December 2014 - galaxy-dev - lists.galaxyproject.org

Mercurial is out of date for Toolshed
by Ryan G 08 Jan '15

08 Jan '15

I've been trying to track down why I can't get anything from the toolshed installed and finally have it figured out. Whenever I tried to install anything I always got an Error with no explanation of what the error was. After enabling Debug messages into the log file, I see the error is: tool_shed.util.hg_util DEBUG 2014-12-22 14:47:48,910 Error cloning repository: httpsconnection instance has no attribute '_set_hostport' I googled around and found out this is a known bug/issue with older version of Mercurial and was fixed in v3. I added a line to hg_util.py to see where it picks up hg. Its using version 2.2.3. Indeed, one of the eggs downloaded by Galaxy is mercurial-2.2.3. I have the newest version of mercurial installed in my site-packages folder but I guess that's not what galaxy wants. So my question is, how do I get Galaxy to use the latest version of Mercurial? And, Why did it download an older version?

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GCC2015 Training Day Topic Nominations are Open through January 6
by Dave Clements 05 Jan '15

05 Jan '15

Hello all, GCC2015 Training Day <http://gcc2015.tsl.ac.uk/training-day/> topics are nominated by you <http://bit.ly/gcc2015tdnom>, the Galaxy Community. Please take a few minutes to nominate a topic. Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one. If you are looking for ideas, see the topics nominated in 2013 <http://bit.ly/1i2j1gN> and 2014 <http://bit.ly/1s6NtMN>, and the Events <https://wiki.galaxyproject.org/Events> and the Events Archives <https://wiki.galaxyproject.org/Events/Archive> pages. Nominated topics will be published on the Training Day <http://gcc2015.tsl.ac.uk/training-day/> page as they come in. *Nominations close 6 January*. Topics will be compiled into a uniform list by the GCC2015 Organising Committee <http://gcc2015.tsl.ac.uk/organisers>, and topics will be voted on by the Galaxy Community 12-23 January. Topics will then be selected and scheduled based on topic interest, and the organisers' ability to confirm instructors for each session. Some very popular sessions may be scheduled more than once. The final schedule will be posted before registration opens. Cheers, GCC2015 Organising Committee <http://gcc2015.tsl.ac.uk/organisers> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Create a package with binaries
by KRESS Arnaud (ESP) 05 Jan '15

05 Jan '15

Hi gentlemen, I am currently struggling to create a custom package (to share via a toolshed) that would include a tool definition file and the associated binary. Once installed, I can launch a job but I get the following error message: mytool.sh: line 14: mytool: unknown command It seems that the PATH was not correctly set. What am I doing wrong ? My directory tree in my package: . ├── mytool.sh ├── mytool.xml ├── bin │ └── mytool └── tool_dependencies.xml Here is my tool_dependencies.xml file content: <?xml version="1.0"?> <tool_dependency> <package name="mytool" version="1.0"> <install version="1.0"> <actions> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> </readme> </package> </tool_dependency> Thank you, AK

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Re: [galaxy-dev] [Spam:*****] Re: How galaxy workflow work ?
by Ruslan Forostianov 05 Jan '15

05 Jan '15

galaxy.web.framework.decorators ERROR 2014-12-18 12:22:04,760 Uncaught exception in exposed API method: Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py", line 244, in decorator rval = func( self, trans, *args, **kwargs) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/workflows.py", line 231, in create populate_state=True, File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/run.py", line 18, in invoke modules.populate_module_and_state( trans, workflow, workflow_run_config.param_map ) File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line 843, in populate_module_and_state step_errors = module_injector.inject( step, step_args=step_args ) File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line 830, in inject state, step_errors = module.compute_runtime_state( trans, step_args ) File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line 264, in compute_runtime_state state = self.decode_runtime_state( trans, step_updates.pop( "tool_state" ) ) KeyError: 'tool_state' Cheers, Ruslan Forostianov

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run_test.sh - ImportError: cannot import name _args_from_interpreter_flags
by Ryan G 05 Jan '15

05 Jan '15

I'm trying to run the functional tests my local installation, and see this error come up when the test web server comes up. Google didn't turn up much other than that other people see this. Most of my tests then proceed to fail so I suspect this is pretty important. How do I get around this? Is there a solution?

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samtools installation problems
by Nathan Kipniss 02 Jan '15

02 Jan '15

Hi All, New to galaxy here. I'm having an issue uploading bam files into a local instance of galaxy. I understand that it requires samtools, and I installed the appropriate dependency from the toolshed. However, I get the following error: Traceback (most recent call last): File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 407, in <module> __main__() File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 396, in __main__ add_file( dataset, registry, json_file, output_path ) File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 324, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 147, in dataset_content_needs_grooming version = self._get_samtools_version() File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 129, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/usr/lib/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory Which leads me to believe something is wrong with the install (can't find samtools). The dependency directory is also set. Is there another step I'm missing, or is it better to not install dependencies via the toolshed? Best, Nathan Kipniss

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Trouble with async data sources
by Eric Rasche 30 Dec '14

30 Dec '14

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inconsistency in data library display
by Ryan G 23 Dec '14

23 Dec '14

I'm uploading a bunch of fastq.gz files to a data library. I'm currently doing this one file at a time to test some API functionality. I noticed that right after the web page refreshes itself, the file name is displayed with a '.gz' at the end. If I navigate to the data library by clicking on 'Manage Data Libraries", etc, the file is displayed without the '.gz'. Not a big deal, but it was throwing me off for a while trying to figure out how to use the underlying API.

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Feature Request: Ability to you keyword to move through items in the main window similar to Gmail
by Ryan G 23 Dec '14

23 Dec '14

When browsing a data library, clicking on entries I want to select is a bit cumbersome. It would be nice to use arrow keys, etc to select items, just like when selecting mail in Gmail.

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rpy vs rpy2
by Ryan G 22 Dec '14

22 Dec '14

I'm trying to install rpy for Galaxy, however it seems to not be available anymore. rpy2 is supposed to be the replacement. Does/will Galaxy migrate to rpy2? Some of the tools rely on rpy but since its not available anymore, the tools can't run. Also, why use a R python wrapper? Why not just create an R script and run 'Rscript' directly? Ryan

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