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)
>
>
>----------------------------------------------------------------------
>
>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
>
>
>------------------------------
>
>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.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>
>>
>>
>>
>>
>> ___________________________________________________________
>> 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/
>>
>>
>>
>>
>> ___________________________________________________________
>> 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/
>>
>
>
>------------------------------
>
>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.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>
>
>
>
>
>___________________________________________________________
>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/
>
>
>
>
>___________________________________________________________
>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/
>
>
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>
>------------------------------
>
>Message: 4
>Date: Tue, 16 Dec 2014 15:16:50 +0000
>From: "Wang, Yu" <Yu.Wang@lrz.de>
>To: Björn Grüning <bjoern.gruening@gmail.com>
>Cc: "galaxy-dev@lists.galaxyproject.org"
> <galaxy-dev@lists.galaxyproject.org>
>Subject: [galaxy-dev] bx_python_0_7 installation error
>Message-ID: <8BEC9B22-6CB8-4927-BF39-7A3B08BEB3E6@lrz.de>
>Content-Type: text/plain; charset="utf-8"
>
>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.no<http://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.de<mailto:wang@lrz.de>
>
>On 16 Dec 2014, at 11:08, Björn Grüning <bjoern.gruening@gmail.com<mailto: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.de<mailto:wang@lrz.de><mailto:wang@lrz.de>
>
>On 16 Dec 2014, at 04:07, Björn Grüning <bjoern@gruenings.eu<mailto: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><mailto:wang@lrz.de>
>
>On 15 Dec 2014, at 16:12, John Chilton <jmchilton@gmail.com<mailto: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><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><mailto:wang@lrz.de>
>
>
>
>
>___________________________________________________________
>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/
>
>
>
>
>___________________________________________________________
>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/
>
>
>
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>------------------------------
>
>Message: 5
>Date: Thu, 18 Dec 2014 10:19:51 +0100
>From: Loraine Guéguen <loraine.gueguen@sb-roscoff.fr>
>To: galaxy-dev@lists.galaxyproject.org
>Subject: [galaxy-dev] visualization in anonymous mode ?
>Message-ID: <54929C37.1070508@sb-roscoff.fr>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>Hi,
>
>I'd like to use the visualization in anonymous mode, but the visualize
>icon on the dataset is not available in anonymous mode (although it
>works fine when connected).
>Is it possible to activate the dataset visualization in anonymous mode ?
>
>Thanks,
>
>Loraine
>
>
>
>--
>Loraine Guéguen
>
>Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
>Service Informatique et Bioinformatique
>Station Biologique de Roscoff
>FR 2424 CNRS UPMC
>Place Georges Teissier
>CS 90074
>29688 Roscoff cedex
>tel: ++33 (0)2 98 29 56 46 (interne : 415)
>http://abims.sb-roscoff.fr/
>http://www.sb-roscoff.fr/
>
>
>
>------------------------------
>
>Message: 6
>Date: Thu, 18 Dec 2014 16:55:29 +0100
>From: Ruslan Forostianov <ruslan@thehyve.nl>
>To: jmchilton@gmail.com
>Cc: galaxy-dev@lists.galaxyproject.org, "Bruijn, Freek de"
> <f.debruijn@vumc.nl>
>Subject: Re: [galaxy-dev] [Spam:*****] Re: How galaxy workflow work ?
