August 2011 - galaxy-dev - lists.galaxyproject.org

Wrapper generator.
by J. F. J. Laros 31 Aug '11

31 Aug '11

Dear, I need to add a number of tools to my local Galaxy installation, but the size of the wrappers I've seen keep me from writing one. Are there wrapper generators to make this task easier? If not, I might want to make one. A possible implementation I'm considering is to first make a (WSDL) description of any command line tool (using soaplab2 for example) and by making a general wrapper builder that takes WSDL as input. Does something similar already exist and if not, does this idea sound okay? With kind regards, Jeroen. -- Jeroen F. J. Laros - J.F.J.Laros(a)lumc.nl

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August 30, 2011 Galaxy Development News Brief
by Jennifer Jackson 30 Aug '11

30 Aug '11

August 30, 2011 Galaxy Development News Brief http://galaxyproject.org/wiki/News%20Briefs/2011_08_30 Source: http://getgalaxy.org new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 949e4f5fa03a What's New ISMB/ECCB, BOSC, and 3DSIG 2011 Slides Recent Publications GalaxyProject.org Wiki Tool Shed Upcoming Events Updated & Improved Data Tools Visualization (Trackster) Workflows API Source Quotas Bug Fixes

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Tools requiring java can't find java
by Chorny, Ilya 30 Aug '11

30 Aug '11

This is probably a question for our sys admin but when I run tools such as GATK I get an error java command not found. I can execute java from the command line and it works. Further I can grab the drmaa submission script (ie galaxy_job_id.sh) and qsub it from the command line and it finds JAVA. Any thoughts? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

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[API] Get the hashed dataset id within Galaxy
by Louise-Amélie Schmitt 30 Aug '11

30 Aug '11

Hi, I would need to make a tool that can get the API dataset id out of the input dataset of the tool, how can I do that?

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install with EPD python?
by Paul Tanger 30 Aug '11

30 Aug '11

Has anyone gotten galaxy installed on a mac 10.5 with EPD (enthought) python 2.6 (EPD version 6.1-1)? I get this error which I suspect is related to the fact that I have EPD python, not the generic python that was preinstalled? Any ideas? Thanks! Some eggs are out of date, attempting to fetch... Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 30, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 184, in resolve if e.args[0].project_name != self.distribution.project_name: AttributeError: 'str' object has no attribute 'project_name' Fetch failed.

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set metadata step
by Shantanu Pavgi 30 Aug '11

30 Aug '11

Hi, There is a 'set_metadata_externally' setting in universe_wsgi.ini file. What is involved in this step? Is it run for every dataset/output being generated in the galaxy? -- Thanks, Shantanu.

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API keys and id encryption (silly questions)
by Louise-Amélie Schmitt 30 Aug '11

30 Aug '11

Hello everyone, These questions are a bit silly but I'm really ignorant when it comes to security. Sorry about that. Why use API keys instead of user names? Is it to to prevent anyone from figuring out who is behind an URL? Or did I miss the point? Also, why encrypt the dataset/library/folder ids when a simple display is enough to get them? Thanks L-A

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migrate the database schema from 80 to 81
by Jack Zhu 29 Aug '11

