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Fwd: Installing data for Galaxy
by Guruprasad Ananda 01 Feb '10

01 Feb '10

Begin forwarded message: > From: Guruprasad Ananda <gua110(a)bx.psu.edu> > Date: February 1, 2010 11:01:00 AM EST > To: Iwe Muiser <e.c.muiser(a)gmail.com> > Subject: Re: [galaxy-dev] Installing data for Galaxy > > Hello Iwe, > > I apologise for not covering data integration in detail on our wiki. > Here's how you add a new sequence to your Galaxy instance. In your case, for hg18, please download hg18.2bit file from http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/, and then update tool-data/alignseq.loc file with the following line: > seq hg18 PATH_TO_hg18.2bit > Also, in future if you want to find out which ".loc" file to use, you can check the validator tag under the input parameter in the tool's xml file. > Please let us know if you need any more information. > > Thanks, > Guru > Galaxy team. > > > On Feb 1, 2010, at 9:39 AM, Iwe Muiser wrote: > >> Hello, >> >> I have some questions about installing data onto my Ubuntu linux box. Mainly genomic data that can be used by the extract_genomic_dna.py script. I have done some attempts to get this working but now I'm quite stuck. First I downloaded this data from the UCSC ftp site. (ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes to be precise). Then I added the following line to "faseq.loc" as instructed: "hg18 /home/muiser/data/Human_data/HG18/chromosomes". >> After this I restarted the galaxy deamon but nothing seems to have happened. I have the idea that I am missing certain steps. >> >> The ultimate goal is to get a local galaxy install working like the one on "http://main.g2.bx.psu.edu/" >> >> The wiki is helpful to install new tools and to get an idea of how stuff works but sparsely mentions data integration. Except for MAFs which I tried as well. I'm now building an index for these .maf files which I assume will take quite some time. >> >> I hope you can help me out a bit. >> >> Thanks in advance, >> >> Iwe Muiser >> _______________________________________________ >> galaxy-dev mailing list >> galaxy-dev(a)lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-dev > > Guruprasad Ananda > Graduate Student > Bioinformatics and Genomics > The Pennsylvania State University > > > > Guruprasad Ananda Graduate Student Bioinformatics and Genomics The Pennsylvania State University

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Issues when using mysql with galaxy
by Sriram Raghuraman 01 Feb '10

01 Feb '10

Hi I am using python 2.6.4 and the latest version of galaxy. I am attempting to install galaxy on my local ubuntu desktop. I can upload files and the history is updated correctly with sqlite In order to use mysql I get the schema from sqlite using sqlite3 universe.sqlite .dump > ./temp.sql I edited temp.sql to replace some quote around column names with `` . I also moved the lone insert statement to the bottom.(file attached) I use this sql script to initialize the mysql d/b named galaxy. I use this line for the database connection in universe_wsgi.ini database_connection = mysql://{username}:{password}@localhost/galaxy?unix_socket=/var/run/mysqld/mysqld.sock When i start galaxy it seems ok until i try uploading a file when i get |a RuntimeError: maximum recursion depth exceeded in the history pane on the right. Traceback attached. |When I actually upload a file in sqlite and them dump out the schema it generates additional inserts for event etc. When I apply those inserts and then start up galaxy, I don't get this error on uploading the file. However the file upload never completes even for a really small file. I get the animated upload sign forever. Thanks Sriram

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Installing data for Galaxy
by Iwe Muiser 01 Feb '10

01 Feb '10

Hello, I have some questions about installing data onto my Ubuntu linux box. Mainly genomic data that can be used by the extract_genomic_dna.py script. I have done some attempts to get this working but now I'm quite stuck. First I downloaded this data from the UCSC ftp site. ( ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes to be precise). Then I added the following line to "faseq.loc" as instructed: "hg18 /home/muiser/data/Human_data/HG18/chromosomes". After this I restarted the galaxy deamon but nothing seems to have happened. I have the idea that I am missing certain steps. The ultimate goal is to get a local galaxy install working like the one on " http://main.g2.bx.psu.edu/" The wiki is helpful to install new tools and to get an idea of how stuff works but sparsely mentions data integration. Except for MAFs which I tried as well. I'm now building an index for these .maf files which I assume will take quite some time. I hope you can help me out a bit. Thanks in advance, Iwe Muiser

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[hg] galaxy 3302: Revert bowtie wrapper -- accidently committed ...
by Greg Von Kuster 29 Jan '10

29 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e17d80f7e2b6 changeset: 3302:e17d80f7e2b6 user: James Taylor <james(a)jamestaylor.org> date: Fri Jan 29 11:40:23 2010 -0500 description: Revert bowtie wrapper -- accidently committed change from testing diffstat: tools/sr_mapping/bowtie_wrapper.xml | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r 200091ad2b6d -r e17d80f7e2b6 tools/sr_mapping/bowtie_wrapper.xml --- a/tools/sr_mapping/bowtie_wrapper.xml Thu Jan 28 16:41:15 2010 -0500 +++ b/tools/sr_mapping/bowtie_wrapper.xml Fri Jan 29 11:40:23 2010 -0500 @@ -186,7 +186,7 @@ </command> <inputs> <conditional name="refGenomeSource"> - <param name="genomeSourceFood" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> + <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> <option value="indexed">Use a built-in index</option> <option value="history">Use one from the history</option> </param>

