the toolshed the
dependency should be added automatically. I am really not sure why it looks
for ReorderSam.jar in the top directory /. Any clues?
Best wishes,
Alex
--
Alexander Kurze, DPhil
University of Oxford
Department of Biochemistry
South Parks Road
Oxford, OX1 3QU
United Kingdom
Tel: +44
,
Bjoern
Am 17.03.2014 15:48, schrieb Alexander Kurze:
Hi there,
we are running a local instant of galaxy and when running Picard tools
Reorder Sam files I get following error message:
An error occurred with this dataset: *## exit code=1; stdout= Error:
Unable to access jarfile /ReorderSam.jar
Hi there,
We have installed a local copy of galaxy but there seems to be a strange
behavior with deleting data sets in the history panel. A few users complain
that they have deleted their data sets (I can confirm that) but somehow the
quota limit still doesn't show the appropriate freed space.
Perfect! This solved my problem.
Alex
On Fri, Mar 14, 2014 at 1:23 PM, Peter Cock p.j.a.c...@googlemail.comwrote:
On Fri, Mar 14, 2014 at 12:28 PM, Alexander Kurze
alexander.ku...@gmail.com wrote:
Hi there,
We have installed a local copy of galaxy but there seems to be a strange
Hi there,
I have a local copy of galaxy and I am trying to install bowtie2 2.1.0 onto
the system via the toolshed. However it just doesn't work. I always get a
Server Error message. I have checked if the dependencies are installed and
they are all installed in the toolshed depenencies folders.
will be installed and you should see your wrapper.
Ciao,
Bjoern
2014-01-31 Alexander Kurze alexander.ku...@bioch.ox.ac.uk:
Hi there,
I have a local copy of galaxy and I am trying to install bowtie2 2.1.0
onto the system via the toolshed. However it just doesn't work. I always
get a Server Error
,
To help determine the cause of this, could you paste the output of the
following commands run from the root of your Galaxy installation?
hg heads
hg id
--Dave B.
On 01/31/2014 09:05 AM, Alexander Kurze wrote:
Thanks for your quick answers.
I actually have installed the dependencies first
, but will the
AD also mount the share drives? If yes, is there a wrapper that allows to
download Galaxy Histories onto the shared drive?
Alex
--
Alexander Kurze
70 Sunningwell Road
Oxford, OX1 4SX
Tel: +44 1865-243-609
Mobile: +44 7962-425-865
Hi there,
I have a server set up of galaxy. I would like to have a system setup where
people can login via their active directory name and then use their mounted
share drive to download processed data from the galaxy server.
I saw that it is possible via apache to login through the AD, but will
Hi there,
I have a server set up of galaxy. I would like to have a system setup where
people can login via their active directory name and then use their mounted
share drive to download processed data from the galaxy server.
I saw that it is possible via apache to login through the AD, but will
Hi there,
I am running my own instance of galaxy (April 2013 version) and I have
problems with saved histories. Sometimes the histories do NOT show up at
all at the right hand side (panel remains white with no error message). I
then have make a clone of the history and then I can use it again. I
Hello,
I am running a local galaxy server and tried to add the downsampling script
for SAM/BAM files from Brad Longhorst which I found on Github. It uses a
modified picard_wrapper.py. I get everything running except that the end
file shows up empty. I realised when looking at the log file that
to fix it or at least tell me what it means.
Thank you for your help in advance.
Keep up the great work!
Best wishes,
Alex
--
Alexander Kurze, DPhil
University of Oxford
Department of Biochemistry
South Parks Road
Oxford, OX1 3QU
United Kingdom
Tel: +44 1865 613 230
Fax:+44 1865 613 341
Hello,
I am running a local galaxy server where I have restricted the amount of
data for each user to a 100gb. Users are able to delete their own history
to regain diskspace. However, for some users deleting the histories (all
saved histories and datasets) only frees ~80% of their allowance. As
Hi there,
we have a 32 core server but I realised that a lot of programs are only
using a fraction of that. I was able to adjust bowtie, bowtie2 and Tophat
to use all of the cores but couldn't find an thread/core option for Macs14,
Macs2 or PeakRanger. Does anyone know if these programs are
...@googlemail.comwrote:
On Tue, Mar 26, 2013 at 10:15 AM, Alexander Kurze
alexander.ku...@gmail.com wrote:
Hi there,
we have a 32 core server but I realised that a lot of programs are only
using a fraction of that. I was able to adjust bowtie, bowtie2 and
Tophat to
use all
in the longer term - what do other people on this list do?)
HTH, best wishes, Peter
On 25/02/13 11:29, Alexander Kurze wrote:
Hello,
I am using the bowtie-wrapper on my locally installed galaxy server to
align reads. However I missing the stats read-out. Is there any
possibility to include
saved in the stderr but unfortunatly the
stderr is somehow deleted after the alignment job is done in bowtie under
galaxy.
Any idea how I can still access the stats?
Thanks,
Alex
--
Alexander Kurze, DPhil
University of Oxford
Department of Biochemistry
South Parks Road
Oxford, OX1 3QU
United
it should
do.
Does anyone now how I can fix it?
Thanks,
Alex
--
Alexander Kurze, DPhil
University of Oxford
Department of Biochemistry
South Parks Road
Oxford, OX1 3QU
United Kingdom
Tel: +44 1865 613 230
Fax:+44 1865 613 341
___
Please keep
19 matches
Mail list logo
