galaxy-dev October 2010

galaxy-dev@lists.galaxyproject.org

47 participants
83 discussions

run_functional_tests.sh -sid option
by Peter 11 Feb '13

11 Feb '13

Hi, I'm trying to use run_functional_tests.sh to run all the tests for a section (group of tools). I've read the output from: ./run_functional_tests.sh help For example, from the tools_conf.xml.sample we have <section name="ENCODE Tools" id="EncodeTools"> <tool file="encode/gencode_partition.xml" /> <tool file="encode/random_intervals.xml" /> </section> And looking at these tools' XML files, <tool id="gencode_partition1" name="Gencode Partition"> and: <tool id="random_intervals1" name="Random Intervals"> I'd like to run the functional tests for the ENCODE tools, Using the switch for an individual tool id (-id) works, ./run_functional_tests.sh -id gencode_partition1 ... Ran 1 test in 22.302s ... and so does this (well, it say the tool doesn't have any tests which is true in this example): ./run_functional_tests.sh -id random_intervals1 ... Ran 1 test in 0.027s ... However, I also tried using the section id switch (-sid), ./run_functional_tests.sh -sid EncodeTools ... Ran 0 tests in 0.000s ... I also tried using the section name, /run_functional_tests.sh -sid "ENCODE Tools" Is this (-sid not working) a known issue, or am I using it wrong? Thanks, Peter

4 5

Sharing tool definitions between XML files
by Peter 02 Jun '11

02 Jun '11

Hi all, I'm wondering if there is any established way to share parameter definitions between tool wrapper XML files? For example, I am currently working on NCBI BLAST+ wrappers, and these tools have a lot in common. For example, the output format option will be a select parameter, and it will be the same for blastn, blastp, tblastn, etc. I can just cut and paste the definition but this seems inelegant and will be a long term maintenance burden if it ever needs updating (lots of places would need to be updated the same way). I'd like to have a shared XML snippet defining this parameter which I could then reference/include from each tool wrapper than needs it. I'm thinking of something like XML's <!ENTITY ...> might work. Is this possible? Peter

2 2

Output file naming / dataset's label
by Tanguy Le Carrour 14 Apr '11

14 Apr '11

Dear Galaxy Team, I started using Galaxy few months ago. I'm now setting up my first "real" workflows. I would like to keep the name of my input file through the various steps as dataset's label, maybe also modify it a bit, and finally give a "proper" name to the result file downloaded. A simple example: 1) date-sample_name.gff3 --[step1]-> date-sample_name-step1.tsv 2) date-sample_name-step1.tsv --[step2]-> date-sample_name-step1-step2.txt 3 download date-sample_name-step1-step2.txt I've seen that I can use the 'label' attribute in the tool config "data" tag to do so. But I don't know how to access the ${input.label} (?) and how to modify it. I doesn't stop me using my workflows, but it would definitely help my users not to get lost when they use them. Best regards, Tanguy Le Carrour -- Tanguy LE CARROUR Functional Genomics Center Zurich ETH Zurich / University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland

4 8

swap issue
by Isabelle Phan 22 Mar '11

22 Mar '11

Hello, I am running galaxy, using a postgres backend. The galaxy server systematically gets killed whenever I try uploading a bam file. The samtools process is still running. This is the end of the log: 2010-08-26 18:08:11,371 INFO sqlalchemy.engine.threadlocal.TLEngine.0x...4610 {'param_1': 8} sqlalchemy.engine.threadlocal.TLEngine.0x...4610 INFO 2010-08-26 18:08:11,371 {'param_1': 8} 2010-08-26 18:08:11,378 INFO sqlalchemy.pool.QueuePool.0x...4ed0 Connection <connection object at 0x567bf30; dsn: 'dbname=galaxy host=/var closed: 0> being returned to pool sqlalchemy.pool.QueuePool.0x...4ed0 INFO 2010-08-26 18:08:11,378 Connection <connection object at 0x567bf30; dsn: 'dbname=galaxy host=/var closed: 0> being returned to pool 10.1.20.44 - - [26/Aug/2010:18:08:06 -0700] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy:8080/history" "Mozilla/5.0 (X1 (x86_64); en-US; rv:1.9.2.8) Gecko/20100722 Firefox/3.6.8" Killed I have the following options set in universe_wsgi.ini: database_engine_option_server_side_cursors = True database_engine_option_strategy = threadlocal It seems to be running out of swap. I monitored memory usage with 'top' and galaxy died when available swap hit 0k free. I am not superuser on the machine where galaxy is running and I have no other server available. Is there something I could do to prevent galaxy from dying? Thanks, Isabelle -- Isabelle Phan, DPhil Seattle Biomedical Research Institute +1(206)256 7113

