galaxy-dev April 2012

galaxy-dev@lists.galaxyproject.org

101 participants
198 discussions

Output files from Galaxy
by Jennifer Jackson 19 Apr '12

19 Apr '12

I have installed local galaxy and am using it to run some programs. The output files in the history seems to be stored in the directory .../galaxy-dist/database/files/000/, there are files dataset_100.dat, dataset_120.dat etc. My question is that: If I run a program, is there a way to check which dataset is the output file for a running ? I think the number after underscore of dataset should be able to identify it ? right ? Where can I find this number ? Thanks a lot. Jianpeng

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Fw: Potential database corruption with local galaxy instance
by David O'Connor 19 Apr '12

19 Apr '12

To keep the list in the loop, I'm sending this response that I wrote to Jeremy, with some of our system's identifying information stripped out. dave -- David O'Connor http://labs.pathology.wisc.edu/oconnor ph: 608-301-5710 Forwarded message: > From: David O'Connor <david.h.oconnor(a)gmail.com> > To: Jeremy Goecks <jeremy.goecks(a)emory.edu> > Cc: Simon Lank <Simon.Lank(a)gmail.com>, galaxy-dev(a)bx.psu.edu > Date: Wednesday, April 18, 2012 10:01:28 AM > Subject: Re: [galaxy-dev] Potential database corruption with local galaxy instance > > Hi Jeremy, > > Thanks for the troubleshooting help. I've done what you've suggested and embedded the responses below: > > SELECT * FROM migrate_version; > > > > What is the version? Also, for completeness, what database are you using? > repository_id: Galaxy > repository_path: lib/galaxy/model/migrate > version: 93 > > > > Something else you can try is downgrading your database revision and then upgrading to see if you can find the problem. From a command line in your galaxy directory, do this: > > > > % sh manage_db.sh (http://manage_db.sh) downgrade 92 > > % sh manage_db.sh (http://manage_db.sh) upgrade > > > > > > > > The downgrade to 92 and upgrade created job.params. > > > > You may want to back up your database before trying anything to ensure that you can rollback if something goes wrong. > > > > J. > Unfortunately, we are still getting errors about duplicate key values. The debug output when I try to export a history to a file is shown below my signature. Is there anything that was updated recently that would change primary keys? Thanks again for your help, I'm not really sure why we are suddenly encountering these problems after running a stable local Galaxy instance for nearly two years. > > Thanks, > > dave > > > Server ErrorURL: < (http://xdhofs.primate.wisc.edu:8080/history/export_archive)snip> > Module paste.exceptions.errormiddleware:143 in __call__ > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)app_iter = self.application(environ, start_response) > Module paste.debug.prints:98 in __call__ > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)environ, self.app) > Module paste.wsgilib:539 in intercept_output > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)app_iter = application(environ, replacement_start_response) > Module paste.recursive:80 in __call__ > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)return self.application(environ, start_response) > Module paste.httpexceptions:632 in __call__ > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)return self.application(environ, start_response) > Module galaxy.web.framework.base (http://web.framework.base):160 in __call__ > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)body = method( trans, **kwargs ) > Module galaxy.web.controllers.history (http://web.controllers.history):679 in export_archive > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)history_exp_too… trans, incoming = params, set_output_hid = True ) > Module galaxy.tools:1661 in execute > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history,**kwargs ) > Module galaxy.tools.actions.history_imp_exp:121 in execute > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)trans.sa_sessio…) > Module sqlalchemy.orm.scoping:127 in do > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)return getattr(self.registry(), name)(*args, **kwargs) > Module sqlalchemy.orm.session:1356 in flush > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)self._flush(obj…) > Module sqlalchemy.orm.session:1434 in _flush > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)flush_context.e…) > Module sqlalchemy.orm.unitofwork:261 in execute > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)UOWExecutor().e…, tasks) > Module sqlalchemy.orm.unitofwork:753 in execute > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)self.execute_sa…, task) > Module sqlalchemy.orm.unitofwork:768 in execute_save_steps > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)self.save_objec…, task) > Module sqlalchemy.orm.unitofwork:759 in save_objects > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)task.mapper._sa…, trans) > Module sqlalchemy.orm.mapper:1424 in _save_obj > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)c = connection.execute(statement.values(value_params), params) > Module sqlalchemy.engine.base:824 in execute > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)return Connection.executors[c](self, object, multiparams, params) > Module sqlalchemy.engine.base:874 in _execute_clauseelement > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)return self.__execute_context(context) > Module sqlalchemy.engine.base:896 in __execute_context > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)self._cursor_ex…, context.statement, context.parameters[0], context=context) > Module sqlalchemy.engine.base:950 in _cursor_execute > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)self._handle_db…, statement, parameters, cursor, context) > Module sqlalchemy.engine.base:931 in _handle_dbapi_exception > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) > IntegrityError: (IntegrityError) duplicate key value violates unique constraint "job_export_history_archive_pkey" 'INSERT INTO job_export_history_archive (id, job_id, history_id, dataset_id, compressed, history_attrs_filename, datasets_attrs_filename, jobs_attrs_filename) VALUES (%(id)s, %(job_id)s, %(history_id)s, %(dataset_id)s, %(compressed)s, %(history_attrs_filename)s, %(datasets_attrs_filename)s, %(jobs_attrs_filename)s)' {'job_id': 142241L, 'jobs_attrs_filename': [path to galaxy]/galaxy_dist/database/tmp/tmpxvS9aW/tmpbAz3Bx', 'history_id': 2320, 'datasets_attrs_filename': '[path to galaxy]/galaxy_dist/database/tmp/tmpxvS9aW/tmpsYUMXS', 'history_attrs_filename': '[path to galaxy]/galaxy_dist/database/tmp/tmpxvS9aW/tmplIz1m6', 'dataset_id': 185986L, 'id': 2L, 'compressed': True} > extra data (http://xdhofs.primate.wisc.edu:8080/history/export_archive#extra_data) > > CGI Variables > CONTENT_LENGTH > '0' > > HTTP_ACCEPT > 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' > > HTTP_ACCEPT_CHARSET > 'ISO-8859-1,utf-8;q=0.7,*;q=0.3' > > HTTP_ACCEPT_ENCODING > 'gzip,deflate,sdch' > > HTTP_ACCEPT_LANGUAGE > 'en-US,en;q=0.8' > > HTTP_CONNECTION > 'keep-alive' > > HTTP_COOKIE > '__utma=66120872.977517160.1310045015.1325861530.1330104947.7;__utmz=66120872.1311045198.4.4.utmcsr=news.wisc.edu|utmccn=(referral)|utmcmd=referral|utmcct=/19571; __unam=a09e0f7-1312ec609b3-18b6bbaa-11; _saml_idp=aHR0cHM6Ly9sb2dpbi53aXNjLmVkdS9pZHAvc2hpYmJvbGV0aA%3D%3D+;galaxysession=c6ca0ddb55be603a4f09296d70d12dd2ed57e5d59af9de061cbc7c473ecbb378aecb2e3d2b895568' > > HTTP_HOST > ' > > < (http://xdhofs.primate.wisc.edu:8080/history/export_archive)snip> > > > > > > ' > > HTTP_REFERER > '< (http://xdhofs.primate.wisc.edu:8080/history/export_archive)snip>' > > HTTP_USER_AGENT > 