October 2012 - galaxy-dev - lists.galaxyproject.org

error uploading BAM file
by Sukha Malladi 17 Oct '12

17 Oct '12

Hi, I was trying to upload a 43Gb BAM file to Galaxy when I encountered this problem. I am new to galaxy and python. I have tried uploading files in other formats and they have worked fine. I am using galaxy as a local installation and appreciate any thoughts on how to fix this. Thanks Sukha =========== Traceback (most recent call last): File "/Data/galaxy/galaxy-dist/tools/data_source/upload.py", line 384, in <module> __main__() File "/Data/galaxy/galaxy-dist/tools/data_source/upload.py", line 373, in __main__ add_file( dataset, registry, json_file, output_path ) File "/Data/galaxy/galaxy-dist/tools/data_source/upload.py", line 312, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/Data/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 113, in dataset_content_needs_grooming version = self._get_samtools_version() File "/Data/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 97, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/Data/galaxy/Python-2.7.1/Lib/subprocess.py", line 672, in __init__ errread, errwrite) File "/Data/galaxy/Python-2.7.1/Lib/subprocess.py", line 1202, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory ============== Report this error to the Galaxy Team The Galaxy team regularly reviews errors that occur in the application. However, if you would like to provide additional information (such as what you were trying to do when the error occurred) and a contact e-mail address, we will be better able to investigate your problem and get back to you. ___________________________________________________________

1 0

Odd issue with updateucsc.dh
by Fields, Christopher J 17 Oct '12

17 Oct '12

I had an odd error with wigToBigWig that I tracked back to the *.len files generated by the updateucsc.sh script. With my last UCSC update, a majority of the assemblies have this as the single line: <META http-equiv="Content-Script-Type" content="text/javascript"> but others, like Zea_mays_B73_RefGen_v2, are fine. Rerunning this gives the same problem. Any clues? chris

1 0

Number of outputs = number of inputs
by Sascha Kastens 17 Oct '12

17 Oct '12

Hi all! I have a tool which takes one ore more input files. For each input file one output is created, i.e. 1 input file -> 1 output file, 2 input files -> 2 output files, etc. What is the best way to handle this? I used the directions for handlin multiple output files where the ?Number of Output datasets cannot be determined until tool run? which in my opinion is a bit inappropriate. BTW: The input files are added via the <repeat>-Tag, so maybe there is a similar thing for outputs? Thanks in advance! Cheers, Sascha

4 3

the comtent syntax of command and configfile
by welkin zzp 17 Oct '12

17 Oct '12

Hi, In the command tag of the tools/update.xml file, the paramfile was setted by the result of some statements followed, I want to know what syntax is and if it is OK that I move the statements to configfile tag? Thanks, welkin

1 0

Which bam_to_bigwig to use
by Andreas Kuntzagk 17 Oct '12

17 Oct '12

In the main toolshed I find bam_to_bigwig 2 times. Description, Version and Requirements seem the same. How am I to decide which one to use? regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich

2 1

problems when install galaxy locally with python2.7.3 interpreter and platform ubuntu12.04
by 王聃 17 Oct '12

17 Oct '12

Hello, galaxy developers and maintainers: I'm a user from the Chinese mainland. I have ubuntu 12.04 OS and python2.7.3 interpreter. After confirming that I've installed openssl-dev and bzip-dev and python version >2.5, I use virtualenv to create galaxy_env and just run "hg clone https:xxxxxxxx/galaxy-dist; cd galaxy-dist; sh run.sh" in the directory of galaxy. It seems that it's not the problem of linux w/r/x permission. After downloading some egg of python, the shell display as follows: ############################################################################################ /home/don/galaxy-dist/lib/galaxy/__init__.py:79: UserWarning: Module markupsafe was already imported from /usr/lib/python2.7/dist-packages/markupsafe/__init__.pyc, but /home/don/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg is being added to sys.path self.check_version_conflict() .................. .................. Starting server in PID 12288. Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/home/don/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/home/don/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/home/don/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 218, in run result = self.command() File "/home/don/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 303, in command serve() File "/home/don/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 287, in serve server(app) File "/home/don/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 151, in server_wrapper **context.local_conf) File "/home/don/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/home/don/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1314, in server_runner serve(wsgi_app, **kwargs) File "/home/don/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1264, in serve threadpool_options=threadpool_options) File "/home/don/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1114, in __init__ RequestHandlerClass, ssl_context) File "/home/don/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1094, in __init__ RequestHandlerClass, ssl_context) File "/home/don/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 358, in __init__ HTTPServer.__init__(self, server_address, RequestHandlerClass) File "/usr/lib/python2.7/SocketServer.py", line 408, in __init__ self.server_bind() File "/usr/lib/python2.7/BaseHTTPServer.py", line 108, in server_bind SocketServer.TCPServer.server_bind(self) File "/usr/lib/python2.7/SocketServer.py", line 419, in server_bind self.socket.bind(self.server_address) File "/usr/lib/python2.7/socket.py", line 224, in meth return getattr(self._sock,name)(*args) socket.error: [Errno 98] Address already in use ############################################################################################ And I really have no idea what's wrong with galaxy and python. Thanks for your help and advice. Wangdan 2012.10.17