3 4

Problems with run_functional_tests.sh and history?
by Peter 21 Feb '11

21 Feb '11

Hi all, I'm having trouble with the Galaxy functional tests. On our Linux server things seem to work, but I'm having trouble on my Mac. This affects multiple tests. For example, using a test for my own tool wrapper, on Linux my test passes. On my Mac, the tool is missing the required binary so I expect the test to fail with error level 127 and a message to stderr. However, I get the following cryptic error: $ ./run_functional_tests.sh -id tmhmm2 ... functional_tests.py INFO 2010-10-28 11:57:01,129 Embedded web server started functional_tests.py INFO 2010-10-28 11:57:01,185 Functional tests will be run against localhost:8980 nose.plugins.manager DEBUG 2010-10-28 11:57:01,210 DefaultPluginManager load plugin sqlalchemy = sqlalchemy.test.noseplugin:NoseSQLAlchemy nose.plugins.manager DEBUG 2010-10-28 11:57:01,215 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML TMHMM 2.0 ( tmhmm2 ) > Test-1 ... Error - <type 'exceptions.TypeError'>: 'NoneType' object is not callable URL: http://localhost:8980/history File '/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Paste-1.7.2-py2.5.egg/paste/exceptions/errormiddleware.py', line 144 in __call__ app_iter = self.application(environ, sr_checker) File '/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Paste-1.7.2-py2.5.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Paste-1.7.2-py2.5.egg/paste/httpexceptions.py', line 636 in __call__ return self.application(environ, start_response) File '/Users/xxx/repositories/galaxy-central/lib/galaxy/web/framework/base.py', line 154 in __call__ return body( environ, start_response ) File '/Users/xxx/repositories/galaxy-central/lib/galaxy/web/framework/__init__.py', line 668 in render template.render_context( context ) File '/Users/xxx/repositories/galaxy-central/eggs/Mako-0.2.5-py2.5.egg/mako/template.py', line 146 in render_context runtime._render_context(self, self.callable_, context, *args, **kwargs) File '/Users/xxx/repositories/galaxy-central/eggs/Mako-0.2.5-py2.5.egg/mako/runtime.py', line 381 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/Users/xxx/repositories/galaxy-central/eggs/Mako-0.2.5-py2.5.egg/mako/runtime.py', line 414 in _exec_template callable_(context, *args, **kwargs) File '/Users/xxx/repositories/galaxy-central/database/compiled_templates/root/history.mako.py', line 55 in render_body __M_writer(u'\n<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\n\n<html>\n\n<head>\n<title>') File '/Users/xxx/repositories/galaxy-central/lib/galaxy/web/framework/__init__.py', line 665 in write response_write( d.encode( 'utf-8' ) ) TypeError: 'NoneType' object is not callable CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT: 'text/html; */*' HTTP_ACCEPT_ENCODING: 'identity' HTTP_CONNECTION: 'close' HTTP_COOKIE: '$Version=1; galaxysession=eb142648ac45b770a711a07bbd8189c4a80d9868f9ceff96f0635391728a47dfe5161bca180a2aae; $Path="/"' HTTP_HOST: 'localhost:8980' PATH_INFO: '/history' REMOTE_ADDR: '127.0.0.1' REQUEST_METHOD: 'GET' SERVER_NAME: '127.0.0.1' SERVER_PORT: '8980' SERVER_PROTOCOL: 'HTTP/1.1' Configuration ------------- static_enabled: False use_translogger: False WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0xbfd2e10> paste.cookies: (<SimpleCookie: galaxysession='eb142648ac45b770a711a07bbd8189c4a80d9868f9ceff96f0635391728a47dfe5161bca180a2aae'>, '$Version=1; galaxysession=eb142648ac45b770a711a07bbd8189c4a80d9868f9ceff96f0635391728a47dfe5161bca180a2aae; $Path="/"') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0xbfd3110> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0xccf1f10> paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True webob._parsed_query_vars: (MultiDict([]), '') wsgi process: 'Multithreaded' ------------------------------------------------------------ ERROR ====================================================================== ERROR: TMHMM 2.0 ( tmhmm2 ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/xxx/repositories/galaxy-central/test/functional/test_toolbox.py", line 160, in test_tool