galaxy-dev January 2010

galaxy-dev@lists.galaxyproject.org

29 participants
156 discussions

Re: [galaxy-dev] Questions about Galaxy!
by WangJun 27 Feb '10

27 Feb '10

Dear Greg Von Kuster, I installed a local Galaxy instance for data submit test for our own GMap project. And I found a question: If I submit from GMap for the first time, then a error page appears. (attached the error information) However, if I use it from "Get Data" in Galaxy for the first time, it works very well. I guess the history_id does not exist when I submit from GMap for the first time. Also I found it's "Server error" if I submit data from UCSC table browser to the public Galaxy instance for the first time. I think I have the same question with them. Can you help to to find a solution? Thanks a lot! Best wishes, Kathleen 2010-01-19 发件人： Greg Von Kuster 发送时间： 2009-11-18 02:10:17 收件人： wangjun 抄送： galaxy-dev 主题： Re: [galaxy-dev] Questions about Galaxy! Kathleen, Please install a local instance of Galaxy and develop a data source tool that works between your Galaxy instance and GMap. You can download Galaxy from http://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy. When you have your tool working, please submit it to us for possible inclusion in the public Galaxy instance. Thanks very much for your interest in doing this. Greg Von Kuster On Nov 17, 2009, at 11:27 AM, wangjun(a)mail.cbi.pku.edu.cn wrote: Hello Greg Von Kuster, You can access test GMap at http://202.38.125.5:8383/. Click the big button "search" and submit using the default params, then you can see four tracks. You can click the entry of the second track, for example the red one, then you can see the detail info in the right panel. Click the "view sequence", there is a button "submit to Galaxy", you can try it. Thanks a lot! Kathleen Kathleen, sorry, I thought you had your own local Galaxy instance. Can you give us more information on GMap? Do you have a wiki or something we can access online to read about it? Thanks! On Nov 17, 2009, at 10:37 AM, wangjun(a)mail.cbi.pku.edu.cn wrote: Hello Greg Von Kuster, I am talking about your public Galaxy instance, and we don't have local one. We find that UCSC's data can be saved in your site directly, so we hope that Galaxy can also save our GMap data directly. We use the same post method like UCSC and the data can be saved now, but the data title is wrong. So I am writing to you to hope that you can help us. Thanks you. Kathleen Hello Kathleen, Are you talking about your own local Galaxy instance or our main public Galaxy instance that is hosted here at Penn State University? Greg Von Kuster On Nov 17, 2009, at 10:10 AM, WangJun wrote: Hello Greg Von Kuster, Thanks for your reply, but I think you misunderstood my meaning. I am now working on a genome browser project GMap, and I hope that I can post request from GMap to Galaxy, then Galaxy can retrieve and save the data in the History space like the UCSC request. Untill now, I can post a request, including a url and params, and Galaxy can retrieve the data and save it. However, the title of the data is still "UCSC Main". I think that's because of the tool_id param's value is still "ucsc_table_direct1". I mean whether you can support us by adding a new tool_id named "CBI GMap". Then our post data can be shown with title "CBI GMap", not "UCSC Main". Thanks a lot! Kathleen 发件人： Greg Von Kuster 发送时间： 2009-11-17 21:49:22 收件人： WangJun 抄送：主题： Re: [galaxy-dev] Questions about Galaxy! Kathleen, I'm not sure I understand the question, but if you are simply creating a new tool that is very similar to the "ucsc_table_direct1" tool , and you want the ID of your new tool to be "CBIGMap" ( I would advise against space characters in the tool ID ), then your tools config tag can be something like this: <tool id="CBIGMap" name="CBIG Map" version="1.0.0" hidden="false" tool_type="data_source" URL_method="post"> If you have questions about how to add a new tool to your Galaxy instance, see our wiki at http://bitbucket.org/galaxy/galaxy- central/wiki/AddToolTutorial On Nov 17, 2009, at 8:38 AM, WangJun wrote: Hello Greg Von Kuster, Now I have solved the second problem.:) And for the first one, could you help me to