[galaxy-dev] Problem with set_user_disk_usage.py script
I recently updated our server to the latest release and have just had a user who ran up a lot of space and isn’t seeing it come back when she purges her data. I’ve tried using the set_user_disk_usage.py script as I’ve previously done to resolve this but now it is failing with the following: (galaxy_env)[galaxy@galaxy scripts]$ ./set_user_disk_usage.py Loading Galaxy model... Traceback (most recent call last): File ./set_user_disk_usage.py, line 85, in module model, object_store, engine = init() File ./set_user_disk_usage.py, line 43, in init for key, value in config_parser.items( app:main ): File /usr/lib64/python2.6/ConfigParser.py, line 565, in items raise NoSectionError(section) ConfigParser.NoSectionError: No section: ‘app:main' Do I need a newer python or is this a bug/regression? Shane Dr. Shane Sturrock Senior Scientist shane.sturr...@biomatters.com | P: +64 9 379 5064 BIOMATTERS ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Problem with set_user_disk_usage.py script
Thanks Martin, That solves it. What I ended up doing (since my install is pretty old now) was to symlink the galaxy-dist/universe_wsgi.ini to galaxy-dist/config/galaxy.ini and then the script started working. Shane On 9/06/2015, at 3:15 pm, Martin Čech mar...@bx.psu.edu wrote: The script by default expects Galaxy config to be at config/galaxy.ini if you have Galaxy config in a diffferent place you can use the --config flag to specify path to it. The config location has been recently changed (from galaxy root folder and a different filename) - that is why the defaults are different then your setup. Sorry for the inconvenience. Martin On Mon, Jun 8, 2015 at 9:43 PM Shane Sturrock sh...@biomatters.com mailto:sh...@biomatters.com wrote: I recently updated our server to the latest release and have just had a user who ran up a lot of space and isn’t seeing it come back when she purges her data. I’ve tried using the set_user_disk_usage.py script as I’ve previously done to resolve this but now it is failing with the following: (galaxy_env)[galaxy@galaxy scripts]$ ./set_user_disk_usage.py Loading Galaxy model... Traceback (most recent call last): File ./set_user_disk_usage.py, line 85, in module model, object_store, engine = init() File ./set_user_disk_usage.py, line 43, in init for key, value in config_parser.items( app:main ): File /usr/lib64/python2.6/ConfigParser.py, line 565, in items raise NoSectionError(section) ConfigParser.NoSectionError: No section: ‘app:main' Do I need a newer python or is this a bug/regression? Shane Dr. Shane Sturrock Senior Scientist shane.sturr...@biomatters.com mailto:shane.sturr...@biomatters.com | P: +64 9 379 5064 BIOMATTERS ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ http://galaxyproject.org/search/mailinglists/ Dr. Shane Sturrock Senior Scientist shane.sturr...@biomatters.com | P: +64 9 379 5064 BIOMATTERS ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Problem with set_user_disk_usage.py script
The script by default expects Galaxy config to be at config/galaxy.ini if you have Galaxy config in a diffferent place you can use the --config flag to specify path to it. The config location has been recently changed (from galaxy root folder and a different filename) - that is why the defaults are different then your setup. Sorry for the inconvenience. Martin On Mon, Jun 8, 2015 at 9:43 PM Shane Sturrock sh...@biomatters.com wrote: I recently updated our server to the latest release and have just had a user who ran up a lot of space and isn’t seeing it come back when she purges her data. I’ve tried using the set_user_disk_usage.py script as I’ve previously done to resolve this but now it is failing with the following: (galaxy_env)[galaxy@galaxy scripts]$ ./set_user_disk_usage.py Loading Galaxy model... Traceback (most recent call last): File ./set_user_disk_usage.py, line 85, in module model, object_store, engine = init() File ./set_user_disk_usage.py, line 43, in init for key, value in config_parser.items( app:main ): File /usr/lib64/python2.6/ConfigParser.py, line 565, in items raise NoSectionError(section) ConfigParser.NoSectionError: No section: ‘app:main' Do I need a newer python or is this a bug/regression? Shane *Dr. Shane Sturrock*Senior Scientist shane.sturr...@biomatters.com | P: +64 9 379 5064 BIOMATTERS ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] errors and questions with run_tests.sh and install_and_test_tool_shed_repositories.sh
Thanks for your answers !