self.do_it( td ) File "/Users/xxx/repositories/galaxy-central/test/functional/test_toolbox.py", line 24, in do_it self.new_history() File "/Users/xxx/repositories/galaxy-central/test/base/twilltestcase.py", line 291, in new_history self.check_history_for_string('Your history is empty') File "/Users/xxx/repositories/galaxy-central/test/base/twilltestcase.py", line 215, in check_history_for_string self.visit_page( "history" ) File "/Users/xxx/repositories/galaxy-central/test/base/twilltestcase.py", line 1040, in visit_page tc.code( 200 ) File "/Users/xxx/repositories/galaxy-central/eggs/twill-0.9-py2.5.egg/twill/commands.py", line 133, in code should_be)) TwillAssertionError: code is 500 != 200 ---------------------------------------------------------------------- Ran 1 test in 0.824s FAILED (errors=1) functional_tests.py INFO 2010-10-28 11:57:02,079 Shutting down functional_tests.py INFO 2010-10-28 11:57:02,079 Shutting down embedded web server ... ############################################################################### Here is my suggested fix: diff -r 82743fcbf23c lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Thu Oct 28 11:41:18 2010 +0100 +++ b/lib/galaxy/web/framework/__init__.py Thu Oct 28 11:56:16 2010 +0100 @@ -660,6 +660,9 @@ ## return template.render( **data ) def render( environ, start_response ): response_write = start_response( self.response.wsgi_status(), self.response.wsgi_headeritems() ) + if response_write is None: + log.error( "Error: this request returned None from start_response: %s" % self.request.browser_url ) + return [] class StreamBuffer( object ): def write( self, d ): response_write( d.encode( 'utf-8' ) ) ############################################################################### With the patch, I get: $ ./run_functional_tests.sh -id tmhmm2 ... functional_tests.py INFO 2010-10-28 11:52:37,742 Embedded web server started functional_tests.py INFO 2010-10-28 11:52:37,800 Functional tests will be run against localhost:9383 nose.plugins.manager DEBUG 2010-10-28 11:52:37,825 DefaultPluginManager load plugin sqlalchemy = sqlalchemy.test.noseplugin:NoseSQLAlchemy nose.plugins.manager DEBUG 2010-10-28 11:52:37,829 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML TMHMM 2.0 ( tmhmm2 ) > Test-1 ... galaxy.web.framework ERROR 2010-10-28 11:52:38,685 Error: this request returned None from start_response: http://localhost:9383/history ERROR ====================================================================== ERROR: TMHMM 2.0 ( tmhmm2 ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/xxx/repositories/galaxy-central/test/functional/test_toolbox.py", line 160, in test_tool self.do_it( td ) File "/Users/xxx/repositories/galaxy-central/test/functional/test_toolbox.py", line 24, in do_it self.new_history() File "/Users/xxx/repositories/galaxy-central/test/base/twilltestcase.py", line 291, in new_history self.check_history_for_string('Your history is empty') File "/Users/xxx/repositories/galaxy-central/test/base/twilltestcase.py", line 217, in check_history_for_string tc.find(subpatt) File "/Users/xxx/repositories/galaxy-central/eggs/twill-0.9-py2.5.egg/twill/commands.py", line 239, in find raise TwillAssertionError("no match to '%s'" % (what,)) TwillAssertionError: no match to 'Your' -------------------- >> begin captured logging << -------------------- galaxy.web.framework: ERROR: Error: this request returned None from start_response: http://localhost:9383/history --------------------- >> end captured logging << --------------------- ---------------------------------------------------------------------- Ran 1 test in 0.821s FAILED (errors=1) functional_tests.py INFO 2010-10-28 11:52:38,691 Shutting down functional_tests.py INFO 2010-10-28 11:52:38,691 Shutting down embedded web server ... ############################################################################### I'm still puzzled about what is going wrong - this affects other Galaxy tests as well - not just mine. Is there something obvious wrong with the setup on this machine? Actually using Galaxy running on this Mac seems to work. Thanks, Peter

