I am having the same issue. The RHEL packages for atlas, blas, and lapack
are installed, but numpy 1.7 won't install, while numpy 1.9 seems to
install successfully.
--
David Lapointe Ph.D.
Sr. Bioinformatics Specialist
Research and Geospatial Technology Services
Tufts Technology Services (TTS)
16 Dearborn Road
Somerville MA 02144
Phone: 617-627-5319
Fax: 617-627-3667
http://it.tufts.edu
On 12/16/14, 5:08 AM, "Björn Grüning"
bjoern.gruening@gmail.com wrote:
>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, ³join² function is not installed on galaxy. When I tried to
>>install ³join², 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
>> wang@lrz.de
mailto:wang@lrz.de
>>
>> On 16 Dec 2014, at 04:07, Björn Grüning
>><bjoern@gruenings.eu
mailto:bjoern@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
>> wang@lrz.de
mailto:wang@lrz.demailto:wang@lrz.de
>>
>> On 15 Dec 2014, at 16:12, John Chilton
>><jmchilton@gmail.com
mailto:jmchilton@gmail.commailto:jmchilton@gmail.c
>om>> 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.Wang@lrz.de
mailto:Yu.Wang@lrz.demailto:Yu.Wang@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/nu
>>mpy/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/nu
>>mpy/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/nu
>>mpy/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/nu
>>mpy/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/nu
>>mpy/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/nu
>>mpy/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
>> wang@lrz.de
mailto:wang@lrz.demailto:wang@lrz.de
>>
>>
>>
>>
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>>
>>
>>
>>
>> ___________________________________________________________
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>>
>___________________________________________________________
>Please keep all replies on the list by using "reply all"
>in your mail client. To manage your subscriptions to this
>and other Galaxy lists, please use the interface at:
>
https://lists.galaxyproject.org/
>
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>
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