Jerico Nico De Leon Revote wrote:
Hi,
I'm just doing a simple get-data from UCSC on our local Galaxy
instance and got the following error:
WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako)
cannot be fetched
The job box then is displayed as red on the history panel.
The
Sending to galaxy-dev ...
On Thu, Oct 27, 2011 at 5:51 AM, Jim Robinson
jrobi...@broadinstitute.org wrote:
Hi Mike,
Someone from the Galaxy team can perhaps give some insight on
what went wrong, I can comment on the error message from IGV.
That error is thrown from Picard, in every case
Hi, I updated my test server today and everything seemed fine. I added
a new library item via a URL. After that my history panel displays
Internal Server Error and I am getting the error below in paster.log:
Any ideas how this has occurred and if there is a fix?
Shaun
Its possible the sorting problem was a specific version and now gives
an error. The incorrect index caused by bad sequence lengths is a
recurrent problem, but I do not know what tool produces such headers.
Perhaps someone who has experienced this can chime in.
I'm not a samtools expert
David,
I looked into this for some time, and although I found strange behavior in the
mercurial environment, it is impossible to determine what caused it. Your
repository was definitely corrupted in some way, perhaps by a network problem
that occurred when you were transferring files, or some
Just realized I didn't reply to all, so the list didn't see this.
No problem at all, it would be much appreciated in fact.
Is there anything I need to do to do so you can do that?
Cheers
David
On Wed, Oct 26, 2011 at 9:28 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello David,
I'm not sure
Hi Nate,
Any updates?
Thanks,
Ilya
-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya
Sent: Friday, October 21, 2011 2:24 PM
To: Nate Coraor (n...@bx.psu.edu)
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re:
Hi Dan,
I want to modify the wrappers to get genome information from the bam/sam
attribute. I did this for the tophat/cufflinks wrappers. I add another option
to select genome called attribute and then I pass $bam.metadata.dkey in the
command line (see example below). Is this something you
Hi Ilya,
You can validate dbkeys using validators including metadata,
dataset_metadata_in_file/data_table, unspecified_build and others.
Could you clarify what GATK tools you are trying to modify and exactly what you
are trying accomplish? A complete example xml file, and any additional files
What I am trying to do is, instead of having to select the genome from a drop
down that points to the loc file, to take the metadata.dbkey attribute of an
input file and use it to select the genome. I want to avoid having a user of my
workflow select a genome n times in each step of a workflow.
I would like to avoid reinventing the wheel if possible, so I wonder if anyone
has wrappers for Garli (https://www.nescent.org/wg_garli/Main_Page) and Tandem
Repeats Finder (http://tandem.bu.edu/trf/trf.html) they could share.
Thanks,
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