- galaxy-dev - lists.galaxyproject.org

Visualisation of VCF files in trackster
by Ulf Schaefer 25 Sep '13

25 Sep '13

Dear all My attempts to visualise a vcf file in trackster fail. I can visualise the corresponding SAM/BAM files fine. I can visualise the same file on Galaxy main too, but not in my local install. I receive the following error message: "Trackster Error Input error: found interval with block-counts not matching starts/sizes on line. sort: write failed: standard output: Broken pipe sort: write error needLargeMem: trying to allocate 0 bytes (limit: 100000000000)" The vcf format is in version 4.1. I am creating it from the sorted BAM file with samtools mpileup in the most basic way. What am I missing? Thanks a lot for your help Ulf ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************

2 3

pbkdf2 encryption - disabling does not work
by Jan Hapala 25 Sep '13

25 Sep '13

Hi, I need to run Galaxy with ProFTPd, therefore I need to disable the PBKDF2 encryption of the passwords (as stated here http://dev.list.galaxyproject.org/disable-PBKDF2-revert-to-SHA1-td4661274.h… ). However, when I do add this line: use_pbkdf2 = false to the universe_wsgi.ini, restart Galaxy, submit the form for the password change (or register as a new user) I get an error "_hashlib.HASH object has no attribute __getitem__". I got the same result with a version as of Jul 2 and the most recent tag (10411:c42567f43aa7, Aug 19). I would be much grateful for your suggestions! Regards, Jan URL: http://127.0.0.1:8080/user/edit_info?cntrller=user&user_id=f2db41e1fa331b3e File '.../eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '.../eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '.../eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '.../lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '.../lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '.../lib/galaxy/webapps/galaxy/controllers/user.py', line 842 in edit_info trans.sa_session.flush() File '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py', line 114 in do File '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py', line 1718 in flush File '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py', line 1789 in _flush File '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py', line 331 in execute File '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py', line 475 in execute File '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py', line 59 in save_obj File '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py', line 485 in _emit_update_statements File '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py', line 1449 in execute File '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py', line 1584 in _execute_clauseelement File '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py', line 1651 in _execute_context File '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py', line 1647 in _execute_context File '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py', line 475 in _init_compiled File '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/types.py', line 626 in process File '.../lib/galaxy/model/custom_types.py', line 125 in process_bind_param value = value[0:self.impl.length] StatementError: '_hashlib.HASH' object has no attribute '__getitem__' (original cause: TypeError: '_hashlib.HASH' object has no attribute '__getitem__') 'UPDATE galaxy_user SET update_time=%(update_time)s, password=%(password)s WHERE galaxy_user.id = %(galaxy_user_id)s' [{u'galaxy_user_id': 1, 'password': <sha1 HASH object @ 0x7338bc0>}]

2 1

cuffdiff wrapper not synchronized with cuffdiff version
by Karen Chait 25 Sep '13

25 Sep '13

Hello, After the latest update of Galaxy I saw that the cuffdiff wrapper is for version 2.0. I updated the $PATH to cuffdiff v. 2.0.2 but when I run cuffdiff in Galaxy I get the following error: Error running cuffdiff. cuffdiff: /lib64/libz.so.1: no version information available (required by cuffdiff) cuffdiff: unrecognized option '--library-norm-method' cuffdiff v1.3.0 (3022) What else do I need to define inorder to run the latest version of cuffdiff. Thank you, Karen

3 10

Want faster dataset import
by Ted Goldstein 25 Sep '13

25 Sep '13

I want to frequently import many tens of thousands of datasets. The files are on the same sever as Galaxy. But the upload based mechanism is really really slow. It takes hours to load this many files, yet the data is not moving at all! What is the best strategy to go about making a faster bulk import? I can imagine a tight loop that is My datatypes are limited. foreach folder new LibraryFolder foreach file in each directory new LibraryDataset new LibraryDatasetDatasetAssociation flush once at the end. Thoughts?

