Hi,

Am 16.12.2014 um 10:39 schrieb Wang, Yu:
> Hi, Björn, my intention was to test a simple workflow (BASIC PROTOCOL 1 
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418382/) on my local galaxy 
> installation.
> By default, “join” function is not installed on galaxy. When I tried to 
> install “join”, it reported error on the installation of bx_python_0_7 
> (Galaxy main tool shed).
> It looks like the automated installation of bx python failed somehow.
> Looking at the package, it will attempt to install NumPy 1.7.1
> https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7

I see, thanks for the information.
Unfortunately, this is a different package from what I was talking. Have
you compiled ATLAS or installed it with your package manager? Are you
running a Linux or OS-X.

The problem is that Galaxy tries to install:

pip install numpy

And this crashes because you don't have all requirements installed. If
possible try to install LAPACK and ATLAS with your package manager, you
need to set a lot of ENV variables if you compile it yourself.

Cheers,
Bjoern


> Then I tried to install NumPy 1.7.1 from Galaxy main tool shed, there were 
> all these errors from LAPACK and ATLAS.
> 
> Cheers,
> Yu
> 
> di29her
> w...@lrz.de<mailto:w...@lrz.de>
> 
> On 16 Dec 2014, at 04:07, Björn Grüning 
> <bjo...@gruenings.eu<mailto:bjo...@gruenings.eu>> wrote:
> 
> Hi Wang,
> 
> can you point me to the exact version your try to install. There is an
> old numpy_1_7 package which should be deprecated. We had a lot of
> trouble installing ATLAS and LAPACK and decided to deprecate all
> packages which depends on LAPACK and ATLAS. Now we do not require both
> libraries anymore.
> 
> Thanks,
> Bjoern
> 
> Am 15.12.2014 um 18:16 schrieb Wang, Yu:
> Hi, John,thanks for your answer. I installed svnversion, and 
> compiled/installed ATLAS/Blas/ LAPACK. I still got error messages like 
> ATLAS/Blas/ LAPACK are not found.
> I could install package_numpy_1_9 by using galaxy main tool shed. There is 
> something wrong with package_numpy_1_7 on my environment.
> 
> Cheers,
> Yu
> 
> di29her
> w...@lrz.de<mailto:w...@lrz.de><mailto:w...@lrz.de>
> 
> On 15 Dec 2014, at 16:12, John Chilton 
> <jmchil...@gmail.com<mailto:jmchil...@gmail.com><mailto:jmchil...@gmail.com>> 
> wrote:
> 
> Looks like this - https://github.com/clarete/curdling/issues/19
> 
> I think you somehow need to install the package svn on your machine - if you 
> have root on that machine the command might be something like "sudo zypper 
> install svn" or may it is "sudo zypper install subversion". If you don't have 
> root on the machine I would ask the operating system maintainer or try to 
> compile and install svn locally and make it available to Galaxy.
> 
> Hope this helps,
> 
> -John
> 
> On Fri, Dec 12, 2014 at 7:14 AM, Wang, Yu 
> <yu.w...@lrz.de<mailto:yu.w...@lrz.de><mailto:yu.w...@lrz.de>> wrote:
> Hi, I am running galaxy on SLSE11, when I tried to install bumpy 1.7.1, I got 
> the following error.
> Can anyone point what goes wrong here?
> 
> 
> Error   Running from numpy source directory.
> /bin/sh: svnversion: command not found
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1494:
>  UserWarning:
>    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
>    Directories to search for the libraries can be specified in the
>    numpy/distutils/site.cfg file (section [atlas]) or by setting
>    the ATLAS environment variable.
>  warnings.warn(AtlasNotFoundError.__doc__)
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1503:
>  UserWarning:
>    Blas (http://www.netlib.org/blas/) libraries not found.
>    Directories to search for the libraries can be specified in the
>    numpy/distutils/site.cfg file (section [blas]) or by setting
>    the BLAS environment variable.
>  warnings.warn(BlasNotFoundError.__doc__)
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1506:
>  UserWarning:
>    Blas (http://www.netlib.org/blas/) sources not found.
>    Directories to search for the sources can be specified in the
>    numpy/distutils/site.cfg file (section [blas_src]) or by setting
>    the BLAS_SRC environment variable.
>  warnings.warn(BlasSrcNotFoundError.__doc__)
> /bin/sh: svnversion: command not found
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1408:
>  UserWarning:
>    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
>    Directories to search for the libraries can be specified in the
>    numpy/distutils/site.cfg file (section [atlas]) or by setting
>    the ATLAS environment variable.
>  warnings.warn(AtlasNotFoundError.__doc__)
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1419:
>  UserWarning:
>    Lapack (http://www.netlib.org/lapack/) libraries not found.
>    Directories to search for the libraries can be specified in the
>    numpy/distutils/site.cfg file (section [lapack]) or by setting
>    the LAPACK environment variable.
>  warnings.warn(LapackNotFoundError.__doc__)
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1422:
>  UserWarning:
>    Lapack (http://www.netlib.org/lapack/) sources not found.
>    Directories to search for the sources can be specified in the
>    numpy/distutils/site.cfg file (section [lapack_src]) or by setting
>    the LAPACK_SRC environment variable.
>  warnings.warn(LapackSrcNotFoundError.__doc__)
> error: must supply either home or prefix/exec-prefix -- not both
> 
> 
> Cheers,
> Yu
> 
> di29her
> w...@lrz.de<mailto:w...@lrz.de><mailto:w...@lrz.de>
> 
> 
> 
> 
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