- galaxy-dev - lists.galaxyproject.org

nglims error: "sequencing results" menu
by Lee Katz 10 Jul '13

10 Jul '13

Hi, I get an internal server error when clicking "sequencing results" under the lab menu. I'm hoping for an easy fix :) This is in my server log file (and I'm removing some data and IP addresses found in the log): 10.xx.xx.xx - - [09/Jul/2013:15:45:21 -0400] "GET /chapman/nglims/list_sqn_results HTTP/1.1" 500 - " http://mydomain/chapman/nglims" "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/27.0.1453.116 Safari/537.36" Error - <class 'sqlalchemy.exc.ArgumentError'>: SQL expression object or string expected. URL: http://mydomain/chapman/nglims/list_sqn_results File '/home/galaxy/bin/chapman-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/home/galaxy/bin/chapman-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/galaxy/bin/chapman-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/galaxy/bin/chapman-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/home/galaxy/bin/chapman-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/home/galaxy/bin/chapman-dist/lib/galaxy/web/framework/__init__.py', line 98 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxy/bin/chapman-dist/lib/galaxy/webapps/galaxy/controllers/nglims.py', line 312 in list_sqn_results return grid(trans, **kwd) File '/home/galaxy/bin/chapman-dist/lib/galaxy/web/framework/helpers/grids.py', line 78 in __call__ query = self.apply_query_filter( trans, query, **kwargs ) File '/home/galaxy/bin/chapman-dist/lib/galaxy/webapps/galaxy/controllers/nglims.py', line 2577 in apply_query_filter ["sqn_run_results.request_id DESC", "lane ASC", "sample_id DESC"]) File '<string>', line 1 in <lambda> File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 50 in generate File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 1239 in order_by File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 204 in _adapt_col_list File 'build/bdist.linux-x86_64/egg/sqlalchemy/sql/expression.py', line 1409 in _literal_as_text ArgumentError: SQL expression object or string expected. CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_ENCODING: 'gzip,deflate,sdch' HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.8' HTTP_CONNECTION: 'Keep-Alive' HTTP_COOKIE: xxxxxxxxxxxxxxxxxxxxx WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x9e68750> is_api_request: False paste.cookies: (<SimpleCookie: __utma='56454061.1423238699.1342718372.1353518961.1353970254.7' __utmz='56454061.1353970254.7.5.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=(not%20provided)' fsr.s.session.11.2.0='{' galaxysession='c6ca0ddb55be603a9c0efb539e40d0336dececb67b847917dbf9a94fc6cf855c6779ace204504c35' s_cc='true' s_ppv='100' s_ria='%7CSilverlight%205.1' s_sq='%5B%5BB%5D%5D' s_vi=''>, 'galaxysession=c6ca0ddb55be603a9c0efb539e40d0336dececb67b847917dbf9a94fc6cf855c6779ace204504c35; __utma=56454061.1423238699.1342718372.1353518961.1353970254.7; __utmz=56454061.1353970254.7.5.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=(not%20provided); fsr.s.session.11.2.0={"v":1,"rid":"d445cf6-83333627-36f4-dc7a-687e3","ru":" https://www.google.com/","r":"www.google.com ","st":"","cp":{"GovDelivery":"N"},"to":3,"c":" http://www.cdc.gov/nchs/health_policy/ADL_tables.htm","pv":1,"lc":{"d0":{"v":1,"s":false}},"cd":0,"f":1373396348260}; s_cc=true; s_ria=%7CSilverlight%205.1; s_sq=%...[CE]; s_ppv=100') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x9e68710> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x27d5e10> paste.recursive.forward: <paste.recursive.Forwarder from /chapman> paste.recursive.include: <paste.recursive.Includer from /chapman> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /chapman> paste.recursive.script_name: '/chapman' paste.throw_errors: True request_id: '1720335ce8d011e296e1b8ac6f45c6b6' webob._parsed_query_vars: (MultiDict([]), '') wsgi process: 'Multithreaded' ------------------------------------------------------------

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Browse Galaxy main tool shed - Connection Reset error
by Ben Warren 09 Jul '13