2 1

Local Galaxy Install - Multiple Input Files for Workflow Missing?
by Adam Brenner 25 Sep '13

25 Sep '13

Howdy, On our local galaxy cluster, I have gotten a report that the multiple input files selection on workflows is missing. How do I enable it? Looking at the past mailing list[1] this is the item that is missing from our setup -- the tooltip icon. We are running a version of galaxy that is roughly ~one month old: c42567f43aa7. [1]: http://dev.list.galaxyproject.org/Looking-for-recommendations-How-to-run-ga… Thanks! -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne(a)uci.edu

2 1

pgcleanup problem
by Eric Kuyt 25 Sep '13

25 Sep '13

Hi All, I'm trying to do some cleanup in my test environment (galaxy-dist) and pgcleanup.py ends with Traceback (most recent call last): > File "./scripts/cleanup_datasets/pgcleanup.py", line 773, in <module> > cleanup = Cleanup() > File "./scripts/cleanup_datasets/pgcleanup.py", line 55, in __init__ > self.__connect_db() > File "./scripts/cleanup_datasets/pgcleanup.py", line 114, in __connect_db > self.conn = psycopg2.connect(**args) > TypeError: 'username' is an invalid keyword argument for this function Unless I add args['user'] = args['username'] del args['username'] Is this a bug or a config error? Eric

2 1

Dependencies for complex datatypes
by Peter Cock 25 Sep '13

25 Sep '13

Hello all, Bjoern and I were talking about doing some work on more datatype definitions, but this raises the question about how to handle dependencies. First of all, complex datatypes in Galaxy are defined using Python code, so any Python dependency must be available to the main Galaxy process (unlike Python dependencies for jobs which are run on separate processes). For example, if I wrote GenBank/EMBL definitions using Biopython, could this dependency be handled via the Tool Shed? Second, the Python code for some datatypes may call a binary command line tool. For example, I was thinking of using the blastdbcmd binary within the BLAST database file format definitions to provide more useful peek information. Again, how could this dependency be handled via the Tool Shed? Thanks, Peter

1 1

error in 2013_08_12 DevNewsBriefs
by Curtis Hendrickson (Campus) 25 Sep '13

25 Sep '13

Dear Galaxy Team I was upgrading our servers with the 8/12 release, and going over the DevNotes<http://wiki.galaxyproject.org/DevNewsBriefs/2013_08_12>. I noted item "Pull Requets Merged #5: SAMtools indexes #188<http://wiki.galaxyproject.org/DevNewsBriefs/2013_08_12#Pull_Requests_Merged>". But the file created by the pull request didn't seem to exist. After looking in bitbucket at the history, it looks like the pull request was backed out<https://bitbucket.org/galaxy/galaxy-central/commits/73d7a93e2f8d0bafbcb0b4d…> before the release. Have I correctly understood the situation? Regards, Curtis

2 1

Patch for deseq_and_sam2counts Galaxy wrapper
by Guest, Simon 25 Sep '13

25 Sep '13

Hi Nikhil, I've been using your Galaxy wrapper for deseq_and_sam2counts. I fixed it up to run the R script from the tool install directory directly, so no manual copying of the script is required after installation in the Galaxy GUI. I attach my patch (as a Mercurial export), and hope you will incorporate this into the official repository, to avoid me having to maintain my own version. If it's more convenient for you to receive the update in a different form, please say. Thanks for making the tool wrapper available. cheers, Simon ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================

1 0

Tool Shed: get_readme_files bug
by Richard Burhans 24 Sep '13

24 Sep '13

It appears that the Tool Shed does not show the correct "readme" file content. 1) get_readme_files() in lib/galaxy/webapps/tool_shed/controllers/ repository.py gets the correct metadata from the database 2) build_readme_files_dict() in lib/tool_shed/util/readme_util.py reads data from whatever revision happens to be there (not the requested revision) As an example, compare the output from: http://toolshed.g2.bx.psu.edu/repository/get_readme_files? name=genome_diversity&owner=miller-lab&changeset_revision=5064f618ec1c and: http://toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/file/ 5064f618ec1c/README -rico

2 7