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 wang@lrz.demailto:wang@lrz.de

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.demailto:wang@lrz.de

On 15 Dec 2014, at 16:12, John Chilton <jmchilton@gmail.commailto:jmchilton@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.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/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 wang@lrz.demailto:wang@lrz.de

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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

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.demailto:wang@lrz.de

On 16 Dec 2014, at 04:07, Björn Grüning <bjoern@gruenings.eumailto: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.demailto:wang@lrz.demailto:wang@lrz.de

On 15 Dec 2014, at 16:12, John Chilton <jmchilton@gmail.commailto:jmchilton@gmail.commailto:jmchilton@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.Wang@lrz.demailto: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/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 wang@lrz.demailto:wang@lrz.demailto:wang@lrz.de

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Hi, Björn, thanks for your tip. I am working on SLES11. After installing LAPACK and ATLAS, I could install numpy1.7.1 by using Galaxy main tool shed.

But installation of bx_python_0_7 produced a new error message: bx-python http://galaxy.srv.lrz.de:8080/admin_toolshed/manage_repository_tool_dependencies?repository_id=a799d38679e985db&operation=browse&tool_dependency_ids=a799d38679e985db 0.7.1 package Error Traceback (most recent call last): File "/home/galaxy/galaxy-dist/tool_deps/__virtualenv_src/virtualenv.py", line 2577, in <module> main() File "/home/galaxy/galaxy-dist/tool_deps/__virtualenv_src/virtualenv.py", line 979, in main no_pip=options.nohttp://options.no_pip) File "/home/galaxy/galaxy-dist/tool_deps/__virtualenv_src/virtualenv.py", line 1091, in create_environment search_dirs=search_dirs, never_download=never_download) File "/home/galaxy/galaxy-dist/tool_deps/__virtualenv_src/virtualenv.py", line 611, in install_setuptools search_dirs=search_dirs, never_download=never_download) File "/home/galaxy/galaxy-dist/tool_deps/__virtualenv_src/virtualenv.py", line 583, in _install_req cwd=cwd) File "/home/galaxy/galaxy-dist/tool_deps/__virtualenv_src/virtualenv.py", line 1057, in call_subprocess % (cmd_desc, proc.returncode)) OSError: Command /home/galaxy/galaxy-...8bca/venv/bin/python -c "#!python """Bootstra...sys.argv[1:])

" /home/galaxy/galaxy-...ols-0.6c11-py2.6.egg failed with error code 1 /bin/sh: /home/galaxy/galaxy-dist/tool_deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/bin/activate: No such file or directory

In order to solve an error message “must supply either home or prefix/exec-prefix -- not both" to install numpy I have created a ~/.pydistutils.cfg file with the following contents:

[install] prefix=

Could this be the reason for the bx-python error? many thanks!

Cheers, Yu

di29her wang@lrz.demailto:wang@lrz.de

On 16 Dec 2014, at 11:08, Björn Grüning <bjoern.gruening@gmail.commailto: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, “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 wang@lrz.demailto:wang@lrz.demailto:wang@lrz.de

On 16 Dec 2014, at 04:07, Björn Grüning <bjoern@gruenings.eumailto:bjoern@gruenings.eumailto: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.demailto:wang@lrz.demailto:wang@lrz.demailto:wang@lrz.de

On 15 Dec 2014, at 16:12, John Chilton <jmchilton@gmail.commailto:jmchilton@gmail.commailto:jmchilton@gmail.commailto:jmchilton@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.Wang@lrz.demailto:Yu.Wang@lrz.demailto: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/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 wang@lrz.demailto:wang@lrz.demailto:wang@lrz.demailto:wang@lrz.de

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Hi David,

do you get the same error message as Wang?

Am 17.12.2014 um 23:10 schrieb Lapointe, David:

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.