On Mon, Feb 17, 2014 at 3:08 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Feb 17, 2014 at 2:57 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
It looks like you made some changes to your tool dependency
recipe since the last test run.
Yeah, the mira de novo test was missing
Hi Peter,
We'll try to get some time to look at your tool_dependencies.xml recipe as soon
as possible.
Greg Von Kuster
On Feb 18, 2014, at 5:47 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Greg, Dave,
RE: http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
Same as
On Tue, Feb 18, 2014 at 11:41 AM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
We'll try to get some time to look at your tool_dependencies.xml recipe as
soon as possible.
Greg Von Kuster
Great.
Re:
https://trello.com/c/HVGrShnC/60-tool-shed-should-test-installation-of-packages
Hi all,
I just updated my development server, and ran into what looks
like a missing dependency:
$ ./run.sh
...
galaxy.jobs.manager DEBUG 2014-02-18 11:58:06,422 Starting job handler
galaxy.jobs INFO 2014-02-18 11:58:06,422 Handler 'main' will load all
configured runner plugins
On Tue, Feb 18, 2014 at 12:00 PM, Peter Cock p.j.a.c...@googlemail.comwrote:
Hi all,
I just updated my development server, and ran into what looks
like a missing dependency:
$ ./run.sh
...
galaxy.jobs.manager DEBUG 2014-02-18 11:58:06,422 Starting job handler
galaxy.jobs INFO 2014-02-18
Hi John,
Fix confirmed - nice timing, I just finished my lunch break :)
Thanks!
Peter
On Tue, Feb 18, 2014 at 12:35 PM, John Chilton jmchil...@gmail.com wrote:
That should be fixed now, sorry about that.
-John
On Tue, Feb 18, 2014 at 6:07 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:
Hi all,
Earlier today I updated my development server, which uses SQLite,
and ran the update schema script (now at v118). With hindsight
there could have been a warning that I missed - because afterwards
despite updating to the galaxy-central tip, trying to use any of
the tools failed with an SQL
On Tue, Feb 18, 2014 at 8:30 AM, Peter Cock p.j.a.c...@googlemail.comwrote:
This fixed the history_dataset_association.extended_metadata_id
error - so is the most likely explanation a failed schema update?
Might a stale migration_tmp table have been to blame?
Yes, I've seen this before when
On Tue, Feb 18, 2014 at 1:40 PM, Dannon Baker dannon.ba...@gmail.com wrote:
On Tue, Feb 18, 2014 at 8:30 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:
This fixed the history_dataset_association.extended_metadata_id
error - so is the most likely explanation a failed schema update?
Might a
Hi all,
If anyone is interested, I've just wrapped a little Python script
I'd prepared early for use in Galaxy for a fairly common need -
back translating a protein alignment into a nucleotide alignment
by threading the unaligned sequence.
We're testing this locally, and barring any major issues
There isn't really a way to set the role usefully at library dataset
creation right now. This was discussed in a recent thread that also
had some local workarounds:
On Fri, Sep 13, 2013 at 9:54 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
I've sent this to both the Galaxy and Biopython developers lists,
and hope this will make sense to both groups. If you've not heard
of Galaxy, start here: http://galaxyproject.org - while the easy to
guess
Hi,
something strange happens with Cufflinks in our Galaxy server. When a
user deletes a running Cufflinks job in fact the associated Cufflinks
process(es) are not terminated. Apart from unneccessary CPU usage, this
prevents other jobs from starting if the max jobs limit has been already
On Tue, Feb 18, 2014 at 2:20 PM, Federico Zambelli
federico.zambe...@unimi.it wrote:
Hi,
something strange happens with Cufflinks in our Galaxy server. When a user
deletes a running Cufflinks job in fact the associated Cufflinks process(es)
are not terminated. Apart from unneccessary CPU
Thanks Peter!
+1 for including that into the Biopython release process
Cheers,
Bjoern
On Fri, Sep 13, 2013 at 9:54 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
I've sent this to both the Galaxy and Biopython developers lists,
and hope this will make sense to both groups. If
Hi Peter,
it runs on a single server since this Galaxy instance is for internal
use of our lab only.
