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 simple (just install
XCode and the command line tools first).

Note that I have not yet updated my Biopython using
tools on the main tool shed to include the automatic
dependency on the Tool Shed Biopython package,
so they require a manual install for now. As soon
as the NumPy/ATLAS packaging issue is solved,
I plan to push those updates from the Test Tool
Shed though.

Peter


On Fri, Sep 20, 2013 at 10:04 AM, Ido Tamir <ta...@imp.ac.at> wrote:
> 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 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.
>>>>>>
>>>>>> I used biopython repository as a guide to write my tool dependency 
>>>>>> definition:
>>>>>> http://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61
>>>>>>
>>>>>> I can confirm biopython repository is failing to install for me with
>>>>>> exactly the same error. I wonder if a recently addition in the test
>>>>>> toolshed broke the treatment of "prior_installation_required".
>>>>>>
>>>>>> Thanks,
>>>>>> Carlos
>>>>>
>>>>> Could be - note that currently Biopython isn't currently
>>>>> installing properly on the Test Tool Shed due to ALTAS
>>>>> failing (a requirement of NumPy which is a requirement
>>>>> of Biopython). Dave and Bjoern are I think looking at this
>>>>> already...
>>>>
>>>> I can't do much I tested it again and for me its working fine on my
>>>> computers I have at hand ... sorry.
>>>>
>>>
>>> In case it helps, this is how the INSTALLATION.log file ends on OS X 10.8.4:
>>> $ tail -n 3 
>>> ~/src/shed_tools_dependencies.central/atlas/3.10.1/iuc/package_atlas_3_10/3508de0ebae1/INSTALLATION.log
>>> x ATLAS/tune/lapack/lanbsrch.c
>>> tar: Error exit delayed from previous errors.
>>> #############################################
>>>
>>> This is the relevant part I can find in Galaxy's log:
>>> [localhost] local: tar xfvj atlas3.10.1.tar.bz2
>>>
>>> Warning: local() encountered an error (return code 1) while executing
>>> 'tar xfvj atlas3.10.1.tar.bz2'
>>>
>>> After noticing this I got what I'm guessing is the original file from
>>> sourceforge:
>>> http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.1/atlas3.10.1.tar.bz2
>>>
>>> I can confirm that trying to untar this file fails with the exact same
>>> error. However, on Ubuntu 13.04 untaring this file works just fine.
>>
>> That is new to me. How can that happen? Anyone with an OS-X can confirm
>> that?
>>
>>> On Ubuntu 13.04 the error I see is:
>>> STDERR
>>> It appears you have cpu throttling enabled, which makes timings
>>> unreliable and an ATLAS install nonsensical.  Aborting.
>>> See ATLAS/INSTALL.txt for further information
>>> #############################################
>>>
>>> Björn, you said cpu throttling can be easily disable on Ubuntu. Can
>>> you comment how? Do I need to disable it completely, or should the
>>> install script do it when installing?
>>
>> ATLAS (once untared ;-)) needs cpu-throttling to be disabled to
>> optimizes its library. If it is not disabled ATLAS compilation will
>> fail. For OS-X I found that:
>>
>> http://apple.stackexchange.com/questions/41045/how-can-i-disable-cpu-throttling-and-cpu-disabling
>>
>> Sorry, I never touched a OS-X. Nevertheless, If its not disabled, it is
>> supposed to fail silently and downstream packages will not be affected.
>> But if its crashing during untarring, I can't do much. What I can do is
>> to repack the tarball and host it elsewhere. What brings me to:
>>
>> http://gmod.827538.n3.nabble.com/RFC-Storing-of-tarballs-and-patches-for-tool-dependencies-to-enable-reproducibility-td4036591.html
>>
>> Bad news for a Friday morning, sorry :(
>> Bjoern
>>
>>
>>> Thanks,
>>> Carlos
>>>
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>>
>>
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>
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