September 2012 - galaxy-dev - lists.galaxyproject.org

Galaxy error
by Kenneth R. Auerbach 12 Sep '12

12 Sep '12

Hello, Can anyone tell me why I keep getting this error when I try to do a blast search in Galaxy? I checked that the nr database file was there and had the right permissions. Does this error mean that Galaxy can't find the nr file or does it mean something else? ------------ An error occurred running this job:BLAST Database error: No alias or index file found for protein database [/9720/genome_references/ncbi/nr-protein-db/nr-newstyle/nr] in search path [/9720/galaxyprod/galaxy-dist/database/job_working_directory/1485::] Return error code 2 from command: blast ------------- Thank you. Ken.

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Manage local data admin tool failed with dbkey KeyError
by Derrick Lin 11 Sep '12

11 Sep '12

Hi guys, I enabled the tool with enable_beta_job_managers = True, server runs fine. But after I clicked on Manage local data, it gave the following error: URL: http://pwbc.garvan.unsw.edu.au/galaxy_dev/data_admin/manage_data [^<http://pwbc.garvan.unsw.edu.au/galaxy_dev/data_admin/manage_data> ] File '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/lib/galaxy/web/framework/__init__.py', line 184 in decorator return func( self, trans, *args, **kwargs ) File '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/lib/galaxy/web/controllers/data_admin.py', line 47 in manage_data genomes[ dbkey ][ table ] = dict( state='Generated', style=self.jobstyles[ 'done' ] ) KeyError: 'phix' I tried to fix it by commenting out all the phix entries in all .loc files. Then it gave the same error but this time caused by "hg18". I think it must have something to do with builts.txt, manual_builts.txt and the loc files? Thanks Derrick

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select with >=20 options renders as autocompleting text box
by Dan Tenenbaum 11 Sep '12

11 Sep '12

Hi, I notice that a <param> with type "select" renders differently depending on how many <option>s there are. If there are < 20 options, it appears as a normal select box. If there are >= 20 options, it looks like a text box (but it has autocompletion and does have a dropdown menu), and Inspect Element in Chrome reveals that it in fact is an <input type="text"> with the classes "text-and-autocomplete-select ac_input". Is this deliberate? If so, can the behavior be turned off? I suppose that there is no functional impact, but it looks sort of odd and jarring to have several select boxes one of which happens to look different just because of the number of options it has. Example: <param name="distance" type="select" help="" label="Distance Method" force_select="FALSE"> <option value="None">1</option> </param> ...renders as a normal select box. <param name="distance" type="select" help="" label="Distance Method" force_select="FALSE"> <option value="None">1</option> <option value="None">2</option> <option value="None">3</option> <option value="None">4</option> <option value="None">5</option> <option value="None">6</option> <option value="None">7</option> <option value="None">8</option> <option value="None">9</option> <option value="None">10</option> <option value="None">11</option> <option value="None">12</option> <option value="None">13</option> <option value="None">14</option> <option value="None">15</option> <option value="None">16</option> <option value="None">17</option> <option value="None">18</option> <option value="None">19</option> <option value="None">20</option> </param> ...renders as a text box with autocomplete. Thanks, Dan

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Migrate Galaxy database from MySQL to Postgres
by Leon Mei 11 Sep '12

11 Sep '12

Dear list members, Did anyone migrate the Galaxy database from MySQL to Postgres lately? Any verified script available? Simple solution by adding a postgres flag in mysqldump (http://dev.list.galaxyproject.org/MySQL-2-Postgres-td4139570.html) didn't work for me. It throws lots of syntax errors on int(), double quote, etc. My mysql version: 14.14, distribution 5.5.25a My postgres version: 9.1 I am now on a quest following the suggested list at: http://wiki.postgresql.org/wiki/Converting_from_other_Databases_to_PostgreS… I appreciate if someone can share his or her experience on this. Thanks a lot, Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - http://ngs.nbic.nl Skype: leon_mei Mobile: +31 6 41709231

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FreeBayes bug - update to a toolshed tool wrapper
by Lance Parsons 11 Sep '12