add a new tool_id named "CBI GMap" to support our data source? This is a project in Center for Bioinformatics in Peking University in China. And I am a PhD student working on it. If you have other questions, please email me.:) <tool id="ucsc_table_direct1" name="UCSC Main" version="1.0.0" hidden="false" tool_type="data_source" URL_method="post"> Thanks a lot! Best, Kathleen 20091117 =================================================================== = Hello Greg Von Kuster, Thanks a lot for your reply. But I still have a question: I have a url, and I include three necessary params in the following form. After I post it to Galaxy, I can see that Galaxy fetch the data. However, there are two point that I want to ask: 1. the "tool_id" param. My data's title is still "UCSC Main", I think that's because I use the "ucsc_table_direct1" value for "tool_id", right? Then how do I change this title? Can I adjust it by other param to change the title? 2. If I submit data from UCSC, then I can see a white box containing the data in the History part. However, I can only see the data info without data if I submit from my own site. (You can refer to attachment for detail. The No.20 data is from UCSC, and I can see the sequence. While the No.22 data is from my site, and I can not see the sequence.) And I don't know why. <form method="POST" action="http://main.g2.bx.psu.edu/tool_runner"> <input type="HIDDEN" value="ucsc_table_direct1" name="tool_id"/> <input type="HIDDEN" value="http://202.38.125.5:8383/entry/ rice_nucleotide_frame_galaxy.jsp" name="URL"/> <input type="HIDDEN" value="<%=id%>" name="id"/> <input type="HIDDEN" value="<%=trackName%>" name="trackName"/> <input type="HIDDEN" value="<%=type%>" name="type"/> <input type="HIDDEN" value="rice" name="db"/> <input type="HIDDEN" value="Rice" name="org"/> <input type="SUBMIT" value="Send query to Galaxy" name="submitGalaxy"/> </form> (test data: http://202.38.125.5:8383/entry/ rice_nucleotide_frame_galaxy.jsp? id=LOC_Os02g01370&trackName=MSU_Osa1_Rice_Loci&type=seq ) Thank a lot! Best, Kathleen 20091117 发件人： Greg Von Kuster 发送时间： 2009-11-17 04:50:55 收件人： WangJun 抄送： galaxy-user(a)bx.psu.edu; galaxy-dev(a)bx.psu.edu 主题： Re: [galaxy-dev] Questions about Galaxy! Hello Kathleen, Please see our wiki at http://bitbucket.org/galaxy/galaxy-central/ wiki/DataSources for details about how Galaxy communicates with external data sources. Your "dataset platform" will need to build an url that includes all of the parameters that are needed to retrieve the data, and send that url to Galaxy in the URL parameter so that Galaxy can execute the post. On Nov 16, 2009, at 9:06 AM, WangJun wrote: Hi, This is a question about Galaxy interaction with UCSC data. I hava a dataset platform, and I want to add a button like the UCSC's "Send query to Galaxy". I find that it's actually a form: <form method="POST" action="http://main.g2.bx.psu.edu/ tool_runner"> <input type="HIDDEN" value="ucsc_table_direct1" name="tool_id"/> <input type="HIDDEN" value="http://genome.ucsc.edu/cgi-bin/ hgTables" name="URL"/> <input type="HIDDEN" value="296389734" name="hguid"/> <input type="HIDDEN" value="hg18" name="db"/> <input type="HIDDEN" value="Human" name="org"/> <input type="HIDDEN" value="multiz28way" name="hgta_table"/> <input type="HIDDEN" value="multiz28way" name="hgta_track"/> <input type="HIDDEN" value="range" name="hgta_regionType"/> <input type="HIDDEN" value="primaryTable" name="hgta_outputType"/> <input type="HIDDEN" value="chr3:130734948-130736581" name="position"/> <input type="HIDDEN" value="get output" name="hgta_doTopSubmit"/> <input type="HIDDEN" value="146683120" name="hgsid"/> <input type="SUBMIT" value="Send query to Galaxy" name="hgta_doGalaxyQuery"/> </form> I have a url and three params, and I tried. But I can't see my data in the right-side green box. And what's the tool_id param used for? Thanks in advance! Best, Kathleen 2009-11-16 _______________________________________________ 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 Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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2010 GMOD Summer School - Americas
by Dave Clements, GMOD Help Desk 16 Feb '10