09 Jul '13

I am running a local instance of galaxy, which has been functioning fine until 2 weeks ago. However, now when I go to the Admin section, then to ‘Search and browse tool sheds’ and click ‘Galaxy main tool shed’ the browser waits for a while then I get a ‘Connection was reset’ error instead of it loading the repository list. My galaxy source code is current (galaxy-central default branch) but the problem persists. There is no error in the pastor.log, just the HTTP get request. Using firebugs's Net monitor I see that the request headers are: ----- GET /admin_toolshed/browse_tool_shed?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1 Host: galaxy-dev.pfr.co.nz User-Agent: Mozilla/5.0 (Windows NT 6.1; WOW64; rv:22.0) Gecko/20100101 Firefox/22.0 Accept: text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8 Accept-Language: en-US,en;q=0.5 Accept-Encoding: gzip, deflate DNT: 1 Referer: http://galaxy-dev.pfr.co.nz/admin_toolshed/browse_tool_sheds Cookie: galaxysession=6b92569b51fb1f456359b57e01e74ed0870e5e1795387640f0c3bfaf4ef313aabbd45f06f75feeb3 Authorization: Basic aHJhYnh3OkdlaWdodDM5 Connection: keep-alive ----- And the response is ok: HTTP/1.1 302 Found Date: Tue, 09 Jul 2013 03:31:54 GMT Server: PasteWSGIServer/0.5 Python/2.6.6 Content-Type: text/html; charset=UTF-8 Location: http://toolshed.g2.bx.psu.edu/repository/browse_valid_categories?galaxy_url… Connection: close Transfer-Encoding: chunked (Response body) Reload the page to get source for: http://galaxy-dev.pfr.co.nz/admin_toolshed/browse_tool_shed?tool_shed_url=h… ----- But then the next request is aborted: GET /repository/browse_valid_categories?galaxy_url=http://galaxy-dev.pfr.co.nz HTTP/1.1 Host: toolshed.g2.bx.psu.edu User-Agent: Mozilla/5.0 (Windows NT 6.1; WOW64; rv:22.0) Gecko/20100101 Firefox/22.0 Accept: text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8 Accept-Language: en-US,en;q=0.5 Accept-Encoding: gzip, deflate DNT: 1 Referer: http://galaxy-dev.pfr.co.nz/admin_toolshed/browse_tool_sheds Cookie: galaxycommunitysession=bbd44e69cb8906b5a39a9cdac7e07561173165e04e61ec5f385274c6a929ecc3b4da275f30092ddc; toolshedgalaxyurl= Connection: keep-alive ----- Then the browser gives the 'The connection was reset' error. The Get request status is changed to 'Aborted'. There is no response Also, my Galaxy instance is behind an http proxy, but all the proxy settings are as they should be (as described in the galaxy wiki). Any ideas as to what could be causing the tool shed browser to fail to load? Kind Regards Ben Warren Research Technologist F: +64 9 925 7001 ben.warren(a)plantandfood.co.nz www.plantandfood.co.nz The New Zealand Institute for Plant & Food Research Limited Postal Address: Plant & Food Research Mt Albert Private Bag 92169, Auckland, 1142, New Zealand Physical Address: Plant & Food Research Mt Albert 120 Mt Albert Road, Sandringham, Auckland, 1025, New Zealand The contents of this e-mail are confidential and may be subject to legal privilege. If you are not the intended recipient you must not use, disseminate, distribute or reproduce all or any part of this e-mail or attachments. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. Any opinion or views expressed in this e-mail are those of the individual sender and may not represent those of The New Zealand Institute for Plant and Food Research Limited.