11 Sep '12

I have been using the FreeBayes tool in our local Galaxy instance for some time. As FreeBayes is a rapidly evolving tool, it has been very helpful to have Daniel Blankenberg work on keeping an updated wrapper. Recently, I've run into a rather troublesome bug in FreeBayes (https://github.com/ekg/freebayes/issues/22) that is causing it to crash on nearly every real dataset. Luckily, the bug has been fixed in the latest version of FreeBayes (0.9.6_9608597d12e127c847ae03aa03440ab63992fedf). Unfortunately, the latest version has a few parameter changes that require an update to the wrapper code. I've taken the liberty to make some changes to the wrapper and they seem to work. However, now that I have the tool installed from the Tool Shed, I'm not sure of the best way to 1) incorporate this update into my local galaxy instance and 2) contribute this change back to the Tool Shed. The best solution is to get the Tool Shed updated and then pull that update into my production Galaxy instance, however, I'm wondering if there is a way I could push "hot-fixes" to my production instance without causing me headaches down the line when the Tool Shed is inevitably updated. As far as coordinating updates of Tool Shed tools, I suppose the process might be different for different tool authors. I was wondering, however, if anyone had thoughts on how this might work best. I've created a clone of the galaxy tool shed repository in Bitbucket (https://bitbucket.org/lance_parsons/freebayes/) and given Daniel and Greg access to it in hopes that would make things easier.Let me know if there is a better way to coordinate, etc. Thanks again. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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Restarting Galaxy
by Kenneth R. Auerbach 11 Sep '12

11 Sep '12

Hello, Can someone tell me if stopping and then restarting the Galaxy process would prevent currently-running jobs from completing after the restart? Will all the jobs remain in the queue after the restart? Also, what is the best way to restart the Galaxy server? Users are complaining that jobs are extremely slow to start running. Is there a way to speed things up? Any info or suggestions would be greatly appreciated. Thank you.

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Shell script to start Galaxy in multi-server environment
by Karger, Amir 11 Sep '12

11 Sep '12

We're upgrading to a late June Galaxy from a last-year Galaxy. We noticed that the docs say you no longer need 2 different .ini files. Great! Unfortunately, the multiprocess.sh in contrib/ still assumes you have multiple .ini files. So the question is, assuming we correctly set up the different web servers, job managers, and job handlers servers in universe_wsgi.ini, what's the command line we should be giving to run Galaxy on each type of server? The wiki Admin/Config pages for Performance and Scaling and Cluster and that sort of thing had some info on editing the .ini, but I didn't see what my .sh should look like there. Pointers to websites, emails, or existing .sh files appreciated. Thanks, -Amir Karger Senior Research Computing Consultant Harvard Medical School Research Computing amir_karger(a)hms.harvard.edu

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hg19 reference genome
by Sandrine Imbeaud 11 Sep '12

11 Sep '12

Hi, We have installed our own Galaxy server and started NGS analysis but during the mapping procedure using either BWA for illumina or BFAST, no reference genome index is available. We have uploaded the hg19.fa file and put it in the Galaxy-dist/database folder. We modified the BWA_index.loc file (the same for BFAST file) indicating the path to the file. We restart the Galaxy. However, still no reference is available through the NGS: mapping modules?. Is there any way to solve this probably simple problem. Kind regards / Sandrine & Abdelhadi -- Sandrine Imbeaud INSERM, UMR U-674, IUH Université Paris Descartes Génomique Fonctionnelle des tumeurs solides 27 rue Juliette Dodu F75010 Paris, France TEL: +33 (0)1 53 72 51 98 FAX: +33 (0)1 53 72 51 92 MOBILE: +33 (0)6 12 69 80 29 http://www.inserm-u674.net/

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GATK v2.x
by David Hoover 11 Sep '12

11 Sep '12

Is anyone working on adapting the GATK tools for a more recent version of GATK? The distributed version is 1.4, and GATK is up to 2.1. David Hoover Helix Systems Staff

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Server Error in history framer when debug = False
by David Roquis 11 Sep '12