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[hg] galaxy 3301: Workflow: deal with case where an input parame...
by Greg Von Kuster 29 Jan '10

29 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/200091ad2b6d changeset: 3301:200091ad2b6d user: James Taylor <james(a)jamestaylor.org> date: Thu Jan 28 16:41:15 2010 -0500 description: Workflow: deal with case where an input parameter that was connected has been removed diffstat: lib/galaxy/web/controllers/workflow.py | 14 +++++++++++++- 1 files changed, 13 insertions(+), 1 deletions(-) diffs (25 lines): diff -r 2772ab12e361 -r 200091ad2b6d lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Thu Jan 28 15:54:46 2010 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Thu Jan 28 16:41:15 2010 -0500 @@ -491,8 +491,20 @@ 'form_html': module.get_config_form(), } # Connections + input_connections = step.input_connections + if step.type is None or step.type == 'tool': + # Determine full (prefixed) names of valid input datasets + data_input_names = {} + def callback( input, value, prefixed_name, prefixed_label ): + if isinstance( input, DataToolParameter ): + data_input_names[ prefixed_name ] = True + visit_input_values( module.tool.inputs, module.state.inputs, callback ) + # Filter + # FIXME: this removes connection without displaying a message currently! + input_connections = [ conn for conn in input_connections if conn.input_name in data_input_names ] + # Encode input connections as dictionary input_conn_dict = {} - for conn in step.input_connections: + for conn in input_connections: input_conn_dict[ conn.input_name ] = \ dict( id=conn.output_step.order_index, output_name=conn.output_name ) step_dict['input_connections'] = input_conn_dict

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[hg] galaxy 3300: Workflow: fix problem with upgrade_messages fo...
by Greg Von Kuster 29 Jan '10

29 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/2772ab12e361 changeset: 3300:2772ab12e361 user: James Taylor <james(a)jamestaylor.org> date: Thu Jan 28 15:54:46 2010 -0500 description: Workflow: fix problem with upgrade_messages for input dataset modules diffstat: lib/galaxy/web/controllers/workflow.py | 2 ++ 1 files changed, 2 insertions(+), 0 deletions(-) diffs (19 lines): diff -r c9d95fd8bfe9 -r 2772ab12e361 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Thu Jan 28 14:52:02 2010 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Thu Jan 28 15:54:46 2010 -0500 @@ -714,6 +714,7 @@ # If kwargs were provided, the states for each step should have # been POSTed for step in workflow.steps: + step.upgrade_messages = {} # Connections by input name step.input_connections_by_name = \ dict( ( conn.input_name, conn ) for conn in step.input_connections ) @@ -771,6 +772,7 @@ else: # Prepare each step for step in workflow.steps: + step.upgrade_messages = {} # Contruct modules if step.type == 'tool' or step.type is None: # Restore the tool state for the step

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[hg] galaxy 3299: require pysqlite in functional_tests to work a...
by Greg Von Kuster 29 Jan '10

29 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/c9d95fd8bfe9 changeset: 3299:c9d95fd8bfe9 user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Jan 28 14:52:02 2010 -0500 description: require pysqlite in functional_tests to work around a bug in nose diffstat: scripts/functional_tests.py | 4 ++++ 1 files changed, 4 insertions(+), 0 deletions(-) diffs (14 lines): diff -r 7173ce5647ce -r c9d95fd8bfe9 scripts/functional_tests.py --- a/scripts/functional_tests.py Thu Jan 28 13:37:53 2010 -0500 +++ b/scripts/functional_tests.py Thu Jan 28 14:52:02 2010 -0500 @@ -17,6 +17,10 @@ eggs.require( "PasteDeploy" ) eggs.require( "Cheetah" ) +# this should not be required, but it is under certain conditions, thanks to this bug: +# http://code.google.com/p/python-nose/issues/detail?id=284 +eggs.require( "pysqlite" ) + import atexit, logging, os, os.path, sys, tempfile import twill, unittest, time import subprocess, sys, threading, random

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[hg] galaxy 3298: Fix another exception error (only in 2.4) with...
by Greg Von Kuster 29 Jan '10

29 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/7173ce5647ce changeset: 3298:7173ce5647ce user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Jan 28 13:37:53 2010 -0500 description: Fix another exception error (only in 2.4) with check_python.py diffstat: scripts/check_python.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (10 lines): diff -r 52d5450e34e4 -r 7173ce5647ce scripts/check_python.py --- a/scripts/check_python.py Thu Jan 28 11:38:38 2010 -0500 +++ b/scripts/check_python.py Thu Jan 28 13:37:53 2010 -0500 @@ -25,5 +25,5 @@ check_python() print check_virtualenv() sys.exit( 0 ) - except Exception: + except StandardError: sys.exit( 1 )

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[hg] galaxy 3297: Workflow: fix for dealing with changes to the ...
by Greg Von Kuster 29 Jan '10

