- galaxy-dev - lists.galaxyproject.org

Problem with Biopython
by Alfredo Guilherme Silva Souza 06 Jan '15

06 Jan '15

Has anyone used the Biopython in Galaxy ? *Traceback (most recent call last):* * File "/home/steve/galaxy-dist/tools/molecular_dynamics/gromacs.py", line 10, in <module>* * import Bio.PDB.PDBParser* *ImportError: No module named Bio.PDB.PDBParser* Researching I saw that I have to work with eggs in the Galaxy. Has anyone done this with Biopython? Is it really necessary? Thanks -- *Alfredo Guilherme da Silva Souza* Distributed Systems and Computer Networks Federal University of São Carlos - UFSCar Contact +55 16 9115-3035 | alfredo.bioinformatics(a)gmail.com <contato(a)gilsonleite.com.br>

2 2

Problem using FastQC in Galaxy
by Waldron, Michael H 05 Jan '15

05 Jan '15

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

6 12

Create a package with binaries
by KRESS Arnaud (ESP) 05 Jan '15

05 Jan '15

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

2 1

Problem using FastQC in Galaxy
by Alfredo Guilherme Silva Souza 05 Jan '15

05 Jan '15

Has anyone used the Biopython in Galaxy ? *Traceback (most recent call last):* * File "/home/steve/galaxy-dist/tools/molecular_dynamics/gromacs.py", line 10, in <module>* * import Bio.PDB.PDBParser* *ImportError: No module named Bio.PDB.PDBParser* Researching I saw that I have to work with eggs in the Galaxy. Has anyone done this with Biopython? Is it really necessary? Thanks -- *Alfredo Guilherme da Silva Souza* Distributed Systems and Computer Networks Federal University of São Carlos - UFSCar Contact +55 16 9115-3035 | alfredo.bioinformatics(a)gmail.com <contato(a)gilsonleite.com.br>

3 3

Creating a new job handler for Galaxy
by Abdulrahman Azab 05 Jan '15

05 Jan '15

Hi Galaxy developers, In our Elixir project (http://www.elixir-europe.org/) Norway, we have five geographically distributed Galaxy instances. Each is working on a local cluster (mostly SLURM). We are planning to interconnect those five clusters using a meta-scheduler ARC (http://www.nordugrid.org/arc/) to achieve load balancing, so that a galaxy job can be reallocated to an external cluster in case that the local cluster is saturated. ARC manages the interconnection very well. What we need is to create a Galaxy job handler for ARC. Is there a general template or interface for a job handler, i.e. for defining job submission commands ... etc.? and how to compile and integrate this new job handler and integrate it into the Galaxy installation? Thank you, Yours sincerely, Abdulrahman Azab Head engineer, ELIXIR.NO / The Genomic HyperBrowser team Department of Informatics, University of Oslo, Boks 1072 Blindern, NO-0316 OSLO, Norway Email: azab(a)ifi.uio.no, Cell-phone: +47 46797339 ---- Senior Lecturer in Computer Engineering Faculty of Engineering, University of Mansoura, 35516-Mansoura, Egypt Email: abdulrahman.azab(a)mans.edu.eg</owa/abdulrahman.azab(a)mans.edu.eg>

2 1

galaxy.tools.parameters.basic.RuntimeValue not str
by Pandori n 05 Jan '15

05 Jan '15

Hi all! Maybe somebody faced with this problem: 1) in my wf used tool with: "u'model_class': u'Conditional', u'type': u'conditional', u'name': u'reference_genome'}], " 2) when i run wf via web - all ok, and on a second step: "Select a reference genome" is "test" (in view details) But, when i run wf via api: param = {u'mapper_easy' :{u'param': u'reference_genome|index', u'value': u'test'}} nuser.workflows.run_workflow(workflow_id=wf_id, dataset_map=dataset_map, params=param, history_id=hist_id) wf started and on a second step is failed... In details: "Select a reference genome" is "<galaxy.tools.parameters.basic.RuntimeValue object at 0x7f5374266850>" Any help is appreciated. Thanks!

2 1

January 2015 Galaxy News!
by Dave Clements 05 Jan '15

05 Jan '15

1 0

Re: [galaxy-dev] [Spam:*****] Re: How galaxy workflow work ?
by Ruslan Forostianov 05 Jan '15

05 Jan '15

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

2 3

run_test.sh - ImportError: cannot import name _args_from_interpreter_flags
by Ryan G 05 Jan '15

05 Jan '15

I'm trying to run the functional tests my local installation, and see this error come up when the test web server comes up. Google didn't turn up much other than that other people see this. Most of my tests then proceed to fail so I suspect this is pretty important. How do I get around this? Is there a solution?

2 1

integrate galaxy with slurm
by xlwang 05 Jan '15

05 Jan '15

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(a)lists.galaxyproject.org wrote: >Send galaxy-dev mailing list submissions to > galaxy-dev(a)lists.galaxyproject.org > >To subscribe or unsubscribe via the World Wide Web, visit > https://lists.galaxyproject.org/listinfo/galaxy-dev >or, via email, send a message with subject or body 'help' to > galaxy-dev-request(a)lists.galaxyproject.org > >You can reach the person managing the list at > galaxy-dev-owner(a)lists.galaxyproject.org > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of galaxy-dev digest..." > > >HEY! This is important! If you reply to a thread in a digest, please >1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread. >2. Strip out everything else in the digest that is not part of the thread you are responding to. > >Why? >1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. >2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. > >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(a)unistra.fr> >To: galaxy-dev(a)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(a)gruenings.eu> >To: "Wang, Yu" <Yu.Wang(a)lrz.de>, John Chilton <jmchilton(a)gmail.com> >Cc: "galaxy-dev(a)lists.galaxyproject.org" > <galaxy-dev(a)lists.galaxyproject.org> >Subject: Re: [galaxy-dev] package_numpy_1_7 can't be installed >Message-ID: <548FA1FD.5010007(a)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(a)lrz.de<mailto:wang@lrz.de> >> >> On 15 Dec 2014, at 16:12, John Chilton <jmchilton(a)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(a)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(a)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(a)lrz.de> >To: Björn Grüning <bjoern(a)gruenings.eu> >Cc: "galaxy-dev(a)lists.galaxyproject.org" > <galaxy-dev(a)lists.galaxyproject.org> >Subject: Re: [galaxy-dev] package_numpy_1_7 can't be installed >Message-ID: <9C386582-2905-44A3-9F7D-1B330A364C81(a)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(a)lrz.de<mailto:wang@lrz.de> > >On 16 Dec 2014, at 04:07, Björn Grüning <bjoern(a)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(a)lrz.de<mailto:wang@lrz.de><mailto:wang@lrz.de> > >On 15 Dec 2014, at 16:12, John Chilton <jmchilton(a)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(a)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(a)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/ > > >

1 0