Hi Ido,
If I might chime in, I am a bit worried about all the automatic installation
going on in galaxy, and it seems that the trend is to enhance this.
A small R or python script calling into well known libraries that come from
well known repositories (bioconductor etc… ) I can check.
(Of
Hi Peter and Carlos,
On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto
carlos.borr...@gmail.com wrote:
I did an extra test. Started with a clean 'galaxy-dist'. This time
both repositories fail with the same error. I guess before something
was cached for the repository with version 0.1.4.
Hi Carlos,
Hi Peter and Carlos,
On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto
carlos.borr...@gmail.com wrote:
I did an extra test. Started with a clean 'galaxy-dist'. This time
both repositories fail with the same error. I guess before something
was cached for the repository
Yes this tar is broken at least on OSX.
Other people have the same issue:
http://code.google.com/p/libarchive/issues/detail?id=299
On Sep 20, 2013, at 10:41 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote:
Hi Carlos,
Hi Peter and Carlos,
On Mon, Sep 16, 2013 at 8:57 PM, Carlos
Hi Ido and Carlos,
can you check if that tarball is working?
http://downloads.sourceforge.net/project/math-atlas/Developer%20%
28unstable%29/3.11.11/atlas3.11.11.tar.bz2
The chance is low, but if its working for you I will consider to create
a new version for it.
Thanks,
Bjoern
Yes this tar
Thanks for posting that Ido,
Right now I would suggest manually installing these
dependencies, rather than ticking the box for the Tool
Shed to do it for you.
If you are using the Apple provided Python to run your
Galaxy on Mac OS X, it comes with NumPy anyway,
so compiling Biopython should be
tar xvfj atlas3.11.11.tar.bz2
shows no errors on OSX and creates one ATLAS folder.
best,
ido
On Sep 20, 2013, at 11:17 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote:
Hi Ido and Carlos,
can you check if that tarball is working?
On Wed, Sep 18, 2013 at 11:47 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, Aug 27, 2013 at 2:18 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
I also tried running the command that returns error code 64 on the same
system that runs the automated tests, and it downloaded the correct
On Fri, Sep 20, 2013 at 10:17 AM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
Hi Ido and Carlos,
can you check if that tarball is working?
http://downloads.sourceforge.net/project/math-atlas/Developer%20%28unstable%29/3.11.11/atlas3.11.11.tar.bz2
The chance is low, but if its working
Hi All,
I'm trying to do some cleanup in my test environment (galaxy-dist)
and pgcleanup.py ends with
Traceback (most recent call last):
File ./scripts/cleanup_datasets/pgcleanup.py, line 773, in module
cleanup = Cleanup()
File ./scripts/cleanup_datasets/pgcleanup.py, line 55, in
Hi,
I tried to things to solve it.
1: I uploaded a new version to:
http://testtoolshed.g2.bx.psu.edu/view/iuc/package_atlas_3_10 this time
with target_filename=ATLAS.tar.bz2. That is a rather new feature, so
you will need a recent Galaxy version. The prosite is that we do not
need to call
Hello all,
I'm looking at how to automatically script setting up a
Galaxy instance with selected tools with dependencies
as part of automated testing [*].
Can the Galaxy API be used to run the dependency
instructions in a tool_dependencies.xml file (without
using a Tool Shed)?
Or more
On Fri, Sep 20, 2013 at 1:48 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
Hi,
I tried to things to solve it.
Was this specifically to solve ATLAS under Mac OS X,
or more generally include the problem shown on the
Galaxy (Test) Tool Shed?
1: I uploaded a new version to:
On Fri, Sep 20, 2013 at 1:48 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
Hi,
I tried to things to solve it.
Was this specifically to solve ATLAS under Mac OS X,
or more generally include the problem shown on the
Galaxy (Test) Tool Shed?
Yes. My hope was to use tarfile from
Il giorno gio, 19/09/2013 alle 12.42 -0500, John Chilton ha scritto:
Feature request received.
The following changeset demonstrates how one could implement this
https://github.com/jmchilton/galaxy-central/commit/b500a24bc1aa94bef48db20a7cc1f3d68855b7fd
Hi John,
that's pretty interesting
On Fri, Sep 20, 2013 at 8:48 AM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
Hi,
I tried to things to solve it.
1: I uploaded a new version to:
http://testtoolshed.g2.bx.psu.edu/view/iuc/package_atlas_3_10 this time
with target_filename=ATLAS.tar.bz2. That is a rather new feature, so
Hi Rico,
The test tool shed is now running my latest commit - 10629:ab20415126a7. I was
successful with installing the genome diversity repository and all of it's
dependencies using that changeset in my local Galaxy environment (although 3
tool dependencies encountered the following errors
Thanks,
I integrated parts of these snippets into our general dynamic_jobs function,
and it works flawlessly.
Best,
Geert
Van: jmchil...@gmail.com [jmchil...@gmail.com] namens John Chilton
[chil...@msi.umn.edu]
Verzonden: donderdag 19 september 2013
The default branch ( i.e., the galaxy-central repository on bitbucket) is
backward compatible to the December 20, 2012 Galaxy release with regard to
communication between a Galaxy instance and a Tool Shed instance. It is not
guaranteed that this communication will be forward compatible as new
Greg,
I still get the same traceback. The issue is with installing a
repository from testtoolshed, which is running code on the default
branch, to a galaxy instance running on the stable branch. My
understanding was that the default branch is supposed to be backward-
compatible to the
Hello Rico,
I'm not seeing a problem here. The revision of the genome_diversity you're
referring to is the repository tip on the main tool shed. The README file on
disk has this content:
g2cmnty@montana:~/galaxy_toolshed/database/community_files/000/repo_200$ cat
README
Source code for the
On Fri, Sep 20, 2013 at 9:08 AM, Nicola Soranzo sora...@crs4.it wrote:
Il giorno gio, 19/09/2013 alle 12.42 -0500, John Chilton ha scritto:
Feature request received.
The following changeset demonstrates how one could implement this
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