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_3) AppleWebKit/535.19 (KHTML, like Gecko) Chrome/18.0.1025.162 Safari/535.19' > > PATH_INFO > '/history/export_archive' > > REMOTE_ADDR > '192.168.1.47' > > REQUEST_METHOD > 'GET' > > SERVER_NAME > '0.0.0.0' > > SERVER_PORT > '8080' > > SERVER_PROTOCOL > 'HTTP/1.1' > > > > > Configuration > __file__ > '[path to galaxy]/galaxy_dist/universe_wsgi.ini' > > admin_users > ' > > < (http://xdhofs.primate.wisc.edu:8080/history/export_archive)snip>' > > > > > > > > allow_library_path_paste > 'True' > > allow_user_creation > 'False' > > allow_user_deletion > 'True' > > database_connection > ' > > < (http://xdhofs.primate.wisc.edu:8080/history/export_archive)snip> > > > > > > ' > > database_engine_option_max_overflow > '100' > > database_engine_option_pool_size > '100' > > datatypes_config_file > 'datatypes_conf.xml' > > debug > 'True' > > enable_api > 'True' > > enable_job_recovery > 'False' > > enable_pages > 'True' > > enable_tracks > 'True' > > file_path > 'database/files' > > here > ' > > [path to galaxy] > > > > > > /galaxy_dist' > > library_import_dir > '<Msnip>' > > local_job_queue_workers > '25' > > new_file_path > 'database/tmp' > > require_login > 'True' > > smtp_server > '< (http://xdhofs.primate.wisc.edu:8080/history/export_archive)snip>' > > static_cache_time > '360' > > static_dir > '[path to galaxy]/galaxy_dist/static/' > > static_enabled > 'True' > > static_favicon_dir > '[path to galaxy]/galaxy_dist/static/favicon.ico' > > static_images_dir > ' > > [path to galaxy] > > > > > > /galaxy_dist/static/images' > > static_scripts_dir > '[path to galaxy]/galaxy_dist/static/scripts/' > > static_style_dir > ' > > [path to galaxy] > > > > > > /galaxy_dist/static/june_2007_style/blue' > > tool_config_file > 'tool_conf.xml' > > tool_data_path > 'tool-data' > > tool_path > 'tools' > > use_interactive > 'False' > > user_library_import_dir > '[path to galaxy]/galaxy_dist/database/directory_upload' > > > > > WSGI Variables > application > <paste.debug.prints.PrintDebugMiddleware object at 0x4cecfd0> > > paste.cookies > (<SimpleCookie: __unam='a09e0f7-1312ec609b3-18b6bbaa-11' __utma='66120872.977517160.1310045015.1325861530.1330104947.7' __utmz='66120872.1311045198.4.4.utmcsr=news.wisc.edu|utmccn=(referral)|utmcmd=referral|utmcct=/19571' _saml_idp='aHR0cHM6Ly9sb2dpbi53aXNjLmVkdS9pZHAvc2hpYmJvbGV0aA%3D%3D+' galaxysession='c6ca0ddb55be603a4f09296d70d12dd2ed57e5d59af9de061cbc7c473ecbb378aecb2e3d2b895568'>, '__utma=66120872.977517160.1310045015.1325861530.1330104947.7;__utmz=66120872.1311045198.4.4.utmcsr=news.wisc.edu|utmccn=(referral)|utmcmd=referral|utmcct=/19571; __unam=a09e0f7-1312ec609b3-18b6bbaa-11; _saml_idp=aHR0cHM6Ly9sb2dpbi53aXNjLmVkdS9pZHAvc2hpYmJvbGV0aA%3D%3D+;galaxysession=c6ca0ddb55be603a4f09296d70d12dd2ed57e5d59af9de061cbc7c473ecbb378aecb2e3d2b895568') > > paste.expected_exceptions > [<class 'paste.httpexceptions.HTTPException'>] > > paste.httpexceptions > <paste.httpexceptions.HTTPExceptionHandler object at 0x4cd8430> > > paste.httpserver.thread_pool > <paste.httpserver.ThreadPool object at 0x1205970> > > paste.printdebug_listeners > [<cStringIO.StringO object at 0x4bc5ac0>, <open file '<stderr>', mode 'w' at 0x350d0>] > > 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.remove_printdebug > <function remove_printdebug at 0x4b939b0> > > paste.throw_errors > True > > webob._parsed_query_vars > (MultiDict([]), '') > > wsgi process > 'Multithreaded' > > > > > > full traceback (http://xdhofs.primate.wisc.edu:8080/history/export_archive#full_traceback) > URL: < (http://xdhofs.primate.wisc.edu:8080/history/export_archive)snip> > Module paste.exceptions.errormiddleware:143 in __call__ > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)app_iter = self.application(environ, start_response) > Module paste.debug.prints:98 in __call__ > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)environ, self.app) > Module