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

[Patch] enhance the toolshed upload error checking
by Björn Grüning 14 Oct '12

14 Oct '12

Hi all! If you upload a tool with a tool_dependencies.xml file that does not fit the <requirement> informations in the wrapper the developer will not be informed about that error. Furthermore, the repository are updated and the only hint a developer get is an empty or missing dependency field in the toolshed. In my opinion the developer should be informed that the specified informations are wrong or insufficient and the upload should be aborted. "Talk is cheap. Show me the code." - please see the attached patch. Regards, Björn

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Empty TopHat output
by 吳正華 13 Oct '12

13 Oct '12

Hi all: After updating our local galaxy installation to the latest build last week, I found that when tophat finished its execution, all its output files showed empty in the history. However, I could execute the exact same command via shell and got correct tophat output files. It seemed that something went wrong when galaxy tried to copy tophat output files to galaxy databases/file. Did anyone encounter the same problem? How could I fix this problem? Thanks a lot. Best John Wu ------------------------------------------------------------- PhD Student Academia Sinica

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Group parameters
by Alfredo Guilherme Silva Souza 13 Oct '12

13 Oct '12

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. -- *Alfredo Guilherme* * *

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Adding metadata to datasets
by Anthonius deBoer 13 Oct '12

13 Oct '12

Hi, Is there an easy way to add meta data to a dataset without having to resort to coding it into the dataset definition? I am looking for things beyond tags and just a simple key value pair association would be enough... I cannot see anything that is obvious, but I feel something must be there... Thanks Thon

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Tool Menu Behavior
by Ganote, Carrie L 12 Oct '12

12 Oct '12

Hi all, I've browsed a few of the public Galaxies to get an idea of what I like and don't like; I've noticed that some of the instances have an "accordion" behavior where when one of the tool sections is expanded, all others collapse. In galaxy main, you can have multiple tool sections open at once. I would prefer the accordion style... does anyone know where this is configured, or do I have to manually change the javascript call to jquery's slide function? Thanks! -Carrie

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fastQC report bug
by David Hoover 12 Oct '12

12 Oct '12

Hi, I have a very recent version of Galaxy installed locally, and when I run FastQC:Read QC, it creates an HTML file with missing links to the plots and images within the HTML. The HTML source looks identical to the HTML source from the main Galaxy server, so there must be something wrong with my local install. Is there some option or modification that I need to enable to allow access to the generated HTML/PNG files in the database/files/000/database_###_files directory? David Hoover Helix Systems Staff

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Re: [galaxy-dev] galaxy-dev Digest, Vol 76, Issue 12
by Mark Johnson 12 Oct '12

12 Oct '12

Galaxy assumes that tools that write to stderr indicate failure. There's apparently some way to set up regexps to get around that, but I don't know where to do that (or if indeed that would work). Command-line debugging works some, except when the web server's environment (path, etc.) differs from command line. Or the problem is in how Galaxy interprets output; e.g. "stderr means error" as described above. John Chilton suggested I try using the logging facility, but binary.py throws an exception when I try to do that: An error occurred running this job:uploaded csra file No handlers could be found for logger "galaxy.datatypes.binary" So it's back to square one. Debugging without even a working print statement is pretty difficult. Even trying log = logging.getLogger() or log = logging.getLogger('wsgi') produces exceptions. I would assume there'd be a way to set up logging in universe_wsgi.ini, but none of the logging parameters seem to set up a root logger that tools can use. --mj On 10/12/12 10:55 AM, galaxy-dev-request(a)lists.bx.psu.edu wrote: > You can get to the captured stdout/stderr in the UI by clicking the > info (i) button for the dataset. The way I would normally debug > outside of the Galaxy UI is to take the command line generated by > Galaxy (which should be logged) and run it outside Galaxy. > > -- jt

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Adding binary datatype: upload problem
by Mark Johnson 12 Oct '12

12 Oct '12

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Database migration error
by Bossers, Alex 12 Oct '12

