Hello again,
I've not have any missing test results for a while, on the main
or test Tool Shed, so this was a bit of a surprise:
http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90d552
This is listed under Latest revision: failing tool tests, but
I see no test results at
On Fri, Sep 20, 2013 at 11:10 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Wed, Sep 18, 2013 at 11:47 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:
On Tue, Aug 27, 2013 at 2:18 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
I also tried running the command that returns error code 64
It's a bit unclear what you mean by private here, but it's possible to at
least force users to login to use a Tool Shed if you include the following
setting in the [app:main] section your tool_shed_wsgi.ini file.
# Force everyone to log in (disable anonymous access)
require_login = True
Greg
Forgot to copy the list on this email.
On Mon, Sep 23, 2013 at 9:32 AM, Carlos Borroto
carlos.borr...@gmail.com wrote:
On Fri, Sep 20, 2013 at 6:12 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Carlos,
Can you try again?
Also the new unstable version if you can.
Hi Peter,
This behavior has been corrected in 10637:216c01ce6625. Thanks for reporting
this.
Greg Von Kuster
On Sep 23, 2013, at 7:09 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
I think I've found a bug, or at least an area for improvement,
1. Goto
Hello!
I hope that everybody has a great day!
In a pre-assemble analysis step I want to perform a k-mer analysis of the
fastq-file to visualize the k-mer coverage distribution (too estimate genome
size, heterozygosity, repeats etc). This would preferably be done with
Jellyfish. Is there an
Greg,
That's part of the issue. Please try the following:
1) Direct your browser to http://toolshed.g2.bx.psu.edu/view/miller-
lab/genome_diversity
2) Choose 33:5064f618ec1c under Repository revision
3) View README under Repository README files - may contain
important installation or
On Mon, Sep 23, 2013 at 1:57 PM, John Chilton chil...@msi.umn.edu wrote:
On Mon, Sep 23, 2013 at 12:51 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Carlos!
Hi,
I have created a tool that depends on biopython. I don't like the idea
of having several copies of
On Mon, Sep 23, 2013 at 1:09 PM, Carlos Borroto
carlos.borr...@gmail.com wrote:
On Mon, Sep 23, 2013 at 1:57 PM, John Chilton chil...@msi.umn.edu wrote:
On Mon, Sep 23, 2013 at 12:51 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Carlos!
Hi,
I have created a tool
On Mon, Sep 23, 2013 at 1:51 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
I'm installing my package using the virtualenv option. As you can see
below I marked biopython as prior_installation_required=True.
However, I can see that virtualenv is installing a copy of
On Mon, Sep 23, 2013 at 1:25 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Am Montag, den 23.09.2013, 12:57 -0500 schrieb John Chilton:
On Mon, Sep 23, 2013 at 12:51 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Carlos!
Hi,
I have created a
On Mon, Sep 23, 2013 at 2:30 PM, Carlos Borroto
carlos.borr...@gmail.com wrote:
On Mon, Sep 23, 2013 at 2:22 PM, John Chilton chil...@msi.umn.edu wrote:
Hi John,
First let me tell you why I think duplicating the biopython install
reduces reproducibility. I have this on my tool setup.py:
Opps, sent that last mail out before I meant to.
On Mon, Sep 23, 2013 at 2:30 PM, Carlos Borroto
carlos.borr...@gmail.com wrote:
On Mon, Sep 23, 2013 at 2:22 PM, John Chilton chil...@msi.umn.edu wrote:
Hi John,
First let me tell you why I think duplicating the biopython install
reduces
On Mon, Sep 23, 2013 at 2:24 PM, Carlos Borroto
carlos.borr...@gmail.com wrote:
Can you try to insert that (maybe adopt, its not checked):
action type=set_environment_for_install
repository name=package_biopython_1_62 owner=biopython
package name=biopython version=1.62 /
I want to frequently import many tens of thousands of datasets. The files are
on the same sever as Galaxy. But the upload based mechanism is really really
slow. It takes hours to load this many files, yet the data is not moving at all!
What is the best strategy to go about making a faster bulk
My bad, I should have been clearer. What I mean is that no one should be
able to access it unless I give explicit permission. Browsing or
installing tools shouldn't be possible either without permission.
Serrano
On 09/23/2013 02:54 PM, Greg Von Kuster wrote:
It's a bit unclear what you mean by
Hello,
I have been having trouble with Galaxy since yesterday. I have been trying
to run cuffdiff which has been waiting to run since Friday afternoon and
now my history will not even load (red error message shows up).
Any incite would be much appreciated.
Maria
Hello,
Galaxy will not load my histories and as a result I can not run the
analysis that I need to run. I have tried repeatedly since 7:00 AM EST to
load them with no luck. I worked on this history yesterday and everything
was fine.
Maria
Peter,
Thank you for reporting this. I've been able to determine that there was
an installation error that should have been recorded, but was not. I
hope to have a fix committed shortly.
--Dave B.
On 09/23/2013 05:59 AM, Peter Cock wrote:
Hello again,
I've not have any missing test
On Mon, Sep 23, 2013 at 2:02 PM, Robert Jackman rais...@gmail.com wrote:
Hi,
For some reason my history has stopped being visible on Galaxy today. I was
using Galaxy a lot last week and this morning I find only this message:
An error occurred getting the history data from the server. Please
Hi Carlos!
Hi,
I have created a tool that depends on biopython. I don't like the idea
of having several copies of biopython around and also for best
practice making workflows using my tool reproducible, I chose to make
my package repository[1] dependent of package_biopython_1_62.
Am Montag, den 23.09.2013, 12:57 -0500 schrieb John Chilton:
On Mon, Sep 23, 2013 at 12:51 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Carlos!
Hi,
I have created a tool that depends on biopython. I don't like the idea
of having several copies of biopython
Dear Galaxy Team
I was upgrading our servers with the 8/12 release, and going over the
DevNoteshttp://wiki.galaxyproject.org/DevNewsBriefs/2013_08_12.
I noted item Pull Requets Merged #5: SAMtools indexes
#188http://wiki.galaxyproject.org/DevNewsBriefs/2013_08_12#Pull_Requests_Merged.
But the
At line ~694:
incoming['__user_name__'] = user_name
+ if job.history and job.history.id:
+ incoming['__history_id__'] = job.history.id
+ else:
+ incoming['__history_id__'] = 'unknown'
I have tested this change and it appears to give me exactly what I
Hi,
For some reason my history has stopped being visible on Galaxy today. I
was using Galaxy a lot last week and this morning I find only this
message:
An error occurred getting the history data from the server. Please
contact a Galaxy administrator if the problem persists.
Robert Jackman
Hi,
I have created a tool that depends on biopython. I don't like the idea
of having several copies of biopython around and also for best
practice making workflows using my tool reproducible, I chose to make
my package repository[1] dependent of package_biopython_1_62.
On Mon, Sep 23, 2013 at 12:51 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Carlos!
Hi,
I have created a tool that depends on biopython. I don't like the idea
of having several copies of biopython around and also for best
practice making workflows using my tool
Hi guys,
Since the last upgrade we have observed this error. When submitting a job
it sometimes come back failed with the following error
tool error
An error occurred with this dataset: *Unable to run this job due to a
cluster error, please retry it later*
*
*
It is not reproducible as when you
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