On Sun, Sep 29, 2013 at 10:43 PM, Guest, Simon
simon.gu...@agresearch.co.nz wrote:
At Fri, 27 Sep 2013 00:23:37 -0500,
John Chilton wrote:
Simon,
What is the advantage of putting that XML definition in the tool shed?
It is not 100% true because of prior_install_required dependencies,
but
I have issued a pull request with a specific implementation of these ideas:
https://bitbucket.org/galaxy/galaxy-central/pull-request/227/tool-dependency-resolver-plugins/diff
Please feel free to comment.
-John
On Fri, Sep 27, 2013 at 12:23 AM, John Chilton chil...@msi.umn.edu wrote:
Simon,
Hi Peter and John,
thanks for your comments and thanks for working on the patch John.
On Thu, Sep 26, 2013 at 10:27 PM, John Chilton chil...@msi.umn.edu wrote:
My recommendation would be make the tool dependency install work on as
many platforms as you can and not try to optimize in such a
On Sun, Sep 29, 2013 at 1:17 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Peter and John,
thanks for your comments and thanks for working on the patch John.
Peter wrote:
In this case, for simplicity I would advocate plain NumPy, without
worrying about needing ATLAS.
At Fri, 27 Sep 2013 00:23:37 -0500,
John Chilton wrote:
Simon,
What is the advantage of putting that XML definition in the tool shed?
It is not 100% true because of prior_install_required dependencies,
but for the most part sourcing/load the environment for tools is a
Galaxy problem, not
On Thu, Sep 26, 2013 at 10:27 PM, John Chilton chil...@msi.umn.edu wrote:
My recommendation would be make the tool dependency install work on as
many platforms as you can and not try to optimize in such a way that
it is not going to work - i.e. favor reproduciblity over performance.
Make the precedence a config option. Otherwise I agree.
In addition, I still like the idea I suggested earlier of dependency provider
plugins. Then you could (for example) have one that uses 'modules' and skips
env.sh entirely.
On Sep 26, 2013, at 9:15 PM, John Chilton chil...@msi.umn.edu
Hi Bjoern,
Is there anything else we (the Galaxy community) can do to help
sort out the ATLAS installation problems?
Another choice might be to use OpenBLAS instead of ATLAS, e.g.
http://stackoverflow.com/questions/11443302/compiling-numpy-with-openblas-integration
However, I think we build
In case this will help, I have the framework implemented (and committed) for
handling pre-compioled binaries for tool dependencies for a supported set of
architectures. Dave B has updated a lot of tool dependency definitions on both
the test and main tool sheds to use this enhancement - those
Hi,
Hi Bjoern,
Is there anything else we (the Galaxy community) can do to help
sort out the ATLAS installation problems?
Thanks for asking. I have indeed a few things I would like some
comments.
Another choice might be to use OpenBLAS instead of ATLAS, e.g.
My recommendation would be make the tool dependency install work on as
many platforms as you can and not try to optimize in such a way that
it is not going to work - i.e. favor reproduciblity over performance.
If a system administrator or institution want to sacrifice
reproduciblity and optimize
Hi John,
On Sep 26, 2013, at 5:27 PM, John Chilton chil...@msi.umn.edu wrote:
My recommendation would be make the tool dependency install work on as
many platforms as you can and not try to optimize in such a way that
it is not going to work - i.e. favor reproduciblity over performance.
If a
I was not even thinking we needed to modify the tool shed to implement
this. I was hoping (?) you could just modify:
lib/galaxy/tools/deps/__init__.py
to implement this. If some tool contains the tag
requirement type=package version=1.7.1numpy/requirement
then if there is a manually
James, it seems I was answering at the same time you were, so to highlight my
comments to John, I'm just wondering how this will work for repositories in the
tool shed that do not contain any tools, but just tool dependency definitions
or complex repository dependency definitions.
Thanks,
At Thu, 26 Sep 2013 22:03:09 -0400,
Greg Von Kuster wrote:
Hi John,
On Sep 26, 2013, at 9:15 PM, John Chilton chil...@msi.umn.edu wrote:
I was not even thinking we needed to modify the tool shed to implement
this. I was hoping (?) you could just modify:
Nothing in the Tool Shed
Simon,
What is the advantage of putting that XML definition in the tool shed?
It is not 100% true because of prior_install_required dependencies,
but for the most part sourcing/load the environment for tools is a
Galaxy problem, not so much a tool shed one. What if we did this
instead?
Add an
On Thu, Sep 26, 2013 at 9:10 PM, Greg Von Kuster g...@bx.psu.edu wrote:
James, it seems I was answering at the same time you were, so to highlight my
comments to John, I'm just wondering how this will work for repositories in
the tool shed that do not contain any tools, but just tool
Forgot to copy the list on this email.
On Mon, Sep 23, 2013 at 9:32 AM, Carlos Borroto
carlos.borr...@gmail.com wrote:
On Fri, Sep 20, 2013 at 6:12 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Carlos,
Can you try again?
Also the new unstable version if you can.
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 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,
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
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
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
On Thu, Sep 19, 2013 at 5:15 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
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
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