Dear Jermy,
Thanks for the Toolshed link,
I installed it in the galaxy and tried running it by choosing build
backend database using cuffdiff output and added additional plot as
Heatmap. The Job was run successfully but i could'nt view the HTML page..
it shows as Galaxy - cummeRbund Output
Dear Galaxy developers,
I am a beginner in galaxy development and I would like to build a tool
to send a file from galaxy to an external URL.
I tried to work with the following tutorial :
http://wiki.galaxyproject.org/Admin/Tools/External%20Display%20Applications%20Tutorial
But I couldn't make
Hi Bjoern Greg,
The Biopython package looks OK on the test tool shed,
http://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61
This includes the lines:
package name=numpy version=1.7.1
repository changeset_revision=ad6ebe2c75ef
name=package_numpy_1_7 owner=bgruening
Hello all,
While trying to install the Glimmer3 wrapper from the Tool Shed
I noticed some very wrong looking paths, including this warning
at the terminal where run.sh was open,
Warning: local() encountered an error (return code 1) while executing
'echo
Hi,
Hi Bjoern Greg,
The Biopython package looks OK on the test tool shed,
http://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61
This includes the lines:
package name=numpy version=1.7.1
repository changeset_revision=ad6ebe2c75ef
name=package_numpy_1_7
On Wed, Apr 24, 2013 at 5:05 PM, Iry Witham iry.wit...@jax.org wrote:
Hi Team,
I am trying to get GATK tools added to my cloud instance and keep getting
the following error: [Errno 2] No such file or directory:
Hi all,
I'm currently trying out installation of tools from the Tool Shed
on a secondary Galaxy server (not our production server nor
my development setup). This is running galaxy-dist, current
latest stable I believe:
$ sudo -u galaxy hg heads
changeset: 10201:ebe87051fadf
tag: tip
Hi Peter,
On Wed, Apr 24, 2013 at 5:05 PM, Iry Witham iry.wit...@jax.org wrote:
Hi Team,
I am trying to get GATK tools added to my cloud instance and keep getting
the following error: [Errno 2] No such file or directory:
On Mon, 2013-08-12 at 12:50 +0100, Peter Cock wrote:
Hi all,
I'm currently trying out installation of tools from the Tool Shed
on a secondary Galaxy server (not our production server nor
my development setup). This is running galaxy-dist, current
latest stable I believe:
$ sudo -u galaxy
This looks to be a guppy bug that has now been fixed (
http://sourceforge.net/p/guppy-pe/bugs/10/) so we'll update the egg from
our end, thanks!
For now, you can either build your own guppy 0.1.9+ egg to fix it or
disable use_memdump in your universe (to skip it completely). Unless
you're
Hello,
I started a new cloudman instance two days ago.
I am stuck with two problems.
1. When I try to upload my fastq files to FTP server using Filezilla (I typed
my ec2... address as the host and entered my cloudman registered email address
and password), Filezilla connects to 220-Galaxy
Dear Bjoern,
I was using ubuntu with Turkish language. Your answer gave me clue about the
problem. Turkish language contains some special characters that may confuse
Galaxy. So, I turned it into English. Voila! Problem solved. :)
Thank you so much Bjoern. :) You are the best!
Can Holyavkin
Hi will see what the problem with sqlite is and give feedback later
On 8 August 2013 19:14, Nate Coraor n...@bx.psu.edu wrote:
On Aug 8, 2013, at 12:50 PM, Adam Brenner wrote:
The issue here is the last line:
OperationalError: (OperationalError) disk I/O error u'PRAGMA
On Mon, Aug 12, 2013 at 12:51 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
Hi Peter,
On Wed, Apr 24, 2013 at 5:05 PM, Iry Witham iry.wit...@jax.org wrote:
Hi Team,
I am trying to get GATK tools added to my cloud instance and keep getting
the following error: [Errno 2] No such
On Mon, Aug 12, 2013 at 12:54 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
On Mon, 2013-08-12 at 12:50 +0100, Peter Cock wrote:
Hi all,
I'm currently trying out installation of tools from the Tool Shed
on a secondary Galaxy server (not our production server nor
my development setup).