>Message-ID:
> <CAK_DDJu1njn7AxQt_MwmdRZBKFc0Mv3tW=tZ_XoPXAZkj39pEA@mail.gmail.com>
>Content-Type: text/plain; charset="utf-8"
>
>galaxy.web.framework.decorators ERROR 2014-12-18 12:22:04,760 Uncaught
>exception in exposed API method:
>Traceback (most recent call last):
> File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py",
>line 244, in decorator
> rval = func( self, trans, *args, **kwargs)
> File
>"/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/workflows.py", line
>231, in create
> populate_state=True,
> File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/run.py", line 18, in
>invoke
> modules.populate_module_and_state( trans, workflow,
>workflow_run_config.param_map )
> File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line 843,
>in populate_module_and_state
> step_errors = module_injector.inject( step, step_args=step_args )
> File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line 830,
>in inject
> state, step_errors = module.compute_runtime_state( trans, step_args )
> File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line 264,
>in compute_runtime_state
> state = self.decode_runtime_state( trans, step_updates.pop(
>"tool_state" ) )
>KeyError: 'tool_state'
>
>Cheers,
>Ruslan Forostianov
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>
>------------------------------
>
>Message: 7
>Date: Fri, 19 Dec 2014 22:21:11 +0100
>From: Ruslan Forostianov <ruslan@thehyve.nl>
>To: John Chilton <jmchilton@gmail.com>
>Cc: "galaxy-dev@lists.galaxyproject.org"
> <galaxy-dev@lists.galaxyproject.org>, "Bruijn, Freek de"
> <f.debruijn@vumc.nl>
>Subject: Re: [galaxy-dev] [Spam:*****] Re: How galaxy workflow work ?
>Message-ID:
> <CAK_DDJuOMLkXTVRvM1SxtD=HULqfmMx7Usck4dzVr8xcaC_iMA@mail.gmail.com>
>Content-Type: text/plain; charset="utf-8"
>
>Hi John,
>
>I did some investigation.
>I added logging statement to line 843 of lib/galaxy/workflow/modules.py
>file:
>
>for step in workflow.steps:
> step_args = param_map.get( step.id, {} )
> * log.info <http://log.info>('step.id <http://step.id>=' +
>str(step.id <http://step.id>) + ', step_args=' + str(step_args))*
> step_errors = module_injector.inject( step, step_args=step_args )
>
>It gives:
>galaxy.workflow.modules INFO 2014-12-18 13:39:31,464 step.id=21,
>step_args={'contrast': u'Female-Male'}
>
>See http post below. It looks like somehow runtime parameter appears among
>steps.
>
>4 * Client out-bound request
>4 > POST
>http://galaxy.thehyve.net/api/workflows?key=5c4f870bc0108a60dc7435a000fb7874
>4 > Content-Type: application/json
>4 > Accept: application/json
>{"parameters":{"21":{"contrast":"Female-Male"}},"workflow_id":"d4bec7f9d7e8cf4d","history":"hist_id=59bd7ef52a8ce0e8","ds_map":{"21":{"id":"fb94345e0a2a5a2c","src":"hda"},"22":{"id":"9384bb69863b3f9e","src":"hda"}},"no_add_to_history":"true"}
>
>Here is link to ga file for completeness:
>https://github.com/thehyve/trait_workflow_runner/blob/master/src/main/resources/nl/vumc/biomedbridges/galaxy/rna-seq-dge.ga
>
>On Fri, Dec 19, 2014 at 7:47 PM, John Chilton <jmchilton@gmail.com> wrote:
>
>> That is odd. Does that workflow run through the UI? It looks like it
>> was missing a tool during import. Certainly the API should indicate
>> that overtly instead of failing in this fashion.
>>
>> If it does run, can you export it to JSON and send it to me?
