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> 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.de

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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.de>

On 15 Dec 2014, at 16:12, John Chilton <jmchilton@gmail.com<mailto: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.de<mailto: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.de<mailto:wang@lrz.de>

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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.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.de><mailto:wang@lrz.de>

On 15 Dec 2014, at 16:12, John Chilton <jmchilton@gmail.com<mailto:jmchilton@gmail.com><mailto: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.de<mailto:Yu.Wang@lrz.de><mailto: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.de<mailto:wang@lrz.de><mailto:wang@lrz.de>

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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.de><mailto:wang@lrz.de>

On 15 Dec 2014, at 16:12, John Chilton <jmchilton@gmail.com<mailto:jmchilton@gmail.com><mailto: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.de><mailto: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.de><mailto:wang@lrz.de>

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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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Hi, Peter, thanks for your answer. I found that package_numpy_1_7 can’t be installed by galaxy on my environment. Although I have installed ATLAS/Blas/ LAPACK. I still got error messages like ATLAS/Blas/ LAPACK are not found. Cheers, Yu di29her wang@lrz.de<mailto:wang@lrz.de> On 11 Dec 2014, at 17:24, Peter Cock <p.j.a.cock@googlemail.com<mailto:p.j.a.cock@googlemail.com>> wrote: On Wed, Dec 10, 2014 at 4:31 PM, Wang, Yu <Yu.Wang@lrz.de<mailto:Yu.Wang@lrz.de>> wrote: Hi, I am testing Basic Protocol 1 on my local galaxy instance. But Join didn't work. What did I do wrong? I installed join from galaxy main tool shed, bx_python_0_7 was installed but with installation Status "missing tool dependencies". ... Traceback (most recent call last): File "/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/join/de21bdbb8d28/join/gops_join.py<http://toolshed.g2.bx.psu.edu/repos/devteam/join/de21bdbb8d28/join/gops_join.py>", line 13, in <module> from bx.intervals import * ImportError: No module named bx.intervals 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 Galaxy dev team, why isn't this declaring a dependency on: https://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 Peter