2 1

Error when creating first data library in new Galaxy installation
by Peter Briggs 17 Oct '12

17 Oct '12

Hello I've encountered an error when creating the first data library within a Galaxy installation. The data library appears to be created but an error message appears ("Error attempting to display contents of library (Test Data): No module named controllers.library_common" - see attached screenshot) and although the library name appears, it's not possible to interact further with the library e.g. to add datasets. The original error occurred on our nascent production setup, but I can reproduce it on a brand new vanilla local galaxy instance (changeset 7828:b5bda7a5c345) with the only configuration being to register as a user and set the "admin_users" parameter in universe_wsgi.ini. Then, go to "admin" -> "manage data libraries" -> "create new data library". This error doesn't appear when creating a new data library on an instance which already has existing libraries, and debug output doesn't give me any additional clues about where the "missing module" is coming from. I don't think this problem has been reported previously however apologies if it's already been addressed on the mailing list. Thanks for any help Best wishes, Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

1 1

renaming fastq to fastqsanger
by Pete Schmitt 17 Oct '12

17 Oct '12

When attempting the change the filetype of a fastq file to fastqsanger, the process for changing the type goes on forever. This does not allow any further processing of the data. -- * Pete Schmitt Technical Director: Discovery Cluster NH INBRE Grid Computational Genetics Lab Dartmouth College, HB 6223 L24 Berry/Baker Library Hanover, NH 03755 Phone: 603-646-8109 http://discovery.dartmouth.edu http://columbia.dartmouth.edu/grid http://www.epistasis.org *

4 4

Fwd: Galaxy data upload
by Greg Von Kuster 16 Oct '12

16 Oct '12

Hello Oliver, I've forwarded this to the galaxy-dev mail list since it is the contact point for issues like this. Please send questions like this to the Galaxy mail lists (galaxy-dev, galaxy-user) in the future as there is no guarantee you'll get timely answers from individual contacts. Thanks very much, Greg Von Kuster Begin forwarded message: > From: "Oliver Berkowitz" <O.Berkowitz(a)murdoch.edu.au> > Date: October 14, 2012 11:47:13 PM EDT > To: <greg(a)bx.psu.edu> > Subject: Galaxy data upload > > Dear Greg, > > not sure if you are the right person to contact… > > I have tried several times to upload data to the galaxy server via ftp. Trying to connect leads to error 530, max number of clients already connected, like this: > > Status: Resolving address of main.g2.bx.psu.edu > Status: Connecting to ..... > Status: Connection established, waiting for welcome message... > Response: 220 ProFTPD 1.3.4b Server (Galaxy Main Server FTP) [::ffff:128.118.250.4] > Command: USER xxxxxxxxxxxxxxxxxx > Response: 331 Password required for xxxxxxxxxxxxxxx > Command: PASS ******* > Response: 530 Sorry, the maximum number of clients (3) for this user are already connected. > Error: Critical error > Error: Could not connect to server > > > Do you have an idea what I am doing wrong (or the server J) ? > > Cheers > Oliver > > > ____________________________________________________ > Dr. Oliver Berkowitz > Murdoch University > Centre for Phytophthora Science and Management > School of Biological Sciences and Biotechnology > 90 South Street, Murdoch WA 6150, Australia > P: 61 - (0)8 9360 6335 > E: o.berkowitz(a)murdoch.edu.au > W: http://profiles.murdoch.edu.au/myprofile/oliver-berkowitz/ >

2 1

Re: [galaxy-dev] Group parameters
by Joachim Jacob 16 Oct '12

16 Oct '12

Hi, I assume you mean to group the parameters visually. What I have seen people doing is adding HTML code to the value of the label attribute of a <param> tag set, like ending the label with e.g. "<br/><hr>". Otherwise, if the two groups of parameters are mutually exclusive, you can use the <conditional> tag set. cheers, Joachim Message: 10 Date: Sat, 13 Oct 2012 12:07:03 -0300 From: Alfredo Guilherme Silva Souza<alfredo.bioinformatics(a)gmail.com> To:galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Group parameters Message-ID: <CAL39R3o+JupW225QZ7q4mqf8wMX3MbsmjtnLzA2XqDis5U+ZCg(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hello I'm needing some grouping parameters into a tool that I'm developing, so I did not find any answers in the wiki galaxy. Attached is a picture with the example of the way that the parameters are in my tool currently, and the manner in which I need to leave. Thank you. -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

3 5