I will try ./run_tests.sh -installed and see if it can solve the 2
first points. By the way, I didn't know this option (not displayed with
run_tests.sh --help) or documented on the wiki if I'm not mistaken.
For point 3, I'll try the new planemo shed_test subcommand. The
subcommand planemo test uses the run_tests.sh script, isn't it ? Does
the planemo shed_test subcommand use all or any part of the Tool Shed
Install and Test Framework
(https://wiki.galaxyproject.org/AutomatedToolTests) or is it completely
different ?
Is there any way to launch the tool tests against an external server
(point 4) with Planemo ?
Loraine
Le 02/06/2015 15:16, John Chilton a écrit :
On Tue, Jun 2, 2015 at 4:14 AM, Loraine Guéguen
loraine.gueg...@sb-roscoff.fr wrote:
Hi,
I have investigated the testing possibilities within a Galaxy local instance
and within a toolshed. I met some difficulties and I have 4 questions listed
below.
1- Tests on tools installed in a local Galaxy instance (with run_tests.sh) :
It seems that it is only possible to test the tools that have been manually
installed (run_test.sh -id ...), not the tools that have been installed
through a toolshed. Is that true ? When I try to launch the tests of a
toolshed installed tool, I have the following error message :
#
Failure: ValueError (No such test TestForTool_sartools_edger) ... ERROR
==
ERROR: Failure: ValueError (No such test TestForTool_sartools_edger)
--
Traceback (most recent call last):
File
/projet/htdocs/galaxy-dev/galaxy-dist/eggs/nose-0.11.1-py2.7.egg/nose/failure.py,
line 39, in runTest
raise self.exc_class(self.exc_val)
ValueError: No such test TestForTool_sartools_edger
--
Ran 1 test in 0.002s
FAILED (errors=1)
./run_tests.sh -installed runs the tests of all installed tool shed
tools. It might be possible to combine that with -id - for a specific
tool but I am not sure. It may be possible to construct that test even
if -id doesn't work - but it is probably pretty hacky. Let me know if
-installed works for you but not when combined with -id and we can
work out the details.
#
2- Tests on tools installed in a local Galaxy instance (with run_tests.sh) :
Is it possible to test tools which have repository or tool dependencies ? I
have a tool (manually installed in galaxy-dist/tools/) with a dependence to
a datatype installed from a toolshed. The datatype (no_unzip.zip) is defined
in the param input tag (in test) with attribute ftype. When running
run_tests.sh, it seems that the dataype is not known :
#
==
ERROR: test_tool_01 (functional.test_toolbox.TestForTool_sartools_edger)
SARTools edgeR ( sartools_edger ) Test-2
--
Traceback (most recent call last):
File
/w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py, line
268, in test_tool
self.do_it( td )
File
/w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py, line
37, in do_it
stage_data_in_history( galaxy_interactor, testdef.test_data(),
test_history, shed_tool_id )
File /w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py, line
36, in stage_data_in_history
upload_waits.append( galaxy_interactor.stage_data_async( test_data,
history, shed_tool_id ) )
File /w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py, line
182, in stage_data_async
raise Exception(submit_response)
Exception: {u'message': {u'type': u'error', u'data': {u'file_type': uAn
invalid option was selected for file_type, u'no_unzip.zip', please verify.,
u'files_metadata': [uAn invalid option was selected for file_type,
u'no_unzip.zip', please verify.]}}}
#
It is possible it is the case that tool shed datatypes are not loaded
unless running with the -installed flag. I would either setup the
tests to run locally (manually add datatypes and tools) or run
installed tools with -installed.