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Build the Galaxy under Cluster
by shenwiyn 09 Jul '13

09 Jul '13

Hi everyone, I want to install my local Galaxy under the Cluster with TORQUE.I have a question about how they work together successfully.In addition,after my local Galaxy and TORQUE install successfully,anything else should I do to the Cluster Galaxy?Thank you very much. shenwiyn

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Browse Galaxy main tool shed - Connection Reset error
by Ben Warren 09 Jul '13

09 Jul '13

Hi, I am running a local instance of galaxy, which has been functioning fine until 2 weeks ago. However, now when I go to the Admin section, then to ‘Search and browse tool sheds’ and click ‘Galaxy main tool shed’ the browser waits for a while then I get a ‘Connection was reset’ error instead of it loading the repository list. My galaxy source code is current (galaxy-central default branch) but the problem persists. There is no error in the pastor.log, just the HTTP get request. Using firebugs's Net monitor I see that the request headers are: ----- GET /admin_toolshed/browse_tool_shed?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1 Host: galaxy-dev.pfr.co.nz User-Agent: Mozilla/5.0 (Windows NT 6.1; WOW64; rv:22.0) Gecko/20100101 Firefox/22.0 Accept: text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8 Accept-Language: en-US,en;q=0.5 Accept-Encoding: gzip, deflate DNT: 1 Referer: http://galaxy-dev.pfr.co.nz/admin_toolshed/browse_tool_sheds Cookie: galaxysession=6b92569b51fb1f456359b57e01e74ed0870e5e1795387640f0c3bfaf4ef313aabbd45f06f75feeb3 Authorization: Basic aHJhYnh3OkdlaWdodDM5 Connection: keep-alive ----- And the response is ok: HTTP/1.1 302 Found Date: Tue, 09 Jul 2013 03:31:54 GMT Server: PasteWSGIServer/0.5 Python/2.6.6 Content-Type: text/html; charset=UTF-8 Location: http://toolshed.g2.bx.psu.edu/repository/browse_valid_categories?galaxy_url… Connection: close Transfer-Encoding: chunked (Response body) Reload the page to get source for: http://galaxy-dev.pfr.co.nz/admin_toolshed/browse_tool_shed?tool_shed_url=h… ----- But then the next request is aborted: GET /repository/browse_valid_categories?galaxy_url=http://galaxy-dev.pfr.co.nz HTTP/1.1 Host: toolshed.g2.bx.psu.edu User-Agent: Mozilla/5.0 (Windows NT 6.1; WOW64; rv:22.0) Gecko/20100101 Firefox/22.0 Accept: text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8 Accept-Language: en-US,en;q=0.5 Accept-Encoding: gzip, deflate DNT: 1 Referer: http://galaxy-dev.pfr.co.nz/admin_toolshed/browse_tool_sheds Cookie: galaxycommunitysession=bbd44e69cb8906b5a39a9cdac7e07561173165e04e61ec5f385274c6a929ecc3b4da275f30092ddc; toolshedgalaxyurl= Connection: keep-alive ----- Then the browser gives the 'The connection was reset' error. The Get request status is changed to 'Aborted'. There is no response Also, my Galaxy instance is behind an http proxy, but all the proxy settings are as they should be (as described in the galaxy wiki). Any ideas as to what could be causing the tool shed browser to fail to load? Kind Regards Ben Warren Research Technologist F: +64 9 925 7001 ben.warren(a)plantandfood.co.nz www.plantandfood.co.nz The New Zealand Institute for Plant & Food Research Limited Postal Address: Plant & Food Research Mt Albert Private Bag 92169, Auckland, 1142, New Zealand Physical Address: Plant & Food Research Mt Albert 120 Mt Albert Road, Sandringham, Auckland, 1025, New Zealand The contents of this e-mail are confidential and may be subject to legal privilege. If you are not the intended recipient you must not use, disseminate, distribute or reproduce all or any part of this e-mail or attachments. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. Any opinion or views expressed in this e-mail are those of the individual sender and may not represent those of The New Zealand Institute for Plant and Food Research Limited.