12 Oct '12

After a fresh galaxy-dist pull today (no update for various reasons) the instance was running ok on the default sqlight database. When I migrated back the setting to use the MySQL database it complained during startup about having found an old version of the database and I need to upgrade. Database upgrade started and the first few migrations were successful, but now it hangs every time at 99->100. Any clue what might be wrong? Here is the lengthy trace log. thanks Alex ==================================================== 99 -> 100... Migration script to alter the type of the tool_dependency.version column from TrimmedString(40) to Text. Traceback (most recent call last): File "./scripts/manage_db.py", line 63, in <module> main( repository=repo, url=db_url ) File "/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/shell.py", line 150, in main ret = command_func(**kwargs) File "/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/api.py", line 221, in upgrade return _migrate(url, repository, version, upgrade=True, err=err, **opts) File "/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/api.py", line 349, in _migrate schema.runchange(ver, change, changeset.step) File "/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/schema.py", line 184, in runchange change.run(self.engine, step) File "/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/script/py.py", line 101, in run func() File "lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py", line 30, in upgrade ToolDependency_table = Table( "tool_dependency", metadata, autoload=True ) File "/opt/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/schema.py", line 108, in __call__ return type.__call__(self, name, metadata, *args, **kwargs) File "/opt/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/schema.py", line 236, in __init__ _bind_or_error(metadata).reflecttable(self, include_columns=include_columns) File "/opt/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py", line 1265, in reflecttable self.dialect.reflecttable(conn, table, include_columns) File "/opt/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/databases/mysql.py", line 1664, in reflecttable sql = self._show_create_table(connection, table, charset) File "/opt/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/databases/mysql.py", line 1835, in _show_create_table raise exc.NoSuchTableError(full_name) sqlalchemy.exc.NoSuchTableError: tool_dependency Error in sys.excepthook: Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/apport_python_hook.py", line 66, in apport_excepthook from apport.fileutils import likely_packaged, get_recent_crashes ImportError: No module named apport.fileutils Original exception was: Traceback (most recent call last): File "./scripts/manage_db.py", line 63, in <module> main( repository=repo, url=db_url ) File "/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/shell.py", line 150, in main ret = command_func(**kwargs) File "/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/api.py", line 221, in upgrade return _migrate(url, repository, version, upgrade=True, err=err, **opts) File "/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/api.py", line 349, in _migrate schema.runchange(ver, change, changeset.step) File "/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/schema.py", line 184, in runchange change.run(self.engine, step) File "/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/script/py.py", line 101, in run func() File "lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py", line 30, in upgrade ToolDependency_table = Table( "tool_dependency", metadata, autoload=True ) File "/opt/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/schema.py", line 108, in __call__ return type.__call__(self, name, metadata, *args, **kwargs) File "/opt/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/schema.py", line 236, in __init__ _bind_or_error(metadata).reflecttable(self, include_columns=include_columns) File "/opt/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py", line 1265, in reflecttable self.dialect.reflecttable(conn, table, include_columns) File "/opt/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/databases/mysql.py", line 1664, in reflecttable sql = self._show_create_table(connection, table, charset) File "/opt/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/databases/mysql.py", line 1835, in _show_create_table raise exc.NoSuchTableError(full_name) sqlalchemy.exc.NoSuchTableError: tool_dependency ========================================================

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Small bug with "search tools" in the lastest version of Galaxy
by David Roquis 11 Oct '12

11 Oct '12

Dear Galaxy community, I have noticed that since I have upgraded to the latest galaxy distribution (October 5th, b5bda7a5c345), the "search tools" function in the left frame doesn't seem to work properly. For example, in previous distributions, if I typed "fastx", it would display all the tools under the "FASTX-Toolkit for FASTQ data" section. Now, I don't get anything (but the FASTX-Toolkit for FASTQ data and the tools in it are still available if I look manually in the tool list). Similar problem when I search with the keyword "draw". I get some results, but I would miss some. For example, "Draw quality score boxplot for SOLiD data""Draw quality score boxplot", "Draw nucleotides distribution chart" (and some more) does not appear in the search results. I haven't tested all the possible keywords to search, but my guess is that this problem probably happens with other search terms. The same situation occurs on the penn state instance of galaxy (https://main.g2.bx.psu.edu/) so I guess this problem is not related to my local version. This is not a major bug, but I thought it was worth mentioning it. Sincerely David University of Perpignan

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