16 Feb '10

Hello all, I am pleased to announce that we are now accepting applications for: 2010 GMOD Summer School - Americas 6-9 May 2010 NESCent, Durham, NC, USA http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas This will be a hands-on multi-day course aimed at teaching new GMOD users/administrators how to get GMOD Components up and running. The course will introduce participants to the GMOD project and then focus on installation, configuration and integration of popular GMOD Components. The course will be held May 6-9, at NESCent in Durham, NC. These components will be covered: * Apollo - genome annotation editor * Chado - a modular and extensible database schema * Galaxy - workflow system * GBrowse - the Generic Genome Browser * GBrowse_syn - A generic synteny browser * JBrowse - genome browser * MAKER - genome annotation pipeline * Tripal - web front end for Chado The deadline for applying is the end of Friday, February 22. Admission is competitive and is based on the strength of the application (especially the statement of interest). In 2009 there were over 50 applications for the 25 slots. Any applications received after the deadline will be placed on the waiting list. See the course page for details and an application link: http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas Thanks, Dave Clements GMOD Help Desk PS: We are also investigating holding a GMOD course in the Asia/Pacific region, sometime this fall. Watch the GMOD mailing lists and the GMOD News page/RSS feed for updates. -- Please keep responses on the list! http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas http://gmod.org/wiki/GMOD_News Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback

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Re: [galaxy-dev] [galaxy-bugs] /tmp directory
by juan perin 05 Feb '10

05 Feb '10

Thanks for the answer! I've copied this response to the dev list email instead, after realizing its probably best there. I'm also having some trouble getting our PBS system configured. I have pbs://hostname/ as my pbs parameter in the universe file, as well as everything else specified in the documentation. I'm getting no error in the interface, and the backend never actually gets the job. The error I see in the logs says: galaxy.jobs.runners.pbs ERROR 2009-10-30 13:40:27,762 Uncaught exception queueing job Traceback (most recent call last): File "/home/perin/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 144, in run_next self.queue_job( obj ) File "/home/perin/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 219, in queue_job script = pbs_symlink_template % (job_wrapper.galaxy_lib_dir, " ".join(job_wrapper.get_input_fnames() + output_fnames), self.app.config.pbs_stage_path, exec_dir, command_line) TypeError: sequence item 1: expected string, DatasetPath found I'm guessing this has something to do with my config parameters, and the queue its trying to submit to. the pbs://hostname/ value was used under the assumption that it would default to the 'default' queue on our cluster, so I'm wondering if I need to hard code those values into the connection string? I'm a little confused as to how the syntax translates to the actual required string. My guess is, for our values: pbs://variome.chop.edu/default Perhaps its related to the scrambling of the egg instead? I simply passed LIBTORQUE_DIR to the directory containing my libtorqure.so etc... ? Thanks in advance. Juan Perin On Fri, Oct 30, 2009 at 12:07 PM, Nate Coraor <nate(a)bx.psu.edu> wrote: > Juan Perin wrote: > > I'm hosting galaxy locally and am trying to figure out how to change the >> temporary upload location of files from the root / /tmp folder to something >> else. My /tmp partition is too small to handle large fastq files and this >> is causing me problems. I see where to change things in the universe file, >> but that's the final location, not the temporary space. >> > > Hi Juan, > > A quick solution is to set $TEMP in your shell environment. In the future, > we'll force uploads to honor new_file_path in universe_wsgi.ini. > > --nate >

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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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galaxy-dev January 2010