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ToolShed dependencies KeyError: 'invalid_repository_dependencies'
by Peter Cock 08 Jul '13

08 Jul '13

Hi Greg, Previously my workflows had hard coded dependencies on the main Tool Shed, which currently is a bit of a problem on the Test Tool Shed. Therefore I'm update my Tool Shed workflows using a repository_dependencies.xml with implicit repository and revision fields (i.e. the latest revision within the current ToolShed). It worked for one example but not the other - this turned out to be my own error, but the Tool Shed did not handle it gracefully. Perhaps this class of error could be caught instead? Thanks! ---------------------------------------------------------------- This worked, secreted_protein_workflow, Revision: 2:aecb871dfe4c http://testtoolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow Input: <?xml version="1.0"?> <repositories description="This requires my SignalP and TMHMM wrapers, and my FASTA filtering tool.">  <repository name="tmhmm_and_signalp" owner="peterjc" />  <repository name="seq_filter_by_id" owner="peterjc" /> </repositories> ---------------------------------------------------------------- This failed, rxlr_venn_workflow, Revision: 3:65d174589251 http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow On uploading the tar-ball I got this error in the browser: <quote> Internal Server Error Galaxy was unable to sucessfully complete your request URL: http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=20a9f7389ced5… Module galaxy.web.framework.middleware.error:149 in __call__ >> app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ >> environ, self.app) Module paste.wsgilib:543 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:84 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request >> body = method( trans, **kwargs ) Module galaxy.web.framework:98 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.tool_shed.controllers.upload:219 in upload >> invalid_repository_dependencies_message = repository_dependency_util.generate_message_for_invalid_repository_dependencies( metadata_dict ) Module tool_shed.util.repository_dependency_util:252 in generate_message_for_invalid_repository_dependencies >> invalid_repository_dependencies = invalid_repository_dependencies_dict[ 'invalid_repository_dependencies' ] KeyError: 'invalid_repository_dependencies' extra data full traceback text version This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. </quote> Input repository_dependencies.xml where for the tmhmm_and_signalp entry I am missing the 'n' in name: <?xml version="1.0"?> <repositories description="This requires my SignalP and TMHMM wrapers, and my FASTA filtering tool.">  <repository ame="tmhmm_and_signalp" owner="peterjc" />  <repository name="seq_filter_by_id" owner="peterjc" />  <repository name="venn_list" owner="peterjc" /> </repositories> Output repository_dependencies.xml with mangled tmhmm_and_signalp entry: <?xml version="1.0"?> <repositories description="This requires my SignalP and TMHMM wrapers, and my FASTA filtering tool.">  <repository ame="tmhmm_and_signalp" owner="peterjc" toolshed="http://testtoolshed.g2.bx.psu.edu" />  <repository changeset_revision="66d1ca92fb38" name="seq_filter_by_id" owner="peterjc" toolshed="http://testtoolshed.g2.bx.psu.edu" />  <repository changeset_revision="51fe47a5a803" name="venn_list" owner="peterjc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </repositories> I corrected the ame/name error, and re-uploaded a fresh tar-ball which worked, Revision: 4:25e0ffd4f762 Peter

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Error Uploading Directory of Files
by Nicholas Kline 08 Jul '13

08 Jul '13

Hi, Our lab recently installed a local version of Galaxy on a mid-2012 Mac Pro computer. We can access the Galaxy server and sign in as an administrator. Today we tried creating a Data Library, adding a dataset to it, and uploading a directory of files. We followed this Galaxy documentation ( http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles?act… ) to setup this feature: - Admin > Data Library > Add datasets > Upload directory of files - file format was set to auto-detect - and we chose the option to link to files instead of copying them Galaxy confirmed that the files were successfully uploaded. However, in the data library, under the Message column, is a message in red saying "Job error (click name for more info)". Clicking on one of the uploaded files displays a page with this information: Date uploaded: 2013-06-28 File size: 7.5 GB Data type: auto Build: sacCer2 Miscellaneous information: Traceback (most recent call last): File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 386, in __main__() File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 357, in __main__ output_paths = Job Standard Error Traceback (most recent call last): File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 386, in __main__() File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 357, in __main__ output_paths = parse_outputs( sys.argv[4:] ) File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 64, in parse_outputs id, files_path, path = arg.split( ':', 2 ) ValueError: need more than 1 value to unpack error Database/Build: sacCer2 Number of data lines: None Disk file: /Volumes/G-SPEED Q/data/Person 2012 project/DCP2 mef.fastq Questions: 1. Should we be concerned about this error? 2. If so, what is the right way to fix it? 3. If not, how do we remove the red error message next to each file: "Job error (click name for more info)" ? Thank you

