- galaxy-dev - lists.galaxyproject.org

install with EPD python?
by Paul Tanger 31 Aug '11

31 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 Some eggs are out of date, attempting to fetch...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 31 Aug '11

31 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 30 Aug '11

30 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 30 Aug '11

30 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 30 Aug '11

30 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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[API] Error message forwarding
by Louise-Amélie Schmitt 30 Aug '11

30 Aug '11

Hi, I ran into a little something that is a bit annoying for debug when trying to upload files through the API with library_upload_from_import_dir.py. When the specified folder is wrong, python tries to process the error tuple like a dict, so the original error is hard to find. I modified a little the code to avoid that. It might not work in all cases but at least it solved my problem. Here is the original code: lib/galaxy/web/api/contents.py l.145->end else: rval = [] for k, v in output.items(): if type( v ) == trans.app.model.LibraryDatasetDatasetAssociation: v = v.library_dataset encoded_id = trans.security.encode_id( create_type + '.' + str( v.id ) ) rval.append( dict( id = encoded_id, name = v.name, url = url_for( 'content', library_id=library_id, id=encoded_id ) ) ) return rval Here is how I modified it: else: rval = [] try: for k, v in output.items(): if type( v ) == trans.app.model.LibraryDatasetDatasetAssociation: v = v.library_dataset encoded_id = trans.security.encode_id( create_type + '.' + str( v.id ) ) rval.append( dict( id = encoded_id, name = v.name, url = url_for( 'content', library_id=library_id, id=encoded_id ) ) ) return rval except: log.debug( 'HTTP Error %s: %s' % ( output[0], output[1] ) ) return None Since it saves me some time & energy I just wanted to share it, so I hope it can help. Best L-A

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next galaxy-dist update
by Glen Beane 29 Aug '11

29 Aug '11

We are in need of a galaxy upgrade (we missed the last galaxy-dist update at the end of June). However, we don't want to update to a 2 month old release only to have a new release come out shortly after. Could someone on the development team give me an estimate of when the next galaxy-dist update will happen? -- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153

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contribute tools to galaxy?
by Dongjun Chung 28 Aug '11

28 Aug '11

Hi All, I'm a newbie to galaxy and enjoying it a lot these days. Thanks for the great work. I have a question regarding contribution of software to galaxy. We developed a ChIP-seq peak calling algorithm and software (R package) and hope to contribute it to galaxy. I have read the wiki and prior mailing list about the contribution system but it is still somewhat confusing to me. 1. It seems that I can contribute our software to "tool shed" if I prepare appropriate code & definition files. Then, users can download and use it with their locally installed galaxy. However, these files committed to tool shed will not appear in galaxy main or test servers. Am I correct? 2. What is clear relationship between main/test servers & tool shed? Can we contribute our software to main or test servers as well? Or only galaxy core developers can add new tools to galaxy main or test servers? If so, which software is considered to be added to servers? Are they chosen from tools contributed to tool shed? 3. If our software is a R package, then users need to download and install it first in their R system before they use our software within their galaxy system even in the case they have appropriate definition files. Am I right? Or is there any better solution for this? Thanks! Best, Dongjun

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Database migration
by Jack Zhu 27 Aug '11

27 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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