Hi Starr
I will try to answer some of your questions. Next time I recommend to
ask just one question (with a corresponding subject line). This will
make it much easier for the community to help you, and for others with
similar problems to find the correct e-mail thread.
see below for my
Hi all,
I'd like to change the output dataset labelling in Galaxy file format
conversion tools.
e.g. If the input is history entry 1 (e.g My Genes) then the output
from tabular_to_fasta.xml is currently named FASTA-to-Tabular on data
1.
I would prefer this was FASTA-to-Tabular on data My Genes
Hi Peter,
thanks for raising this important topic.
I think the following trello card has a similar idea and a patch
attached.
https://trello.com/c/JnhOEqow
It would be great if we can simplify the naming of datasets, especially
if you run a workflow with several input, you would like to keep
On Thu, Nov 7, 2013 at 12:29 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
Hi Peter,
thanks for raising this important topic.
I think the following trello card has a similar idea and a patch
attached.
https://trello.com/c/JnhOEqow
It would be great if we can simplify the naming of
On Thu, Nov 7, 2013 at 12:21 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Related to this, would people prefer if the $on_string in the case of
a single input file was the input file's name (e.g. My Genes) rather
than data 1? (When there are multiple input files, $on_string needs
to be
Hi list,
I would need a memory refresher about tasked jobs. When testing some
larger analyses on a local installation, I thought the
local_task_queue_workers setting in universe_wsgi.ini would be the
limiting factor for how many tasks can be executed at the same time. In
our setup, it is
Hi all,
There are two copies of the wiggle_to_simple tool in the main repository,
and this duplication appears to have happened back in 2009.
$ grep wiggle_to_simple tool_conf.xml.sample
tool file=filters/wiggle_to_simple.xml /
tool file=stats/wiggle_to_simple.xml /
$ diff
On Thu, Nov 7, 2013 at 3:18 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Nov 7, 2013 at 12:21 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Related to this, would people prefer if the $on_string in the case of
a single input file was the input file's name (e.g. My Genes) rather
Dear Galaxy mailing-list,
Once again I come seeking for your help. I hope someone already had this
issue or will have an idea on where to look to solve it. :)
One of our users reported having workflows failing because some steps were
executed before all their inputs where ready.
You can find a
Hi Michiel,
Did you finish wrapping samtools idxstats? I can't see it on the Tool Shed...
If not, I may tackle this shortly.
Peter
On Wed, May 22, 2013 at 2:39 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote:
Galaxy stores a BAI for each BAM internally; you can access it in a tool
wrapper
Hello Ido,
The project has had a lot of contributors over the years, it is
probably not safe to assume they have all been experts and
frequently experts know of little tricks or shortcuts that can
result in a lot of trouble (this case in point) - a less sophisticated
developer probably would
I think you want to set local_job_queue_workers instead or set the
number on the local job runner plugin element in the newer
job_conf.xml style configuration - the task runner delegates to the
underlying job runners once it has split out the tasks. The parameter
you were setting I am guessing
John just made it to the Wiki:
http://wiki.galaxyproject.org/Develop/SecurityToolTips
Feel free to add/edit/delete.
M.
On Thu, Nov 7, 2013 at 12:27 PM, John Chilton chil...@msi.umn.edu wrote:
Hello Ido,
The project has had a lot of contributors over the years, it is
probably not safe to
There are still two copies in central but I have synchronized the test
cases and fixed the newlines per your suggestion. I imagine the
easiest way to fix the fact there are two copies is just wait until
they get migrated to the tool shed - it seems like progress is being
made on that front very
Galaxy is not optimized for this kind of use case, I like to think of
it as sort of file centric - but it is clear more and more people
are using it to process data in this fashion. Hopefully someone chimes
in with better advice than I have :).
The way I would probably implement this is create a
On Thu, Nov 7, 2013 at 1:46 AM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Am Donnerstag, den 07.11.2013, 00:25 -0600 schrieb John Chilton:
My two cents below.
On Wed, Nov 6, 2013 at 4:20 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Dave,
We're
Please see my inline comments. Thanks!
Greg Von Kuster
On Nov 7, 2013, at 1:33 PM, John Chilton chil...@msi.umn.edu wrote:
On Thu, Nov 7, 2013 at 1:46 AM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Am Donnerstag, den 07.11.2013, 00:25 -0600 schrieb John Chilton:
My
Dear all,
I have found a solution but I can unfortunately not explain why your solution
on the Admin pages is not working. The following entries in httpd.conf solved
the problem in our environment. Maybe this is useful for other CAS users.
Best,
Sandra
RewriteEngine on
Location /
# Define
Hi Curtis,
This is still open but I expect to correct this very soon, along with
new data additions (but corrections first on the list!). We definately
consider this important and apologize that this has impacted your
paper's supplemental creation.
There is a Trello ticket containing the
Hello Mary,
The underlying data is not complete for all mm9 reference genomes for
the Bowtie2/Tophat2 tools, causing the error. It is a known issue and we
expect to have it corrected very soon now. We consider this important
and high priority, our apologies for the confusion it caused.
A
The potential problem I see here is that environment variables are not
name spaced in any way, so if all env.sh files are sourced no matter
what, there is the potential for a certain environment variable to get
set to a certain dependency version, and then later during the
installation
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