Hi Dave,
Thanks for the clarification. Our testing shows that the local data manager
works in the vanilla Galaxy (simply hg clone, then run.sh). It failed on
our clustered instance that it has been configured to use multiple web
threads, one job manager and two job handlers.
Local data manager is
Hello,
Can anyone tell me why I keep getting this error when I try to do a blast
search in Galaxy? I checked that the nr database file was there and had the
right permissions. Does this error mean that Galaxy can't find the nr file or
does it mean something else?
An error occurre
Hi,
I notice that a with type "select" renders differently
depending on how many s there
are. If there are < 20 options, it appears as a normal select box. If
there are >= 20 options, it looks like a text box (but it has
autocompletion and does have a dropdown menu), and Inspect Element in
Chrome
Dear all,
After playing with several different tools, I got the conversion
working by using this python program:
http://pypi.python.org/pypi/py-mysql2pgsql
Just follow the program manual. Both the installation and the
execution are quite straight forward.
Hope this may help someone in future.
C
Thanks Greg. I used you're updated version and added numpy as a separate
dependency. It seems to work in my development system. I haven't
updated my qa or production versions yet, so I can't check there.
Perhaps you could test it and let me know if there are issues, etc.
Glad I can be of hel
I'm using the CloudMap SNP mapping workflow and have come across a disk
quota error. Is it possible to increase my allocated disk quota to finish
my workflow?
Thanks,
Cole
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in your
Today I ran into a new issues with installing a specific version of
Freebayes. It turns out to be an issue with how git deals with
submodules, something I'm only just learning about myself. In order to
ensure that FreeBayes is built with the correct versions of all of the
various submodules f
Thanks for information Greg. Actually, it turned out to be two things
causing my issues:
1) My copy of tool-data/sam_fa_indices.loc.sample was not owned by the
galaxy user (though it was writable by that user). This caused the
exception which caused the installation to get "stuck" at "cloning
On Aug 25, 2012, at 10:07 PM, Kenneth R. Auerbach wrote:
> Hello,
>
> Can someone tell me if stopping and then restarting the Galaxy process would
> prevent currently-running jobs from completing after the restart? Will all
> the jobs remain in the queue after the restart? Also, what is the b
On Aug 17, 2012, at 10:54 AM, Karger, Amir wrote:
> Replying to myself.
>
> The reason the runner was in a "sleep" state is the logic in
> lib/galaxy/web/config.py says:
>
>if ( len( self.job_handlers ) == 1 ) and ( self.job_handlers[0] ==
> self.server_name ) and ( self.job_manager == s
Hi,
We have installed our own Galaxy server and started using the NGS modules
through it but during the mapping procedure using either BWA for illumina
or BFAST, no reference genome index is available.
We have uploaded the hg19.fa file and put it in the Galaxy-dist/database
folder. We modified the
David, because of the restrictive licensing terms of GATK2 the main
Galaxy Team will not continue to develop any GATK tools except for
those which remain under the open source license (basically, GATK
1.6).
We will be very happy to have wrappers for these and other
non-open-source tools contribute
Is anyone working on adapting the GATK tools for a more recent version of GATK?
The distributed version is 1.4, and GATK is up to 2.1.
David Hoover
Helix Systems Staff
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On Aug 3, 2012, at 10:42 AM, David Roquis wrote:
> Dear Galaxy community,
>
> I have noticed on forums that some users are experiencing this problem too,
> but no clues on how to fix it. When I set debug = false in universe.wsgi.ini,
> I get a server error in the history frame (history works pe
Galaxy imported a library which already existed in the python system
folder. See the error message below.
/home/x/work/galaxy-dist/lib/galaxy/__init__.py:79: UserWarning: Module
markupsafe was already imported from
/usr/lib64/python2.6/site-packages/markupsafe/__init__.pyc, but
/home/x/wor
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On Tue, Sep 11, 2012 at 3:37 PM, wrote:
> Hi Peter,
>
>
>
> This is what I get:
>
>
>
> [auerbach@babar ~]$ ls
> /9720/genome_references/ncbi/nr-protein-db/nr-newstyle/nr*
>
> /9720/genome_references/ncbi/nr-protein-db/nr-newstyle/nr
>
> /9720/genome_refer
Hi,
We have installed our own Galaxy server and started NGS analysis but
during the mapping procedure using either BWA for illumina or BFAST, no
reference genome index is available.
We have uploaded the hg19.fa file and put it in the Galaxy-dist/database
folder. We modified the BWA_index.loc f
On Tue, Sep 11, 2012 at 3:11 PM, wrote:
> Hello,
>
>
>
> Can any one please tell me what could be causing this error message when I
> try to submit a blast job to Galaxy?
>
>
> An error occurred running this job:BLAST Database error: No alias or index
> file found for protein database
> [/9720/ge
Hello,
Can any one please tell me what could be causing this error message when I try
to submit a blast job to Galaxy?
An error occurred running this job:BLAST Database error: No alias or index file
found for protein database
[/9720/genome_references/ncbi/nr-protein-db/nr-newsty
Derrick,
I have not actually tested the local data manager on CloudBioLinux, but
that sounds like something worth looking into.
As for the rsync server mentioned in another email, the data manager
checks our rsync server first, then tries generating indexes if the
rsync server doesn't have t
Hi all,
I wonder if somebody with experience could enlighten me on these issues
regarding authentication of users.
- is it possible to have LDAP integration simultaneously with local
Galaxy users. What I want to reach is when LDAP integration is working,
that I can still add users through th
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