[galaxy-dev] integrate galaxy with slurm

hi, I want to integrate galaxy with slurm, but I don't know how to do it. And Galaxy wiki don't mention it yet. Whether I should install slurm-drmaa first? and then what should I do?

At 2015-01-04 01:00:01, galaxy-dev-request@lists.galaxyproject.org wrote:

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Today's Topics:

1. Create a package with binaries (KRESS Arnaud (ESP))
2. Re: package_numpy_1_7 can't be installed (Björn Grüning)
3. Re: package_numpy_1_7 can't be installed (Wang, Yu)
4. bx_python_0_7 installation error (Wang, Yu)
5. visualization in anonymous mode ? (Loraine Guéguen)
6. Re: [Spam:*****] Re: How galaxy workflow work ? (Ruslan Forostianov)
7. Re: [Spam:*****] Re: How galaxy workflow work ? (Ruslan Forostianov)
8. Problem using FastQC in Galaxy (Waldron, Michael H)
9. Re: samtools installation problems (Nathan Kipniss)
10. Re: Problem using FastQC in Galaxy (Björn Grüning)
11. Re: Problem using FastQC in Galaxy (Waldron, Michael H)

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Message: 1 Date: Tue, 16 Dec 2014 15:43:34 +0100 From: "KRESS Arnaud (ESP)" akress@unistra.fr To: galaxy-dev@lists.galaxyproject.org Subject: [galaxy-dev] Create a package with binaries Message-ID: 3d9e-54904500-a5-9499850@57904884 Content-Type: text/plain; charset="utf-8"

Hi gentlemen, I am currently struggling to create a custom package (to share via a toolshed) that would include a tool definition file and the associated binary. Once installed, I can launch a job but I get the following error message:

mytool.sh: line 14: mytool: unknown command

It seems that the PATH was not correctly set. What am I doing wrong ?

My directory tree in my package: . ├── mytool.sh ├── mytool.xml ├── bin │ └── mytool └── tool_dependencies.xml

Here is my tool_dependencies.xml file content:

<?xml version="1.0"?>

<tool_dependency> <package name="mytool" version="1.0"> <install version="1.0"> <actions> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> </readme> </package> </tool_dependency>

Thank you, AK

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Message: 2 Date: Tue, 16 Dec 2014 04:07:41 +0100 From: Björn Grüning bjoern@gruenings.eu To: "Wang, Yu" Yu.Wang@lrz.de, John Chilton jmchilton@gmail.com Cc: "galaxy-dev@lists.galaxyproject.org" galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] package_numpy_1_7 can't be installed Message-ID: 548FA1FD.5010007@gruenings.eu Content-Type: text/plain; charset=utf-8

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.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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Message: 3 Date: Tue, 16 Dec 2014 09:39:39 +0000 From: "Wang, Yu" Yu.Wang@lrz.de To: Björn Grüning bjoern@gruenings.eu Cc: "galaxy-dev@lists.galaxyproject.org" galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] package_numpy_1_7 can't be installed Message-ID: 9C386582-2905-44A3-9F7D-1B330A364C81@lrz.de Content-Type: text/plain; charset="utf-8"

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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To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

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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/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/