paste.wsgilib:539 in intercept_output > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)app_iter = application(environ, replacement_start_response) > Module paste.recursive:80 in __call__ > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)return self.application(environ, start_response) > Module paste.httpexceptions:632 in __call__ > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)return self.application(environ, start_response) > Module galaxy.web.framework.base (http://web.framework.base):160 in __call__ > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)body = method( trans, **kwargs ) > Module galaxy.web.controllers.history (http://web.controllers.history):679 in export_archive > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)history_exp_too… trans, incoming = params, set_output_hid = True ) > Module galaxy.tools:1661 in execute > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history,**kwargs ) > Module galaxy.tools.actions.history_imp_exp:121 in execute > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)trans.sa_sessio…) > Module sqlalchemy.orm.scoping:127 in do > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)return getattr(self.registry(), name)(*args, **kwargs) > Module sqlalchemy.orm.session:1356 in flush > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)self._flush(obj…) > Module sqlalchemy.orm.session:1434 in _flush > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)flush_context.e…) > Module sqlalchemy.orm.unitofwork:261 in execute > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)UOWExecutor().e…, tasks) > Module sqlalchemy.orm.unitofwork:753 in execute > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)self.execute_sa…, task) > Module sqlalchemy.orm.unitofwork:768 in execute_save_steps > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)self.save_objec…, task) > Module sqlalchemy.orm.unitofwork:759 in save_objects > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)task.mapper._sa…, trans) > Module sqlalchemy.orm.mapper:1424 in _save_obj > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)c = connection.execute(statement.values(value_params), params) > Module sqlalchemy.engine.base:824 in execute > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)return Connection.executors[c](self, object, multiparams, params) > Module sqlalchemy.engine.base:874 in _execute_clauseelement > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)return self.__execute_context(context) > Module sqlalchemy.engine.base:896 in __execute_context > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)self._cursor_ex…, context.statement, context.parameters[0], context=context) > Module sqlalchemy.engine.base:950 in _cursor_execute > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)self._handle_db…, statement, parameters, cursor, context) > Module sqlalchemy.engine.base:931 in _handle_dbapi_exception > >> (http://xdhofs.primate.wisc.edu:8080/history/export_archive#)raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) > IntegrityError: (IntegrityError) duplicate key value violates unique constraint "job_export_history_archive_pkey" 'INSERT INTO job_export_history_archive (id, job_id, history_id, dataset_id, compressed, history_attrs_filename, datasets_attrs_filename, jobs_attrs_filename) VALUES (%(id)s, %(job_id)s, %(history_id)s, %(dataset_id)s, %(compressed)s, %(history_attrs_filename)s, %(datasets_attrs_filename)s, %(jobs_attrs_filename)s)' {'job_id': 142241L, 'jobs_attrs_filename': '[path to galaxy]/galaxy_dist/database/tmp/tmpxvS9aW/tmpbAz3Bx', 'history_id': 2320, 'datasets_attrs_filename':[path to galaxy]/galaxy_dist/database/tmp/tmpxvS9aW/tmpsYUMXS', 'history_attrs_filename': '[path to galaxy]/galaxy_dist/database/tmp/tmpxvS9aW/tmplIz1m6', 'dataset_id': 185986L, 'id': 2L, 'compressed': True}

