It appears that the Tool Shed does not show the correct "readme" file
content.
1) get_readme_files() in lib/galaxy/webapps/tool_shed/controllers/
repository.py gets the correct metadata from the database
2) build_readme_files_dict() in lib/tool_shed/util/readme_util.py
reads data from whatev
On Fri, Sep 20, 2013 at 9:08 AM, Nicola Soranzo 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
>>
>> https://github.com/jmchilton/galaxy-central/commit/b500a24bc1aa94
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
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 st
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
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
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 whil
On Fri, Sep 20, 2013 at 8:48 AM, Bjoern Gruening
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
> you will need a
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 interesti
> On Fri, Sep 20, 2013 at 1:48 PM, Bjoern Gruening
> 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 python and not
On Fri, Sep 20, 2013 at 1:48 PM, Bjoern Gruening
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:
> http://testtoolshed.g2.bx.psu.edu
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 generally,
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 'tar
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
> cleanup = Cleanup()
> File "./scripts/cleanup_datasets/pgcleanup.py", line 55, in __i
On Fri, Sep 20, 2013 at 10:17 AM, Bjoern Gruening
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 for you I will consi
On Wed, Sep 18, 2013 at 11:47 AM, Peter Cock wrote:
> On Tue, Aug 27, 2013 at 2:18 PM, Dave Bouvier 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 file for
>> that operating syst
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 wrote:
> Hi Ido and Carlos,
>
> can you check if that tarball is working?
>
> http://downloads.sourceforge.net/project/math-atlas/Developer%20%28unstable%
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 si
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
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 wrote:
> Hi Carlos,
>
>>> Hi Peter and Carlos,
>>>
On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto
wrot
Hi Carlos,
> > Hi Peter and Carlos,
> >
> >> On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto
> >> 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
Hi Peter and Carlos,
> On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto
> 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.
> >
> > I used biop
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.
>
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