, file_type, etc. But can I pass to it additional keys and
it will
On Tue, Jan 10, 2012 at 11:43 AM, Ryan Golhar
ngsbioinformat...@gmail.comwrote:
Hi Ryan,
You could check it in lib/galaxy/config.py, after it's read. By any
chance, are you using galaxy-central vs. galaxy-dist? It's possible that
due to a bug I recently fixed and a certain combination of