>>
>> -John
>>
>> On Thu, Dec 18, 2014 at 10:55 AM, Ruslan Forostianov <ruslan@thehyve.nl>
>> wrote:
>> > galaxy.web.framework.decorators ERROR 2014-12-18 12:22:04,760 Uncaught
>> > exception in exposed API method:
>> > Traceback (most recent call last):
>> > File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py",
>> > line 244, in decorator
>> > rval = func( self, trans, *args, **kwargs)
>> > File
>> > "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/workflows.py",
>> line
>> > 231, in create
>> > populate_state=True,
>> > File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/run.py", line 18, in
>> > invoke
>> > modules.populate_module_and_state( trans, workflow,
>> > workflow_run_config.param_map )
>> > File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line
>> 843,
>> > in populate_module_and_state
>> > step_errors = module_injector.inject( step, step_args=step_args )
>> > File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line
>> 830,
>> > in inject
>> > state, step_errors = module.compute_runtime_state( trans, step_args )
>> > File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line
>> 264,
>> > in compute_runtime_state
>> > state = self.decode_runtime_state( trans, step_updates.pop(
>> "tool_state"
>> > ) )
>> > KeyError: 'tool_state'
>> >
>> > Cheers,
>> > Ruslan Forostianov
>> >
>>
>
>
>
>--
>Ruslan Forostianov,
>*Software Developer*
>www.thehyve.nl
>*E* ruslan@thehyve.nl
>*M* +31(0)6 83 51 30 81
>*Skype* foro.ru
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>
>------------------------------
>
>Message: 8
>Date: Fri, 2 Jan 2015 20:22:06 +0000
>From: "Waldron, Michael H" <mwaldron@email.unc.edu>
>To: "galaxy-dev@bx.psu.edu" <galaxy-dev@bx.psu.edu>
>Subject: [galaxy-dev] Problem using FastQC in Galaxy
>Message-ID:
> <9678294B07E1BA4084DA67BD4DC53D9E87D556EF@ITS-MSXMBS2F.ad.unc.edu>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Having a problem with directing FastQC output in Galaxy. User is running a job whose command line looks like this:
>
># FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13836_files /proj/galaxy/job_working_directory/010/10467/dataset_13836_files/SRR016862.fastq
>
>Job output looks like this:
>
>## odpath=None: No output found in None. Output for the run was:
># FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13827_files /proj/galaxy/job_working_directory/010/10467/dataset_13827_files/SRR016862.fastq
>Started analysis of SRR016862.fastq
>Approx 5% complete for SRR016862.fastq
>Approx 10% complete for SRR016862.fastq
>Approx 15% complete for SRR016862.fastq
>Approx 20% complete for SRR016862.fastq
>Approx 25% complete for SRR016862.fastq
>Approx 30% complete for SRR016862.fastq
>Approx 35% complete for SRR016862.fastq
>Approx 40% complete for SRR016862.fastq
>Approx 45% complete for SRR016862.fastq
>Approx 50% complete for SRR016862.fastq
>Approx 55% complete for SRR016862.fastq
>Approx 60% complete for SRR016862.fastq
>Approx 65% complete for SRR016862.fastq
>Approx 70% complete for SRR016862.fastq
>Approx 75% complete for SRR016862.fastq
>Approx 80% complete for SRR016862.fastq
>Approx 85% complete for SRR016862.fastq
>Approx 90% complete for SRR016862.fastq
>Approx 95% complete for SRR016862.fastq
>Analysis complete for SRR016862.fastq
>
>The job_working_directory/010/10467 directory is created, however it is empty. It appears this "odpath" needs to be set somehow?
>
>Does anyone know a solution for this?
>
>Mike Waldron
>Systems Specialist
>ITS - Research Computing Center
>University of North Carolina at Chapel Hill
>
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>
>------------------------------
>
>Message: 9
>Date: Fri, 2 Jan 2015 12:57:31 -0800
>From: Nathan Kipniss <nkipniss@gmail.com>
>To: Björn Grüning <bjoern.gruening@gmail.com>,
> p.j.a.cock@googlemail.com, Scott Jeschonek <scottj@averesystems.com>
>Cc: galaxy-dev@lists.galaxyproject.org
>Subject: Re: [galaxy-dev] samtools installation problems
>Message-ID:
> <CAOWYWEyUoudvoi7WMHZcj47-+GN84hnnaZYf1S32eTniOCGUBQ@mail.gmail.com>
>Content-Type: text/plain; charset="utf-8"
>
>Thank you all for the help! Its all running smoothly now.
>
>Best,
>Nathan
>
>On Wed, Dec 31, 2014 at 3:50 PM, Björn Grüning <bjoern.gruening@gmail.com>
>wrote:
>
>> Hi Nathan,
>>
>> please try the following.
>>
>> ln -s /path/to/your/shed_tools/samtools/0.1.19/devteam/what/ever/
>> /path/to/your/shed_tools/samttools/default
>>
>> The important part is that it is samtools < 1.0 and that the default
>> link is a link to the folder in which you find the env.sh file.
