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Creating tool shed repository: installation of dependencies fails.
by Joachim Jacob | VIB | 30 May '13

30 May '13

Hi all, I am building a wrapper around BLAT, and have put it locally in a toolshed. However, the automatic installation of dependencies fails: ************************* Tool dependency installation error: [Errno 2] No such file or directory: '/home/galaxy/galaxy-dist/database/tmp/tmp2J7K_L/database/tmp/tmp2J7K_L/blat ************************* Note that there is a strange duplication in the path. Furthermore, on that Galaxy instance, the database is on /mnt/testgalaxydb/database instead of path mentioned in the error. The tool_dependencies.xml matches the wrapper xml. blat is just downloaded from its url. ************************* <?xml version="1.0"?> <tool_dependency> <package name="blat" version="1.0.0"> <install version="1.0"> <actions> <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</action> <action type="move_file"> <source>blat</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> The BLAT binary for linux x86_64 is retrieved from UCSC. </readme> </package> </tool_dependency> ************************* Thanks for helping me further. Cheers, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team

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Setting up Galaxy interface to motif finding software
by Tom Hait . 30 May '13

30 May '13

Dear Galaxy developers, I hope you could help me with the following issue. I wish to use galaxy tools in our AMADEUS motif finding software: http://acgt.cs.tau.ac.il/amadeus/ AMADEUS helps many users who wish to find motifs in their sequences. AMADEUS has 2 limitations: 1. It can find motifs vs all organism's genome. 2. If the user don't want to find motif vs all organism's genome then The user itself will have to supply the sequences for the motif finding according to his chipSeq peaks he got. We would like that the user won't be troubled with the second limitation by adding locally\cloud Galaxy that downloads to AMADEUS the relevant sequences (~3000 sequences) according to the peaks locations from a BED file supplied by the user. As I see it - the galaxy installation will have to follow the objectives: 1. Work on windows OS. 2. Can be installed in the user computer by a script in AMADEUS 3. downloading time of the relevant sequences (~3000) won't take above 1-2 minutes I will appreciate if someone of you will guide me with the procedure and advise me with the best way to work with Galaxy-AMADEUS interface. Thanks, Tom hait

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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 30 May '13

30 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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