Aside: If I add steps to the beginning of the workfow, the step that
runs too early, typically occurs earlier in the flow. Can this indicate
a race condition where not all dependencies are available (stored?) yet
in the database at the time of querying for job eligible for queueing?
Best,
Hi,
On 21.05.2013 18:06, Dannon Baker wrote:
This interaction is pretty clunky right now (I've made a trello card for
improving it:
https://trello.com/c/eu8XiJLK.
Two options right now are:
1) Import (on main) each workflow you want to copy to your local instance, and
generate the regular
On Wed, May 22, 2013 at 3:12 AM, Andreas Kuntzagk
andreas.kuntz...@mdc-berlin.de wrote:
But how do I get the workflow_id? For example for the workflow
https://main.g2.bx.psu.edu/u/**gm2123/w/cloudmap-unmapped-**
Hey Dannon,
thnx for the info and the quick reply!
On 21.05.2013 18:09, Dannon Baker wrote:
Hey Christian,
This is a bug that surfaced in revision 8333 which should be fixed
in 9326:d07c62f0067a, which is available in the most recent
galaxy-dist (stable branch). If you'd rather not update
Hi,
I would like to inquire whether anyone has attempted to implement the
idxstats tool from samtools into Galaxy?
The xml-file for idxstats is not present in the Galaxy source code,
which led me to try and implement it myself.
However, the main problem I face is that the idxstats tool
Hello,
I am a new Galaxy User.
I am definitely not an expert in informatics, so my questions may sound
silly to you... I apologize if it is the case!
Anyway, I cound not establish a ftp connexion to Galaxy through Filezilla,
and the error message suggests that it comes from an incorrect password
Galaxy stores a BAI for each BAM internally; you can access it in a tool
wrapper like this (assuming the name of your input dataset is 'input_bam':
${input_bam.metadata.bam_index}
Once you have the file path, you can set up a symbolic link to it and the tool
should work fine.
Good luck,
J.
Hey everyone,
I'm having a weird login problem (think it's cookie related) after setting up
Galaxy on a virtual machine and trying to proxy_pass to it using nginx. It says
I'm logged in, but when I get redirected to the front page I'm no longer logged
in. When I visit subsequent pages I'm
I actually fixed the problem by not setting the cookie prefix in the ini file.
Weird.
Sincerely,
Michael E. Cotterell
Ph.D. Student in Computer Science, University of Georgia
Instructor of Record, Graduate RA TA, University of Georgia
mepcotter...@gmail.com (mailto:mepcotter...@gmail.com)
That's not the only thing I changed. I also have the following in my nginx conf
file:
proxy_set_header Host $host;
instead of X-Forwarded-Host $host
Sincerely,
Michael E. Cotterell
Ph.D. Student in Computer Science, University of Georgia
Instructor of Record, Graduate RA TA, University of
Hi all,
I want to include a new tool to galaxy. The tool is written in C++. How
do I write the xml file to execute a cpp program? The tool that I am
trying to integrate ishttps://code.google.com/p/bedtools/
I have the class file to be executed and the command to execute it. For
example,
On Wed, May 22, 2013 at 5:21 PM, vijayalakshmi v...@buffalo.edu wrote:
Hi all,
I want to include a new tool to galaxy. The tool is written in C++. How
do I write the xml file to execute a cpp program? The tool that I am trying
to integrate ishttps://code.google.com/p/bedtools/
I
You might find it instructive to look at the existing bedtools wrappers here:
http://toolshed.g2.bx.psu.edu/view/aaronquinlan/bedtools
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Wed, May 22, 2013 at 12:21 PM, vijayalakshmi v...@buffalo.edu wrote:
Hi all,
I
Hi,
We are trying to put a few reference genomes into the built-in index for bwa,
bowtie, bowtie2 and tophat. For the human hg19 we can find those. However, we
also like to upload the Rhesus macaque genome and haven't been able to find an
indexed version at NCBI or other places.
Are other
Peter,
I have implemented a system that will explicitly exclude a defined list
of repositories from the testing framework, so your repositories' tests
should now be running.
--Dave B.
On 5/21/13 06:26:56.000, Peter Cock wrote:
On Mon, May 13, 2013 at 11:09 AM, Peter Cock
Peter,
Thank you for reporting this issue, it has been resolved in
9827:2a630237801f.
--Dave B.
On 5/21/13 06:10:34.000, Peter Cock wrote:
Hi Greg,
There may be an issue with the new feature to mark a specific revision
to skip tool tests. I ticked this earlier this week on this
On Wed, May 22, 2013 at 6:47 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
I have implemented a system that will explicitly exclude a defined list of
repositories from the testing framework, so your repositories' tests should
now be running.
--Dave B.
Looks good - and now I have some
On Mon, May 20, 2013 at 3:05 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
On Mon, May 20, 2013 at 2:47 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Peter wrote:
Right now the single biggest class of test failures amongst my tools on
the Test Tool Shed is a missing dependencies on the
I cannot guarantee it, but this may be related to a fix I just committed that
populates the repository tag in the dependency definitions with a toolshed
attribute if it is missing (it looks like it is in your case). I used to not
populate the tag, but simply stored the tool shed in the
Hi everyone,
Galaxy is set up on our cluster, and so far everything is working just
fine. However, we'd like to change the submission queue from the default to
a specific one.
To do so, we tryed to set on the universe_wsgi.ini file the
default_cluster_job_runner parameter as following:
Hi all,
I want to include a new tool to galaxy. The tool is written in C++. How
do I write the xml file to execute a cpp program? The tool that I am
trying to integrate ishttps://code.google.com/p/bedtools/
I have the class file to be executed and the command to execute it. For
example,
I'm having a pretty torrid time with this because we've had to implement active
directory authentication for Apache. It works and users can log in with their
AD accounts and that is all fine. The problems arise when I try and get UCSC
to pick up a BAM file. The first problem is that although
Hi,
I upload files which then automatically call execute_workflow.py. The files
background turn to green , but to see the workflow running on the GUI I need to
refresh the display. Does anyone know how I can add a refresh command to the
code, and where in the code to add it.
Thanks
Neil
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