Hi,
I am new user to galaxy. I have installed galaxy on the Linux local server
for ChIP-seq analysis. While running MACS, an error is flagged
"An error occurred running this job: /bin/sh: macs: not found" .
I have set the path for macs in /bin. But still the error persists. It
would be great if a
Hi,
We are attempting to integrate vcftools specifically vcf-merge into
galaxy. We have two or files that we
are attempting to merge, the command when run through terminal does not
give a broken pipe, but
when galaxy runs the command a broken pipe is given at the beginning and
the start of the
Carlos,
The method you describe below for mapping inputs is precisely the intended
approach. One reason for the long identifier being used instead of a simple
step number is that step number (ordering as you would see in the usual run
workflow dialog) can change without it being obvious to the
Leon,
I'm not seeing this behavior in any of my instances. I assume they work
correctly through the standard galaxy interface, but is there anything special
about the workflows in question? Is there perhaps a tool with no inputs in use?
Thanks!
-Dannon
On Jan 6, 2012, at 11:59 AM, Leon M
Hello Galaxy-Dev List,
I am having some issues in getting a script to work correctly in Galaxy. My
script is written in Python, uses RPy2 to pass some data to the R environment
and then calls a custom R function; the output of this function, and of the
greater Python/R tool, is a file. I am h
Hi Jeremy,
thank you for your answer. I followed your hint modifyng
(for example) the ucsc_tablebrowser.xml as follows (not
sure about the tag to have a simple error
message, but this is another problem):
table browser
#if $__user_email__ == ""
You are not authorized
On 01/09/2012 05:04 AM, Vidya .H.K wrote:
Hi,
I am new user to galaxy. I have installed galaxy on the Linux local server
for ChIP-seq analysis. While running MACS, an error is flagged
"An error occurred running this job: /bin/sh: macs: not found" .
I have set the path for macs in /bin. But s
On Mon, Jan 9, 2012 at 9:12 AM, Dannon Baker wrote:
> Carlos,
>
> The method you describe below for mapping inputs is precisely the intended
> approach. One reason for the long identifier being used instead of a simple
> step number is that step number (ordering as you would see in the usual ru
Ivan,
>
>
>table browser
>
>#if $__user_email__ == ""
>You are not authorized to use this tool
>#else
>data_source.py $output $__app__.config.output_size_limit
>#end if
>
>
>
>
> ... and I got the error below, which seems connected to
> the che
On Fri, Jan 6, 2012 at 12:55 PM, Ryan Golhar 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 external metadata setting failed and it's being retried
>> internally (if that
Hi all - I think there is a problem with the Picard HSMetrics wrapper in
Galaxy. The wrapper accepts a BAM files and a BED file. However the BED
file isn't really in a BED format...it requires a SAM header before the BED
lines. This really isn't a BED file format. I'm not quite sure how Galaxy
Hi Dannon,
Thanks for the hint. I got it working by removing "input dataset" step and
adding it back in the workflow canvas. The previous workflow in question
was purely extracted from history.
So now I can check the details via API:
./display.py
http://galaxy.nbic.nl/galaxy/api/workflows/e037f
Glad you got it working, and thanks for the additional information. Now that I
know what's different about the non-working workflows I can probably recreate
and fix this on my end. Extracted workflows *should* function via the API.
-Dannon
On Jan 9, 2012, at 5:06 PM, Leon Mei wrote:
> Hi Dan
Hi Ryan,
Yes, the Picard tool mandates a bizarre bait/target format file for
reasons which might best be addressed to the Picard devs - they may
have some very good reasons although I can't imagine what they are.
:)
Yes, automated conversion of any valid Galaxy bed dataset into the
strange format
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 where can be accessed
clsuter-wide. I have configured
Derrick,
Take a look at the section entitled "Job runner URL" on
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster. But as I
understand it, you don't need to do anything since the drmaa library is
part of your SGE installation. Just make the node Galaxy runs on an exec
host.
Ryan
On M
Thanks Ryan,
I have been following that guide. I can configure the galaxy host to be an
exec host, although it makes more sense to be a submission host.
I hope this can be clarified in the future revise of the documentation.
Cheers,
Derrick
On Tue, Jan 10, 2012 at 12:57 PM, Ryan Golhar
wrote:
Whoops. That's what I mean...a submission host, not an exec host.
On Mon, Jan 9, 2012 at 11:13 PM, Derrick LIN wrote:
> Thanks Ryan,
>
> I have been following that guide. I can configure the galaxy host to be an
> exec host, although it makes more sense to be a submission host.
>
> I hope this
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