galaxy-dev July 2013

galaxy-dev@lists.galaxyproject.org

133 participants
209 discussions

remove already selected options from selection menu
by Tim-Christoph Roloff 10 Jul '13

10 Jul '13

Hi, I am working on a tool that allows to filter on a selected set of contrasts. The contrast names are read from the second column of a history item. In order to allow selection of individual filters for each contrast, I am using the <repeat> tag. Now I would like to make sure that the user selects each contrast at max one time. Can I use the <filter ...> to remove the contrasts that have already been chosen from the selection? Or is there a more elegant way? <repeat name="contrasts" title="Contrast" min="1" max="3"> <param name="contrast" type="select" label="Contrast to filter on" multiple="false"> <options from_dataset="edgercont"> <column name="name" index="1"/> <column name="value" index="1"/> </options> </param> <param name="lfc" type="float" label="Linear fold-change" value="2.0" /> <param name="pval" type="float" label="p-value cutoff" value="0.001" /> </repeat> Thanks for your help in advance Tim

2 3

no metadata for tools in toolshed
by Ido Tamir 10 Jul '13

10 Jul '13

Hi, I grabbed some xml files from Hannons website for his fastx toolkit (improved over galaxys default version). Then I created a repository, uploaded the xml files, but the toolshed complains that it could not find the tools for creating metadata in the xml files. Could somebody please tell me what the problem is with these files? They look like valid tool.xml files to me. http://toolshed.g2.bx.psu.edu/view/idot/fastx_toolkit2 http://idot@toolshed.g2.bx.psu.edu/repos/idot/fastx_toolkit2 thank you very much, ido

2 1

Configuring the time of permanently deleting data sets.
by Perez, Ricardo 10 Jul '13

10 Jul '13

Dear all, I am currently trying to find a way to decrease the time the users need to wait to permanently delete their data sets. In galaxy I read the following "Histories that have been deleted for more than a time period specified by the Galaxy administrator(s) may be permanently deleted."; I am wondering where can I configure this option in my local instance of galaxy. I have looked for such an option in the universe_wsgi.ini file but I have not found it. I would greatly appreciate if someone can point me to the right direction to modify this. Thank you all, --Ricardo Perez

3 2

Tool Error: Failure Preparing Job
by Venice Margarette Juanillas 10 Jul '13

10 Jul '13

Hi all, I'm working on a local Galaxy instance and I want to integrate TASSEL's GLM pipeline into it. But when I run the tool, it prompts: "tool error An error occurred running this job:* failure preparing job*" This is how the log looks like: galaxy.jobs.handler INFO 2013-07-08 16:00:47,648 (73) Job dispatched galaxy.jobs.runners.local DEBUG 2013-07-08 16:00:47,735 Local runner: starting job 73 galaxy.jobs.runners.local ERROR 2013-07-08 16:00:47,939 failure running job 73 Traceback (most recent call last): File "/storage/irri-gsl-galaxy/lib/galaxy/jobs/runners/local.py", line 72, in run_job job_wrapper.prepare() File "/storage/irri-gsl-galaxy/lib/galaxy/jobs/__init__.py", line 184, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/storage/irri-gsl-galaxy/lib/galaxy/tools/__init__.py", line 2435, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/storage/irri-gsl-galaxy/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) UnicodeEncodeError: 'ascii' codec can't encode character u'\u2013' in position 23: ordinal not in range(128) galaxy.datatypes.metadata DEBUG 2013-07-08 16:00:48,206 Cleaning up external metadata files 127.0.0.1 - - [08/Jul/2013:16:00:50 +0800] "GET /api/histories/846c4efa2e1f970a HTTP/1.1" 200 - " http://localhost:8081/history?status=done&show_deleted=False&filename=None&…" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" I figured the problem is that UnicodeEncodeError but I don't have an idea how to fix this or where to begin. I do hope you can help me. Thanks and Best Regards, Venice Margarette B. Juanillas

2 1

allow users for specifying the number of CPUs
by Keilwagen, Jens 10 Jul '13

10 Jul '13

Hi guys, we are currently trying to integrate CLC Bios short read assembler into our local Galaxy version. So far everything went smoothly. However, the command line tool allows for specifying the number of CPU that should be used for computation. We are wondering, whether it is also possible to enable Galaxy users also to specify the number of CPUs. Thanks for any help. Best regards, Jens

3 2

nglims, remove Cycles or autofill
by Lee Katz 09 Jul '13

09 Jul '13

Hi, I would like to autofill "cycles" for next-gen sequencing. Most of our submitters probably don't even know what that means actually and so we want to simplify it. Same goes with paired end reads. How would I fill out the nglims yaml file so that they could skip over that section? Or maybe just hit "next" an extra time? Anything to simplify it. Thank you (and especially Brad)! -- Lee Katz, Ph.D.

2 1

nglims error: "sequencing results" menu
by Lee Katz 09 Jul '13

09 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' ------------------------------------------------------------

2 2

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.

2 1

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

2 1

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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galaxy-dev July 2013