Aborting other long running tools like tophat and bowtie works just as
expected. I have also noticed that at least a couple of times not only
the cufflinks process(es) were not terminated
That should be fixed now, sorry about that.
-John
On Tue, Feb 18, 2014 at 6:07 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, Feb 18, 2014 at 12:00 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
Hi all,
I just updated my development server, and ran into what looks
like a missing
Dear all,
I am looking into options for renaming output files automatically in workflows
and I found this thread :
http://dev.list.galaxyproject.org/Renaming-in-Workflows-td4656426.html#a4656430
I managed to use the following in test workflow:
- ${} to create input variable to the workflow
-
Hi Adam,
This is going to depend entirely on the tools you're using. I'd suggest
running your typical workload and examining the I/O patterns to determine
what makes the most sense. I'd think the temp directory, input dataset, and
output dataset filesystems to be the most utilized.
--nate
On
Hi,
We are trying to add a new tool to our local galaxy instance with the following
requirements.
When a user clicks on the tool in side panel from tools list, a table should
appear where the first element in each row is a clickable link. Users can click
on any of the element, and then see
On Tue, Feb 18, 2014 at 5:19 PM, Saba Sehrish ssehr...@fnal.gov wrote:
Hi,
We are trying to add a new tool to our local galaxy instance with the
following requirements.
When a user clicks on the tool in side panel from tools list, a table should
appear where the first element in each row
I am using *.loc files, to create a bunch of tables I need, but I want to
display complete tables (e.g. from .loc file) with clickable elements for users
so that their input could be captured.
For example if in my .loc file I have the following contents
Model SizePath
M001L180
On Tue, Feb 18, 2014 at 6:14 PM, Saba Sehrish ssehr...@fnal.gov wrote:
I am using *.loc files, to create a bunch of tables I need, but I want to
display complete tables (e.g. from .loc file) with clickable elements
for users so that their input could be captured.
For example if in my .loc
On Feb 18, 2014, at 12:23 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, Feb 18, 2014 at 6:14 PM, Saba Sehrish ssehr...@fnal.gov wrote:
I am using *.loc files, to create a bunch of tables I need, but I want to
display complete tables (e.g. from .loc file) with clickable elements
for
On Tue, Feb 18, 2014 at 7:13 PM, Saba Sehrish ssehr...@fnal.gov wrote:
On Feb 18, 2014, at 12:23 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
On Tue, Feb 18, 2014 at 6:14 PM, Saba Sehrish ssehr...@fnal.gov wrote:
I am using *.loc files, to create a bunch of tables I need, but I want
On Feb 18, 2014, at 3:22 PM, Peter Cock
p.j.a.c...@googlemail.commailto:p.j.a.c...@googlemail.com wrote:
On Tue, Feb 18, 2014 at 7:13 PM, Saba Sehrish
ssehr...@fnal.govmailto:ssehr...@fnal.gov wrote:
On Feb 18, 2014, at 12:23 PM, Peter Cock
On Tue, Feb 18, 2014 at 9:59 PM, Saba Sehrish ssehr...@fnal.gov wrote:
On Feb 18, 2014, at 3:22 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
OK - so no deep changes to the Galaxy parameter data
model etc would be needed (which is good news), 'just'
a new table rendering of a *.loc based
On Feb 18, 2014, at 4:09 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, Feb 18, 2014 at 9:59 PM, Saba Sehrish ssehr...@fnal.gov wrote:
On Feb 18, 2014, at 3:22 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
OK - so no deep changes to the Galaxy parameter data
model etc would be
In experimenting with how we could embed javascript/unsanitized html in
tool output we came across the following method. Given that the current
default is to disallow such activities, we thought it might be useful to
bring it to your attention.
The attached file provides an example, which, when
dear Galaxians,
the users of my galaxy service are quite eterogenous, and would like to
have the toolbar customised only with subsets of the available tools. Such
customisation should be possible
a) at user group level
b) at individual level
A possibility for group-level tool availability could
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