On Thu, Feb 13, 2014 at 7:51 AM, Björn Grüning
bjoern.gruen...@gmail.com wrote:
Am Mittwoch, den 12.02.2014, 10:46 + schrieb Peter Cock:
...
However, at only 5kb the FASTA file is small and fine to bundle -
but the BAM (49kb), log (123kb) and MAF (764kb) quickly add
up so I would prefer
Hi Peter,
The following issue was corrected in change set
https://bitbucket.org/galaxy/galaxy-central/commits/e3a4d4d813fdb8a34cfd6d596e0f4bbdb2d9e211
On Jan 29, 2014, at 12:55 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
I'm getting the following error whenever I'm trying to run SICER
Traceback (most recent call last):
File
/steno-internal/projects/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/sicer/82a8234e03f2/sicer/sicer_wrapper.py,
line 158, in module
if __name__==__main__: __main__()
Hi all,
after the February 2014 galaxy update I'm experiencing errors in Galaxy
Reports.
It only occurs when I'm trying to see which jobs were ran at a specific
date (e.g. I can see how many jobs were ran today, but when I click on the
number to see which ones it returns the following error):
Hi all,
I just wanted to point out that there are several different ways to compare the
history output item to a test file beyond the default “diff”, including
contains, re_match, sim_size, etc, this is set by the “compare” attribute in
the xml tag for the test output. If you really don’t
On Thu, Feb 13, 2014 at 1:58 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi all,
I just wanted to point out that there are several different ways to
compare the history output item to a test file beyond the default
diff, including contains, re_match, sim_size, etc, this is set by
the
Hello Peter,
I'm also sure we could enhance hte twill code to use the dictionary approach
used in the API based testing. However, pervasive use of Javascript is being
introduced into the Galaxy code base at a fast pace and twill does not work
with Javascript. So clearly the use of twill for
I now have 2 versions of snpeff installed from the toolshed on my galaxy server.
Each snpeff version includes an identical datatypes_conf.xml
The galaxy server is setting metadata externally.
When any job runs, (in may case I was running a picard tool), the following
message is written to the
On Thu, Feb 13, 2014 at 4:22 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi JJ,
On Feb 13, 2014, at 11:00 AM, Jim Johnson johns...@umn.edu wrote:
I now have 2 versions of snpeff installed from the toolshed on my galaxy
server.
Each snpeff version includes an identical datatypes_conf.xml
Hi Nikos,
Thank you so much for your report. This issue should be fixed now. Please
update your revision and try again.
Thanks,
Sam
On Thu, Feb 13, 2014 at 7:52 AM, Nikos Sidiropoulos
nikos.sid...@gmail.comwrote:
Hi all,
after the February 2014 galaxy update I'm experiencing errors in
On 2/13/14, 10:22 AM, Greg Von Kuster wrote:
Hi JJ,
On Feb 13, 2014, at 11:00 AM, Jim Johnson johns...@umn.edu wrote:
I now have 2 versions of snpeff installed from the toolshed on my galaxy server.
Each snpeff version includes an identical datatypes_conf.xml
The galaxy server is setting
Hi,
I'm trying to debug file uploads using the file browser. I have nginx setup to
proxy but not to a sub directory.
/usr/sbin/nginx -V
nginx version: nginx/1.4.3
--add-module=/usr/local/src/nginx_upload_module-2.2.0
Here are the settings in my universe_wsgi.ini:
nginx_upload_store =
I'm having some difficulty with external user authentication as described here
-
https://wiki.galaxyproject.org/Admin/Config/ExternalUserDatbases
I've added these two lines to universe_wsgi.ini
use_remote_user = True
remote_user_maildomain = fsu.edu
I've setup ldap authentication in Apache
Hi,
that is just great! Good to see perl packages are working nicely for
you!
Thanks!
Bjoern
Hij Bjoern,
I finally got around to trying your suggestions. It worked out nicely, so
thanks for that!
I've added the modules as an example to the toolshed, as I didn't find an
example yet.
Hi Dan,
Hi all,
I just wanted to point out that there are several different ways to compare
the history output item to a test file beyond the default “diff”, including
contains, re_match, sim_size, etc, this is set by the “compare” attribute in
the xml tag for the test output. If you
Hi Björn,
I think twill is going to be around for a while yet, but it is quickly becoming
more critical to eliminate it. I haven't yet looked at Johns tests using the
API, but my understanding is that they are focused on tools. We're using twill
a lot in other areas besides tools, so it will
Hij Bjoern,
I finally got around to trying your suggestions. It worked out nicely, so
thanks for that!
I've added the modules as an example to the toolshed, as I didn't find an
example yet. Three modules (threads, threads::shared and Thread::Queue) are
bundled in a dependency definition
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