29 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/52d5450e34e4 changeset: 3297:52d5450e34e4 user: James Taylor <james(a)jamestaylor.org> date: Thu Jan 28 11:38:38 2010 -0500 description: Workflow: fix for dealing with changes to the test param name when the conditional is unchanged. Message display is still not perfect for nested messages, but shouldn't cause error's anymore diffstat: lib/galaxy/tools/__init__.py | 12 ++++++++++-- lib/galaxy/tools/parameters/grouping.py | 10 +++++++++- tools/sr_mapping/bowtie_wrapper.xml | 2 +- 3 files changed, 20 insertions(+), 4 deletions(-) diffs (54 lines): diff -r 30cd8d9f8ac9 -r 52d5450e34e4 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Thu Jan 28 11:06:38 2010 -0500 +++ b/lib/galaxy/tools/__init__.py Thu Jan 28 11:38:38 2010 -0500 @@ -1097,8 +1097,16 @@ self.check_and_update_param_values_helper( input.inputs, d, trans, messages, context, rep_prefix ) elif isinstance( input, Conditional ): group_values = values[ input.name ] - current = group_values["__current_case__"] - self.check_and_update_param_values_helper( input.cases[current].inputs, group_values, trans, messages, context, prefix ) + if input.test_param.name not in group_values: + # No test param invalidates the whole conditional + values[ input.name ] = group_values = input.get_initial_value( trans, context ) + messages[ input.test_param.name ] = "No value found for '%s%s', used default" % ( prefix, input.test_param.label ) + current_case = group_values['__current_case__'] + for child_input in input.cases[current_case].inputs.itervalues(): + messages[ child_input.name ] = "Value no longer valid for '%s%s', replaced with default" % ( prefix, child_input.label ) + else: + current = group_values["__current_case__"] + self.check_and_update_param_values_helper( input.cases[current].inputs, group_values, trans, messages, context, prefix ) else: # Regular tool parameter, no recursion needed pass diff -r 30cd8d9f8ac9 -r 52d5450e34e4 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py Thu Jan 28 11:06:38 2010 -0500 +++ b/lib/galaxy/tools/parameters/grouping.py Thu Jan 28 11:38:38 2010 -0500 @@ -359,7 +359,15 @@ def value_from_basic( self, value, app, ignore_errors=False ): rval = dict() current_case = rval['__current_case__'] = value['__current_case__'] - rval[ self.test_param.name ] = self.test_param.value_from_basic( value[ self.test_param.name ], app, ignore_errors ) + # Test param + if ignore_errors and self.test_param.name not in value: + # If ignoring errors, do nothing. However this is potentially very + # problematic since if we are missing the value of test param, + # the entire conditional is wrong. + pass + else: + rval[ self.test_param.name ] = self.test_param.value_from_basic( value[ self.test_param.name ], app, ignore_errors ) + # Inputs associated with current case for input in self.cases[current_case].inputs.itervalues(): if ignore_errors and input.name not in value: # If we do not have a value, and are ignoring errors, we simply diff -r 30cd8d9f8ac9 -r 52d5450e34e4 tools/sr_mapping/bowtie_wrapper.xml --- a/tools/sr_mapping/bowtie_wrapper.xml Thu Jan 28 11:06:38 2010 -0500 +++ b/tools/sr_mapping/bowtie_wrapper.xml Thu Jan 28 11:38:38 2010 -0500 @@ -186,7 +186,7 @@ </command> <inputs> <conditional name="refGenomeSource"> - <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> + <param name="genomeSourceFood" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> <option value="indexed">Use a built-in index</option> <option value="history">Use one from the history</option> </param>

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Re: [galaxy-dev] fancy output
by Greg Von Kuster 28 Jan '10

28 Jan '10

Hello Rich, Line 87 or so in ~/templates/root/history_common.mako can be changed to display differently. it currently looks like this: <div class="info">${_('Info: ')}${data.display_info()}</div> Note that it calls the display_info() method in the file at ~/lib/ galaxy/datatypes/data.py. On Jan 26, 2010, at 2:52 PM, Richard Rauscher wrote: > Hi. > Is there a way to format the “info” output appearing in the history > pain? E.g. I’d like to add some bolding…standard HTML stuff. > Is there a HOW-TO about formatting output? > > Thx, > -Rich > > Richard Rauscher > Director of IT, Biomedical Research & Penn State Cancer Institute > Director, Cancer Biomedical Informatics Core > Penn State University > Hershey, PA > (717) 531-1066 > rrauscher(a)psu.edu > This signature is RFC 3092 compliant. :-) > *****E-Mail Confidentiality Notice***** > This message (including any attachments) contains information > intended for a specific individual(s) and purpose that may be > privileged, confidential or otherwise protected from disclosure > pursuant to applicable law. Any inappropriate use, distribution or > copying of the message is strictly prohibited and may subject you to > criminal or civil penalty. If you have received this transmission > in error, please reply to the sender indicating this error and > delete the transmission from your system immediately. > > _______________________________________________ > galaxy-dev mailing list > galaxy-dev(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-dev Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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