>>
>> I hope this will tell Galaxy how to find samtools for you. Otherwise
>> simply put the samtools binary into your $PATH.
>>
>> Cheers and happy new year!
>> Bjoern
>>
>> Am 31.12.2014 um 19:49 schrieb Nathan Kipniss:
>> > Hi All,
>> >
>> > New to galaxy here. I'm having an issue uploading bam files into a local
>> > instance of galaxy. I understand that it requires samtools, and I
>> installed
>> > the appropriate dependency from the toolshed. However, I get the
>> following
>> > error:
>> >
>> > Traceback (most recent call last):
>> > File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line
>> > 407, in <module>
>> > __main__()
>> > File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line
>> > 396, in __main__
>> > add_file( dataset, registry, json_file, output_path )
>> > File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line
>> > 324, in add_file
>> > if link_data_only == 'copy_files' and
>> > datatype.dataset_content_needs_grooming( output_path ):
>> > File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line
>> > 147, in dataset_content_needs_grooming
>> > version = self._get_samtools_version()
>> > File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line
>> > 129, in _get_samtools_version
>> > output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE,
>> > stdout=subprocess.PIPE ).communicate()[1]
>> > File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
>> > errread, errwrite)
>> > File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
>> > raise child_exception
>> > OSError: [Errno 2] No such file or directory
>> >
>> >
>> > Which leads me to believe something is wrong with the install (can't
>> > find samtools). The dependency directory is also set. Is there another
>> > step I'm missing, or is it better to not install dependencies via the
>> > toolshed?
>> >
>> > Best,
>> > Nathan Kipniss
>> >
>> >
>> >
>> > ___________________________________________________________
>> > 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/
>> >
>>
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>
>------------------------------
>
>Message: 10
>Date: Sat, 03 Jan 2015 12:42:34 +0100
>From: Björn Grüning <bjoern.gruening@gmail.com>
>To: "Waldron, Michael H" <mwaldron@email.unc.edu>,
> "galaxy-dev@bx.psu.edu" <galaxy-dev@bx.psu.edu>
>Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>Message-ID: <54A7D5AA.6050602@gmail.com>
>Content-Type: text/plain; charset=utf-8
>
>Hi Michael,
>
>which version of the FASTQC wrapper are you running? Can you point us to
>the exact build and toolshed version?
>
>Thanks,
>Bjoern
>
>Am 02.01.2015 um 21:22 schrieb Waldron, Michael H:
>> Having a problem with directing FastQC output in Galaxy. User is running a job whose command line looks like this:
>>
>> # FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13836_files /proj/galaxy/job_working_directory/010/10467/dataset_13836_files/SRR016862.fastq
>>
>> Job output looks like this:
>>
>> ## odpath=None: No output found in None. Output for the run was:
>> # FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13827_files /proj/galaxy/job_working_directory/010/10467/dataset_13827_files/SRR016862.fastq
>> Started analysis of SRR016862.fastq
>> Approx 5% complete for SRR016862.fastq
>> Approx 10% complete for SRR016862.fastq
>> Approx 15% complete for SRR016862.fastq
>> Approx 20% complete for SRR016862.fastq
>> Approx 25% complete for SRR016862.fastq
>> Approx 30% complete for SRR016862.fastq
>> Approx 35% complete for SRR016862.fastq
>> Approx 40% complete for SRR016862.fastq
>> Approx 45% complete for SRR016862.fastq
>> Approx 50% complete for SRR016862.fastq
>> Approx 55% complete for SRR016862.fastq
>> Approx 60% complete for SRR016862.fastq
>> Approx 65% complete for SRR016862.fastq
>> Approx 70% complete for SRR016862.fastq
>> Approx 75% complete for SRR016862.fastq
>> Approx 80% complete for SRR016862.fastq
>> Approx 85% complete for SRR016862.fastq
>> Approx 90% complete for SRR016862.fastq
>> Approx 95% complete for SRR016862.fastq
>> Analysis complete for SRR016862.fastq
>>
>> The job_working_directory/010/10467 directory is created, however it is empty. It appears this "odpath" needs to be set somehow?