11 Sep '12

Dear Galaxy community, I have noticed on forums that some users are experiencing this problem too, but no clues on how to fix it. When I set debug = false in universe.wsgi.ini, I get a server error in the history frame (history works perfectly when debug = true). Trying to create a new history, or to upload a saved one, doesn't work either. I use postgresql and nginx, but I this problem also appears on a freshly cloned instance of galaxy-dist. I tried on two machines with Fedora 13 + python 2.6.4 and Fedora 17 + python 2.7.3. As my goal is to use Galaxy in a production environment (with 2 webservers, 1 manager and 2 handlers), I would really like to be able to turn off debug. Here is what I can find in my paster.log when I turn off debug. Thanks a lot if anyone has a solution! David Starting server in PID 4664. serving on 0.0.0.0:8081 view at http://127.0.0.1:8081 127.0.0.1 - - [03/Aug/2012:16:26:49 +0200] "GET / HTTP/1.0" 200 - "-" "Mozilla/5.0 (X11; Linux x86_64; rv:14.0) Gecko/20100101 Firefox/14.0.1" 127.0.0.1 - - [03/Aug/2012:16:26:49 +0200] "GET /root/tool_menu HTTP/1.0" 200 - "http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Linux x86_64; rv:14.0) Gecko/20100101 Firefox/14.0.1" 127.0.0.1 - - [03/Aug/2012:16:26:49 +0200] "GET /history HTTP/1.0" 200 - "http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Linux x86_64; rv:14.0) Gecko/20100101 Firefox/14.0.1" 127.0.0.1 - - [03/Aug/2012:16:26:49 +0200] "GET /history HTTP/1.0" 500 - "http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Linux x86_64; rv:14.0) Gecko/20100101 Firefox/14.0.1" Error - <type 'exceptions.TypeError'>: 'NoneType' object is not callable URL: http://127.0.0.1/history File '/usr/lib/python2.7/site-packages/paste/exceptions/errormiddleware.py', line 144 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/lib/python2.7/site-packages/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/lib/python2.7/site-packages/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/galaxy2ei/galaxy-dist/lib/galaxy/web/framework/base.py', line 169 in __call__ return body( environ, start_response ) File '/home/galaxy2ei/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 772 in render template.render_context( context ) File '/home/galaxy2ei/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 319 in render_context **kwargs) File '/home/galaxy2ei/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/home/galaxy2ei/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/home/galaxy2ei/galaxy-dist/database/compiled_templates/root/history.mako.py', line 62 in render_body __M_writer(u'\n\n') File '/home/galaxy2ei/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 769 in write response_write( d.encode( 'utf-8' ) ) TypeError: 'NoneType' object is not callable 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' HTTP_ACCEPT_LANGUAGE: 'en-us,en;q=0.5' HTTP_CONNECTION: 'close' HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a1a924b5a883eb84f93f9e2c6424cabed485f00c49dc51dd6632e1e679e865175' HTTP_HOST: '127.0.0.1' HTTP_REFERER: 'http://127.0.0.1:8080/' HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64; rv:14.0) Gecko/20100101 Firefox/14.0.1' HTTP_X_FORWARDED_FOR: '127.0.0.1' HTTP_X_FORWARDED_HOST: '127.0.0.1' ORGINAL_HTTP_HOST: 'galaxy_app' ORGINAL_REMOTE_ADDR: '127.0.0.1' PATH_INFO: '/history' REMOTE_ADDR: '127.0.0.1' REQUEST_METHOD: 'GET' SERVER_NAME: '0.0.0.0' SERVER_PORT: '8081' SERVER_PROTOCOL: 'HTTP/1.0' Configuration ------------- __file__: '/home/galaxy2ei/galaxy-dist/universe_wsgi.ini' admin_users: 'david.roquis(a)yahoo.com, galaxytest(a)2ei.com' allow_library_path_paste: 'True' allow_user_dataset_purge: 'True' allow_user_deletion: 'True' allow_user_impersonation: 'True' database_connection: 'postgres://galaxy2ei:galaxy2ei@localhost:5432/galaxyprod' database_engine_option_server_side_cursors: 'True' database_engine_option_strategy: 'threadlocal' datatypes_config_file: 'datatypes_conf.xml' debug: 'False' default_job_handlers: 'handler0' enable_quotas: 'True' file_path: 'database/files' here: '/home/galaxy2ei/galaxy-dist' job_handlers: 'handler0' job_manager: 'manager' job_working_directory: 'database/job_working_directory' library_import_dir: '/home/galaxy2ei/Downloads' new_file_path: 'database/tmp' nginx_upload_path: '/_upload' nginx_upload_store: 'database/tmp/upload_store' nginx_x_accel_redirect_base: '/_x_accel_redirect' nglims_config_file: 'tool-data/nglims.yaml' set_metadata_externally: 'True' static_cache_time: '360' static_dir: '/home/galaxy2ei/galaxy-dist/static/' static_enabled: 'True' static_favicon_dir: '/home/galaxy2ei/galaxy-dist/static/favicon.ico' static_images_dir: '/home/galaxy2ei/galaxy-dist/static/images' static_robots_txt: '/home/galaxy2ei/galaxy-dist/static/robots.txt' static_scripts_dir: '/home/galaxy2ei/galaxy-dist/static/scripts/' static_style_dir: '/home/galaxy2ei/galaxy-dist/static/june_2007_style/blue' tool_config_file: 'tool_conf.xml,shed_tool_conf.xml' tool_data_path: 'tool-data' tool_path: 'tools' upstream_gzip: 'True' use_interactive: 'False' use_nglims: 'False' user_library_import_dir: '/home/galaxy2ei/Downloads' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x8077450> paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603a1a924b5a883eb84f93f9e2c6424cabed485f00c49dc51dd6632e1e679e865175'>, 'galaxysession=c6ca0ddb55be603a1a924b5a883eb84f93f9e2c6424cabed485f00c49dc51dd6632e1e679e865175') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x8077350> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x7f34ec7f5950> 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' ------------------------------------------------------------

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