3- Toolshed Install and Test framework (
install_and_test_tool_shed_repositories.sh) : For my tool, the test fails if
I don't explicitely defined the dbkey attribute to unknown (dbkey=?) in
the param input tag (in test). The default dbkey value seems to be
hg17 (whereas hg17 is not defined on the server running my toolshed). So I
have the following error message if I don't add dbkey=? in test :
#
==
ERROR: test_tool_01
(functional.test_toolbox.TestForTool_galaxy4loraine:9009/repos/lgueguen/sartools_1_0_2/sartools_edger/20150209)
SARTools edgeR (
galaxy4loraine:9009/repos/lgueguen/sartools_1_0_2/sartools_edger/20150209 )
Test-2
Re: [galaxy-dev] galaxy-dev Digest, Vol 108, Issue 8
errors and questions with run_tests.sh and install_and_test_tool_shed_repositories.sh 在 2015年6月8日，17:00，galaxy-dev-requ...@lists.galaxyproject.org 写道： Send galaxy-dev mailing list submissions to galaxy-dev@lists.galaxyproject.org To subscribe or unsubscribe via the World Wide Web, visit https://lists.galaxyproject.org/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-requ...@lists.galaxyproject.org You can reach the person managing the list at galaxy-dev-ow...@lists.galaxyproject.org When replying, please edit your Subject line so it is more specific than Re: Contents of galaxy-dev digest... HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from Galaxy-dev Digest Vol ... to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. Re: Multi-level datatype conversions (Keith Suderman) 2. Re: Bismark doesn't end and blocks the server (Björn Grüning) 3. Re: errors and questions with run_tests.sh and install_and_test_tool_shed_repositories.sh (Loraine Guéguen) -- Message: 1 Date: Sun, 7 Jun 2015 16:37:08 -0400 From: Keith Suderman suder...@cs.vassar.edu To: David Kelly davidke...@uchicago.edu Cc: galaxy-...@lists.bx.psu.edu galaxy-...@lists.bx.psu.edu Subject: Re: [galaxy-dev] Multi-level datatype conversions Message-ID: 12ab4920-b9a0-4993-b320-b225394c2...@cs.vassar.edu Content-Type: text/plain; charset=utf-8 Hi David, On Jun 5, 2015, at 2:10 PM, David Kelly davidke...@uchicago.edu wrote: Hi Keith, I am able to manually convert from a-b and then separately b-c, but not directly from a-c. I'm still thinking about how to approach this as well, but I'll share my thoughts so far. Does Galaxy automatically do the conversions for you in the workflow editor? For example, if you have a tool A that produces format 'a' and another tool B that consumes format 'b' you should be able to drag the noodle from A to B and Galaxy will do an implicit format conversion. If this is working for you then someone from the Galaxy team will have to jump in. If Galaxy is not doing implicit format conversions then it likely means your datatype(s) are not fully defined. I didn't get the implicit format conversion working properly until I implemented the format sniffers. In our use case, we have a collection of climate tools we'd like to use. The tools are written by different groups, so most use their own file formats. Ideally we would like users to be able to upload their data in any of these file formats and use all tools without having to explicitly convert their data. Let's say there are 10 climate datatypes. My understanding is that in order to achieve this kind of interoperability, I'd have to write 90 converters. If Galaxy could chain converters together, I could write 1 converter per datatype and chain them together like this: a - b - c - d - e - f - g - h - i - j - a Another scenario I've been thinking about is picking one data type to be the 'standard'. Let's say it's 'a' in this example. You could write 18 converters: a-b, a-c, a-d,... b-a, c-a, d-a,... This is what we do. We have a standard pivot format then converters from the other formats to/from the pivot format. Cheers, Keith Then suppose you wanted to plug a 'd' file into a 'c' tool. You could first manually convert d-a, then use the automatic conversion for a-c. Not fully automatic, but not too bad. On Thu, Jun 4, 2015 at 5:20 PM, Keith Suderman suder...@anc.org wrote: Hi David, We just got it working for the single conversions, that is, getting Galaxy to automatically convert from a - b when needed. Are you able to do the conversion, i.e a - b and b - c individually? We are just coming to a similar use case and I'm definitely interested in how you make out, even if I can't be much help. Cheers, Keith On Jun 3, 2015, at 4:15 PM, David Kelly davidke...@uchicago.edu wrote: Hello, Suppose I have three custom datatypes defined: a, b, and c I have a datatype converter that converts from a - b I have a datatype converter that converts from b - c Can I then send 'a' files as input into tools that accept type 'c'? This doesn't seem to work in my test case, but I thought it might be worth asking to see if anyone has tried this before. Thanks! Regards, David ___ Please keep all replies on the list by
