May 2013 - galaxy-dev - lists.galaxyproject.org

installing galaxy
by מירב . 30 May '13

30 May '13

hello, I am installing galaxy locally. I tried to upload a ".bam" file and I got this message: Traceback (most recent call last): File "/home/user/galaxy_project/tools/data_source/upload.py", line 386, in <module> __main__() File "/home/user/galaxy_project/tools/data_source/upload.py", line 375, in __main__ add_file( dataset, registry, json_file, output_path ) File "/home/user/galaxy_project/tools/data_source/upload.py", line 314, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/home/user/galaxy_project/lib/galaxy/datatypes/binary.py", line 113, in dataset_content_needs_grooming version = self._get_samtools_version() File "/home/user/galaxy_project/lib/galaxy/datatypes/binary.py", line 97, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/usr/lib/python2.7/subprocess.py", line 679, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1259, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory This file uploaded successfully, to the galaxy on the net. what can it be? thanks for your help merav

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Fwd: installing galaxy
by Ross 30 May '13

30 May '13

---------- Forwarded message ---------- From: מירב . <mermam(a)gmail.com> Date: Wed, May 29, 2013 at 8:40 PM Subject: Re: [galaxy-dev] installing galaxy To: Ross <ross.lazarus(a)gmail.com> It worked!! Thank you very mach [?] Merav 2013/5/29 Ross <ross.lazarus(a)gmail.com> > Hi, Merav. > A fully functional Galaxy server relies on a lot of third party software > and the error message you see is probably because you do not have samtools > available - the upload process needs it to make an index for your bam file. > So the solution may be to install the samtools package - eg for ubuntu > something like: > sudo apt-get install samtools > > After that, if you execute > samtools > at a console, you should see something like: > > rlazarus@iaas1-int:~$ samtools > > Program: samtools (Tools for alignments in the SAM format) > Version: 0.1.18 (r982:295) > > Usage: samtools <command> [options] > > Command: view SAM<->BAM conversion > sort sort alignment file > mpileup multi-way pileup > > > > Please take a look at > http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies > > > > On Wed, May 29, 2013 at 8:00 PM, מירב . <mermam(a)gmail.com> wrote: > hello, > > I am installing galaxy locally. > I tried to upload a ".bam" file and I got this message: > > Traceback (most recent call last): > File "/home/user/galaxy_project/tools/data_source/upload.py", line 386, in <module> > __main__() > File "/home/user/galaxy_project/tools/data_source/upload.py", line 375, in __main__ > add_file( dataset, registry, json_file, output_path ) > File "/home/user/galaxy_project/tools/data_source/upload.py", line 314, in add_file > if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): > File "/home/user/galaxy_project/lib/galaxy/datatypes/binary.py", line 113, in dataset_content_needs_grooming > version = self._get_samtools_version() > File "/home/user/galaxy_project/lib/galaxy/datatypes/binary.py", line 97, in _get_samtools_version > output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] > File "/usr/lib/python2.7/subprocess.py", line 679, in __init__ > errread, errwrite) > File "/usr/lib/python2.7/subprocess.py", line 1259, in _execute_child > raise child_exception > OSError: [Errno 2] No such file or directory > > > This file uploaded successfully, to the galaxy on the net. > > what can it be? > > thanks for your help > > merav > > > > > > > > ___________________________________________________________ > 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: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ

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organizing datasets in the history
by 吳正華 29 May '13

29 May '13

Hi, galaxy community: I’ve set up a local galaxy for our institute, one thing that our users kept complaining is that when dealing with several dozens of datasets, it became hard to find a certain data. I’m wondering is there a way to organize data in history? Say, organizing datasets in folders just like the file arrangement in the shared data library.. Thank you all for your help. Best Regards, John Wu ------------------------------------------ PhD Student Institute of Biomedical Science Academia Sinica

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cufflinks in the main galaxy instance is not able to produce compatible FPKM score
by Nikolay N. 29 May '13

29 May '13

Hi, Most people using the RNA-Seq toolkit use a combination of Tophat/Cufflinks/Cuffdiff. A known issue is that cufflinks and cuffdiff use different normalisation schemes ( http://seqanswers.com/forums/archive/index.php/t-26041.html) Users overcome this problem by running cufflinks with the following flags: --compatible-hits-norm --max-frag-multihits 1 However, in galaxy it is not possible to run cufflinks with these flags. Can you, perhaps, add support for them? many thanks, Nikolay

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Problem to download mercurial egg
by Marc DELOGER 29 May '13

29 May '13

Hello, I tried to download several times the several egg on these following mirrors but the download is always blocked near 50%...I asked several different people and they all have the same problem : http://eggs.g2.bx.psu.edu/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-ucs4… <http://eggs.g2.bx.psu.edu/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-ucs4…> http://eggs.galaxyproject.org/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-… <http://eggs.galaxyproject.org/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-…> Thank you in advance, Marc DELOGER

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Genome not listed
by sridhar srinivasan 29 May '13

29 May '13

Dear developers, 1. I recently installed galaxy locally. now i am trying to run bowtie2. In reference genome section the genome is not listed. 2. Is there any way yo secure our data without using the Proxy(nginx). I Appericiate your suggestions. Thanks Sridhar

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Feature Request - Reload Button
by Michael E. Cotterell 29 May '13

29 May '13

I noticed that if I "touch universe_wsgi.ini" from the terminal (update its timestamp) while Galaxy is running then Galaxy restarts. If this is intended, would it be possible to add a "Reload Galaxy" button/option in the "Server" section of the Admin page that mimics this "feature"? Obviously, you'd want some way of warning an admin if jobs are currently being executed. Thanks. Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA & TA, University of Georgia mepcotterell(a)gmail.com (mailto:mepcotterell@gmail.com) mepcott(a)uga.edu (mailto:mepcott@uga.edu) mec(a)cs.uga.edu (mailto:mec@cs.uga.edu) http://michaelcotterell.com/

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advice on a mixed cloud/SGE architecture
by Nikolay N. 29 May '13

29 May '13

Hi, I was contemplating setting up a galaxy master node on a aws instance but executing the workflows on an internal SGE cluster. I am not yet very familiar with galaxy so wanted to ask whether this is feasible (i.e. the API would support it). Any advice/recommendation is most welcome. many thanks, Nick

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php script integration query
by Prasun Dutta 29 May '13

29 May '13

Hi, If I have some programs in php which I need to integrate in Galaxy as a tool, can I do it? I know if I have some programs written in Perl, python,java,C or C++, I can easily integrate them. Can I do the same with a php script? Regards, Prasun Dutta MSc (Bioinformatics) School of Biological Sciences University of Edinburgh, UK

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Workflow refresh
by Neil.Burdett＠csiro.au 28 May '13

28 May '13

Hi, I upload files which then automatically call execute_workflow.py. The files background turn to green , but to see the workflow running on the GUI I need to refresh the display. Does anyone know how I can add a refresh command to the code, and where in the code to add it. Thanks Neil

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