>>
>> Does anyone know a solution for this?
>>
>> Mike Waldron
>> Systems Specialist
>> ITS - Research Computing Center
>> University of North Carolina at Chapel Hill
>>
>>
>>
>>
>> ___________________________________________________________
>> 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/
>>
>
>
>------------------------------
>
>Message: 11
>Date: Sat, 3 Jan 2015 16:44:29 +0000
>From: "Waldron, Michael H" <mwaldron@email.unc.edu>
>To: Björn Grüning <bjoern.gruening@gmail.com>,
> "galaxy-dev@bx.psu.edu" <galaxy-dev@bx.psu.edu>
>Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>Message-ID:
> <9678294B07E1BA4084DA67BD4DC53D9E87D56874@ITS-MSXMBS2F.ad.unc.edu>
>Content-Type: text/plain; charset="iso-8859-1"
>
>It is FastQC-0.11.2. It's a separate install from Galaxy, and a symlink points to it under tool-data/shared/jars:
>
>$ pwd
>/nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars
>
>FastQC -> /nas02/apps/galaxy-prod/fastqc-0.11.2/FastQC
>
>
>Mike Waldron
>Systems Specialist
>ITS - Research Computing Center
>University of North Carolina at Chapel Hill
>
>
>________________________________________
>From: Björn Grüning [bjoern.gruening@gmail.com]
>Sent: Saturday, January 03, 2015 6:42 AM
>To: Waldron, Michael H; galaxy-dev@bx.psu.edu
>Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>
>Hi Michael,
>
>which version of the FASTQC wrapper are you running? Can you point us to
>the exact build and toolshed version?
>
>Thanks,
>Bjoern
>
>Am 02.01.2015 um 21:22 schrieb Waldron, Michael H:
>> Having a problem with directing FastQC output in Galaxy. User is running a job whose command line looks like this:
>>
>> # FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13836_files /proj/galaxy/job_working_directory/010/10467/dataset_13836_files/SRR016862.fastq
>>
>> Job output looks like this:
>>
>> ## odpath=None: No output found in None. Output for the run was:
>> # FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13827_files /proj/galaxy/job_working_directory/010/10467/dataset_13827_files/SRR016862.fastq
>> Started analysis of SRR016862.fastq
>> Approx 5% complete for SRR016862.fastq
>> Approx 10% complete for SRR016862.fastq
>> Approx 15% complete for SRR016862.fastq
>> Approx 20% complete for SRR016862.fastq
>> Approx 25% complete for SRR016862.fastq
>> Approx 30% complete for SRR016862.fastq
>> Approx 35% complete for SRR016862.fastq
>> Approx 40% complete for SRR016862.fastq
>> Approx 45% complete for SRR016862.fastq
>> Approx 50% complete for SRR016862.fastq
>> Approx 55% complete for SRR016862.fastq
>> Approx 60% complete for SRR016862.fastq
>> Approx 65% complete for SRR016862.fastq
>> Approx 70% complete for SRR016862.fastq
>> Approx 75% complete for SRR016862.fastq
>> Approx 80% complete for SRR016862.fastq
>> Approx 85% complete for SRR016862.fastq
>> Approx 90% complete for SRR016862.fastq
>> Approx 95% complete for SRR016862.fastq
>> Analysis complete for SRR016862.fastq
>>
>> The job_working_directory/010/10467 directory is created, however it is empty. It appears this "odpath" needs to be set somehow?
>>
>> Does anyone know a solution for this?
>>
>> Mike Waldron
>> Systems Specialist
>> ITS - Research Computing Center
>> University of North Carolina at Chapel Hill
>>
>>
>>
>>
>> ___________________________________________________________
>> 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/
>>
>
>
>------------------------------
>
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>
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>
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>
>End of galaxy-dev Digest, Vol 103, Issue 3
>******************************************