2 6

Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?
by Peter 01 Feb '11

01 Feb '11

On Wed, Oct 13, 2010 at 10:22 AM, Peter <peter(a)maubp.freeserve.co.uk> wrote: > On Wed, Oct 13, 2010 at 12:58 AM, Kanwei Li <kanwei(a)gmail.com> wrote: >> >> Hi Peter, >> >> The BLAST+ branch has been transplanted into galaxy-central. Thank you! >> >> Kanwei > > Wow. Thanks :) There are another few change sets on this follow up branch, http://bitbucket.org/peterjc/galaxy-central/src/blastplus2 These are: Include BLAST-XML to tabular in tool_conf.xml.sample http://bitbucket.org/peterjc/galaxy-central/changeset/629448f1a17b Workaround Issue 397 using 'if' in Cheetah template to avoid hidden parameters http://bitbucket.org/peterjc/galaxy-central/changeset/02ce0b68936a Ignore Unix editor backup files ending with tilde (not BLAST+ specific): http://bitbucket.org/peterjc/galaxy-central/changeset/708816ffd451 Ignore # lines in BLAST tabular output in my filter script http://bitbucket.org/peterjc/galaxy-central/changeset/b2dcd6b8d434 And a capitalisation fix in my XML caption: http://bitbucket.org/peterjc/galaxy-central/changeset/6efadbea0cfc > > I mentioned it needs tests: > I've worked out how to add unit tests to the XML wrapper (that is well documented) and run them via run_functional_tests.sh - so adding some BLAST+ tests should be possible now. Peter

5 29

Display of tabular data in Galaxy
by Peter 22 Nov '10

22 Nov '10

Hi all, I've noticed in the right hand column for tabular data Galaxy shows the first few lines with a nice column based layout. Looking at the source, you actually define an HTML table for this. However, on the main central column, when viewing a tabular dataset (by clicking on the eye icon from an entry in the right hand column), the data is shown as raw text. As long as the data in each column is about the same length, this works OK. However, if you have variable length fields then the columns do not line up. It would be nice if the main display showed the data respecting the columns. Has this been considered? My guess is that doing this was rejected due to the computational load to reformat it, and the network load to send the marked up data. (I did try and search the mailing list archives but didn't find any discussion of this) Regards, Peter

2 3

Galaxy wrappers for TMHMM and SignalP
by Peter 15 Nov '10

15 Nov '10

Hello, Are there any existing Galaxy wrappers for the command line tools (or the online services) TMHMM v2.0 (Trans-Membrane Hidden Markov Model) and SignalP v3.0 (Signal Peptide)? http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp Both take protein FASTA files for input, but there are a few extra considerations here like limiting each call to TMHMM to 4000 proteins (IIRC), the possibility to split the job in order to take advantage of multiple cores, and parsing the output into a Galaxy friendly tabular form. Thanks, Peter

2 7

Variabels in label elements
by Bossers, Alex 09 Nov '10

09 Nov '10

Hi All, Does someone know how to get the value of a type="select" param_name displayed in the output file label? I know how to do it if its just a non-nested param setup-up using ${input1.value_label} where the input1 is the select_name. But this fails if the select is inside a conditional..... From cheetah script I can call these values like IF $tool.cmd=="something":..... But whatever I try in the <outputs><data> fails (I though it to be ${tool.cmd.value_label} but that complains on cmd not defined.... All possible iteration tried :( Snippet of a generalised tool.xml below. Any suggestions or hints where to get documentation on this syntax is welcomed! Alex <command> /opt/tools/$tool.cmd $cmd_extra $input_delta #if $tool.cmd=="show-aligns": $tool.extra1 $tool.extra2 #end if > $out_tool </command> <inputs> <conditional name="tool"> <param name="cmd" type="select" value="show-snps" label="Select tool" > <option value="show-snps">show snps</option> <option value="show-aligns">show aligns</option> </param> <when value="show-aligns"> <param name="extra1" type="text" size="40" value="" label="IdR" help="FastA header ref sequence" /> <param name="extra2" type="text" size="40" value="" label="IdQ" help="FastA header query sequence" /> </when> <when value="show-snps" /> </conditional> <param name="input_delta" type="data" format="tabular" label="MUMmer delta file" /> <param name="cmd_extra" type="text" size="40" value="" label="Extra cmd line options" help="see specific cmd line options below for each tool" /> </inputs> <outputs> <data name="out_tool" format="text" label="tool ${tool.cmd.value_label}" /> </outputs>

3 3

How to implement the button "send query to galaxy" in UCSC Main tool
by Zhe Chen 09 Nov '10

09 Nov '10

Hi, How to implement the button "send query to galaxy" in (Get Data)->(UCSC Main tool) on the second page? Do you have a code example of it? Thanks

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galaxy-dev October 2010