29 Aug '11

Hi all, I have problems with updating my local instance of Galaxy. Specifically I can not migrate the database schema from 80 to 81: -------------- $$ sh manage_db.sh upgrade 80 -> 81... Migration script to add a 'tool_version' column to the hda/ldda tables. Traceback (most recent call last): File "./scripts/manage_db.py", line 63, in <module> main( repository=repo, url=db_url ) File "/home/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py", line 150, in main ret = command_func(**kwargs) File "/home/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py", line 221, in upgrade return _migrate(url, repository, version, upgrade=True, err=err, **opts) File "/home/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py", line 349, in _migrate schema.runchange(ver, change, changeset.step) File "/home/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py", line 184, in runchange change.run(self.engine, step) File "/home/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", line 101, in run func() File "lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py", line 17, in upgrade metadata.reflect() File "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py", line 1733, in reflect Table(name, self, **reflect_opts) File "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py", line 108, in __call__ return type.__call__(self, name, metadata, *args, **kwargs) File "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py", line 236, in __init__ _bind_or_error(metadata).reflecttable(self, include_columns=include_columns) File "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1265, in reflecttable self.dialect.reflecttable(conn, table, include_columns) File "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py", line 1673, in reflecttable only=include_columns) File "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py", line 2139, in reflect self._add_column(table, line, charset, only) File "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py", line 2227, in _add_column type_instance = col_type(*type_args, **type_kw) File "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py", line 569, in __init__ super(MSBigInteger, self).__init__(display_width, **kw) TypeError: super(type, obj): obj must be an instance or subtype of type -------------- Your help will be greatly appreciated. Jack

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Galaxy is Hiring
by Dave Clements 29 Aug '11

29 Aug '11

Hello all The Galaxy Project is growing and has open positions in both the Penn State and Emory groups (http://wiki.g2.bx.psu.edu/News/Galaxy%20is%20Hiring) *Penn State: System administrators/analysts* The Nekrutenko Lab <http://www.bx.psu.edu/%7Eanton/> at the Huck Institutes of Life Sciences <http://www.huck.psu.edu/> at Penn State <http://psu.edu/>is currently recruiting system analysts/administrators with experience in building and maintaining complex performance compute environments. The areas of immediate need include: - Storage balancing and tiered storage - Virtualization - Schedulers - Deployment of Galaxy instances and dependence management - Relational databases and query optimization - User management A minimum of 5 year experience with UNIX/Linux system administration is required. Applicants should submit a CV and list of references to jobs(a)galaxyproject.org. <http://bx.mathcs.emory.edu/joining/> *Emory: Software Engineers and Post-Docs* The Taylor Lab <http://bx.mathcs.emory.edu/> in the Biology<http://www.biology.emory.edu/>and Mathematics & Computer Science <http://www.mathcs.emory.edu/> at Emory University<http://emory.edu/>is looking for software engineers <http://bx.mathcs.emory.edu/joining/sw/> and postdoctoral scholars<http://bx.mathcs.emory.edu/joining/postdocs/>to work on the Galaxy project. We are seeking software engineers <http://bx.mathcs.emory.edu/joining/sw/>with expertise in distributed computing and systems programming, web-based visualization and visual analytics, informatics and data analysis and integration, and bioinformatics application areas such as re-sequencing, de novo assembly, metagenomics, transcriptome analysis and epigenetics. These are full time positions located in Atlanta, GA. See the official posting<http://bx.mathcs.emory.edu/joining/sw/>for full details. Postdoctoral applicants <http://bx.mathcs.emory.edu/joining/postdocs/>should have expertise in Bioinformatics and Computational Biology and research interests that complement but extend the lab's current interests<http://bx.mathcs.emory.edu/research/>: The Galaxy project; distributed and high-performance computing for data intensive science; vertebrate functional genomics; and genomics and epigenomic mechanisms of gene regulation, the role of transcription factors and chromatin structure in global gene expression, development, and differentiation. See the announcement<http://bx.mathcs.emory.edu/joining/postdocs/>for full details. If any of these positions describe you then please consider applying. Thanks, Dave C. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Galaxy Test disk quota
by Crystal Goh 29 Aug '11

29 Aug '11

Hi, I am Crystal. As Tophat for SOLiD only available in Galaxy Test (not available in Galaxy Main), I uploaded my csfasta and qual files to Galaxy Test. As the file size very big, the disk space used up is 13.5Gb and I cannot use any tool. This means after uploading raw data, I cannot manipulate any data as the size of raw data itself already exceeds 10Gb. May I know any alternative that I can use? Thank you very much! Best regards, Crystal

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