On Mon, 2013-08-12 at 13:59 +0100, Peter Cock wrote:
On Mon, Aug 12, 2013 at 12:54 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
On Mon, 2013-08-12 at 12:50 +0100, Peter Cock wrote:
Hi all,
I'm currently trying out installation of tools from the Tool Shed
on a secondary Galaxy
Hi Everyone,
Here is an update for the last 2 weeks:
http://galaxy-gsoc2013.blogspot.com/2013/08/week-7-and-week-8-update.html
Saket
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Please keep all replies on the list by using reply all
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On Mon, Aug 12, 2013 at 2:04 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
On Mon, 2013-08-12 at 13:59 +0100, Peter Cock wrote:
On Mon, Aug 12, 2013 at 12:54 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
On Mon, 2013-08-12 at 12:50 +0100, Peter Cock wrote:
Hi all,
I'm
On Mon, 2013-08-12 at 14:13 +0100, Peter Cock wrote:
On Mon, Aug 12, 2013 at 2:04 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
On Mon, 2013-08-12 at 13:59 +0100, Peter Cock wrote:
On Mon, Aug 12, 2013 at 12:54 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
On Mon,
On Mon, Aug 12, 2013 at 2:18 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
On Mon, 2013-08-12 at 14:13 +0100, Peter Cock wrote:
I expect that in the meantime this bug will hit other people
as well (and until the Tool Shed testing is improved I'm a
little worried there could be other
On Mon, 2013-08-12 at 14:30 +0100, Peter Cock wrote:
On Mon, Aug 12, 2013 at 2:18 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
On Mon, 2013-08-12 at 14:13 +0100, Peter Cock wrote:
I expect that in the meantime this bug will hit other people
as well (and until the Tool Shed
On Mon, Aug 12, 2013 at 2:49 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
Ahhh, right the revisions are gone. So the latest is always the one that
are used. Oh oh ... I will screen through my github history and try to
revert the numpy package until next stable is out.
My guess is that
Ok reverted it!
Its now to a normal bash definition and I removed the atlas and lapack
definitions. So it should build but it has performance regressions.
If the new galaxy stable is out, I will upload the new version.
Hope it builds now for you.
Bjoern
bjoern.gruen...@gmail.com wrote:
On Mon, Aug 12, 2013 at 3:10 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
Ok reverted it!
Its now to a normal bash definition and I removed the atlas and lapack
definitions. So it should build but it has performance regressions.
If the new galaxy stable is out, I will upload the new
Hi Bjoern ( Greg),
RE: http://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61
I'm wondering why in the Biopython package dependencies
matplotlib is currently marked as prior installation required? i.e.
package name=numpy version=1.7.1
repository
Hi Peter,
Hi Bjoern ( Greg),
RE: http://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61
I'm wondering why in the Biopython package dependencies
matplotlib is currently marked as prior installation required? i.e.
package name=numpy version=1.7.1
repository
On Mon, 2013-08-12 at 15:55 +0100, Peter Cock wrote:
Maybe I should retitle this thread...
On Mon, Aug 12, 2013 at 3:43 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Aug 12, 2013 at 3:10 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
Ok reverted it!
Its now to a normal
On Mon, Aug 12, 2013 at 4:19 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
Hi Peter,
Hi Bjoern ( Greg),
RE: http://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61
I'm wondering why in the Biopython package dependencies
matplotlib is currently marked as prior
On Mon, 2013-08-12 at 16:26 +0100, Peter Cock wrote:
On Mon, Aug 12, 2013 at 4:19 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
Hi Peter,
Hi Bjoern ( Greg),
RE: http://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61
I'm wondering why in the Biopython package
On Mon, Aug 12, 2013 at 4:25 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
On Mon, 2013-08-12 at 15:55 +0100, Peter Cock wrote:
Maybe I should retitle this thread...
On Mon, Aug 12, 2013 at 3:43 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
Thank you - installing the NumPy
On Mon, 2013-08-12 at 16:32 +0100, Peter Cock wrote:
On Mon, Aug 12, 2013 at 4:25 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
On Mon, 2013-08-12 at 15:55 +0100, Peter Cock wrote:
Maybe I should retitle this thread...
On Mon, Aug 12, 2013 at 3:43 PM, Peter Cock
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