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Galaxy on a server without internet connexion try to contact toolshed.g2.bx.psu.edu
by Ghislain Fournous 08 Jul '13

08 Jul '13

Hi, I installed Galaxy on a server located on a secure Network without internet connexion following this instructions: http://wiki.galaxyproject.org/Admin/Config/Eggs For an offline usage I changed the following parameters: Desable eggs check in run.sh FETCH_EGGS to 0 And the toolshed check option in universe_wsgi.ini enable_tool_shed_check = False On the first run Galaxy run, but when I tried to restart Galaxy try to contact toolshed.g2.bx.psu.edu : #--------------------------- The URL http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=bowtie_… raised the exception: <urlopen error [Errno -3] Temporary failure in name resolution> The URL http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=bowtie_… raised the exception: <urlopen error [Errno -3] Temporary failure in name resolution> The URL http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=lastz&o… raised the exception: <urlopen error [Errno -3] Temporary failure in name resolution> The URL http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=lastz_p… raised the exception: <urlopen error [Errno -3] Temporary failure in name resolution> Traceback (most recent call last): File "/usr/local/Galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/usr/local/Galaxy/galaxy-dist/lib/galaxy/app.py", line 55, in __init__ verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) File "/usr/local/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/migrate/check.py", line 55, in verify_tools tool_shed_accessible, missing_tool_configs_dict = common_util.check_for_missing_tools( app, tool_panel_configs, latest_tool_migration_script_number ) File "/usr/local/Galaxy/galaxy-dist/lib/tool_shed/util/common_util.py", line 67, in check_for_missing_tools return tool_shed_accessible, missing_tool_configs_dict UnboundLocalError: local variable 'missing_tool_configs_dict' referenced before assignment #--------------------------- I Fixed this problem by adding a enable_tool_shed_check check in lib/galaxy/app.py I'm new in the Galaxy World, so perhaps that is not an optimal way to fix this problem. diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -51,8 +51,9 @@ from galaxy.model.migrate.check import create_or_verify_database create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self ) # Alert the Galaxy admin to tools that have been moved from the distribution to the tool shed. - from tool_shed.galaxy_install.migrate.check import verify_tools - verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) + if self.config.get_bool( 'enable_tool_shed_check', False ): + from tool_shed.galaxy_install.migrate.check import verify_tools + verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) # Object store manager self.object_store = build_object_store_from_config(self.config) # Setup the database engine and ORM Regards, Ghislain

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How were liftover and nib files generated?
by Perez, Ricardo 08 Jul '13

08 Jul '13

Dear all, When I rsync files from let say the following command: rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/dm3 . The system will sync files that are related to genome aligments, liftover, and nibs. How did the Galaxy team generated this files? The reason I ask is because I would lather will like to generate similar files to custom genomes to be used in galaxy. Thank you for your time, --Ricardo Perez

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[GSoC2013] Week 2 Accomplishments and Week 3 Plans
by Saket Choudhary 08 Jul '13

08 Jul '13

Not much accomplished this week. I plan to write one more blogspot detailing the datamodel I learnt about galaxy. http://galaxy-gsoc2013.blogspot.com/2013/07/week-2-accomplishments-and-week… On 24 June 2013 14:11, Saket Choudhary <saketkc(a)gmail.com> wrote: > Hi Everyone, > > > Just wrote a blog post for my Week1 tasks and Week 2 to-dos: > > http://galaxy-gsoc2013.blogspot.in/2013/06/week-1-accomplishments-and-week-… > > > I am maintaining a work log in this doc : > https://docs.google.com/document/d/1VCKCpKW6C_Tt1DYWi43GAN_Jo-nebkkj8Ctq7WL… > > > If you have any suggestions for the VCF4.1 issue or otherwise. please do let > me know. > > Thanks > > Saket Choudhary > Undergraduate > Dept. of Chemical Engineering > IIT Bombay >

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Regarding galaxy wrappers: "lumi", "DESeq" "edgeR"
by Sachit Adhikari 08 Jul '13

08 Jul '13

Hi, These are the R libraries. Have anyone written a wrapper for these libraries "lumi", "DESeq" "edgeR"? Thanks, Sachit

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