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Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found
by zhengqiu cai 19 Apr '12

19 Apr '12

Hi All, I was trying to setup the Galaxy tool dependencies, and I met the following problem when running sam-to-bam in samtools: Traceback (most recent call last): File "/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 336, in finish_job drm_job_state.job_wrapper.finish( stdout, stderr ) File "/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/__init__.py", line 637, in finish dataset.set_meta( overwrite = False ) File "/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/model/__init__.py", line 875, in set_meta return self.datatype.set_meta( self, **kwd ) File "/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/datatypes/binary.py", line 179, in set_meta raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found I already set the path of samtools Below I pasted how I set the path: ubuntu@master:/mnt/galaxyTools/tools/samtools$ ll total 8 drwxr-xr-x 4 ubuntu ubuntu 65 2012-04-16 19:09 ./ drwxr-xr-x 38 ubuntu ubuntu 4096 2012-04-16 18:41 ../ drwxr-xr-x 2 ubuntu ubuntu 53 2012-04-16 19:08 0.1.12/ drwxr-xr-x 2 ubuntu ubuntu 53 2012-04-13 20:23 0.1.7/ lrwxrwxrwx 1 ubuntu ubuntu 38 2012-04-16 19:09 default -> /mnt/galaxyTools/tools/samtools/0.1.12/ ubuntu@master:/mnt/galaxyTools/tools/samtools$ more default/env.sh PATH=/mnt/galaxyTools/tools/samtools/0.1.12:$PATH I used the same way to set other programs, such as bwa and bowtie, and they worked perfectly. Only samtools could not work. I even used the full path of samtools in the wrapper file sam_to_bam.py, and it was not working neither. I am wondering if any one met the same problem, or some one can give me some hints. Thank you very much. Cai

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Re: [galaxy-dev] "Fetch taxonomic representation" DOESN'T WORK
by JIE CHEN 18 Apr '12

18 Apr '12

On Tue, Apr 17, 2012 at 1:00 PM, JIE CHEN <jiechenable1987(a)gmail.com> wrote: > Thank you Nate. Your advise is very helpful to me. I installed the > binaries like you said. Right now the binaries can be run successfully in > the command line prompt. However i run into other problems : > > Failed to open input file: /usr/local/projects/galaxy-dist/tool-data/taxonomy/names.dmp > > > What i have done: > 1. downloaded the .tar.gz file from the link you told me > 2. tar zxvf name.tar.gz > 3. then i found the three executables which are: taxBuilder, taxonomy2tree > and tree2PS-fast. > 4. made symbolic link of these files to the /usr/local/bin > > what else shall i do? Thanks. > > Tyler > > On Tue, Apr 17, 2012 at 10:36 AM, Nate Coraor <nate(a)bx.psu.edu> wrote: > >> On Apr 17, 2012, at 1:32 PM, JIE CHEN wrote: >> >> > Dear all, >> > >> > I was trying to run the build-in function "Fetch taxonomic >> representation" on my local instance of Galaxy, however it doesn't work as >> I expect. >> > The error message is: >> > /bin/sh: taxBuilder: not found >> > >> > >> > Anyone has seen this problem before? Please tell me what to do to solve >> this problem? A lot of thanks >> >> Hi Tyler, >> >> Some Galaxy tools depend on external binaries not included in the Galaxy >> distribution, and this is one of those tools. The full list and where to >> get the tools from can be found here: >> >> http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies >> >> This specific tool can be found at: >> >> https://bitbucket.org/natefoo/taxonomy >> >> --nate >> >> > >> > Tyler >> > ___________________________________________________________ >> > Please keep all replies on the list by using "reply all" >> > in your mail client. To manage your subscriptions to this >> > and other Galaxy lists, please use the interface at: >> > >> > http://lists.bx.psu.edu/ >> >> >

2 2

database engine pool size
by Shantanu Pavgi 18 Apr '12

18 Apr '12

I would like to get some idea about 'database_engine_option_pool_size' and 'database_engine_option_max_overflow' settings. We seem to hit both of these limits whenever a user runs a large workflow with following error: {{{ TimeoutError: QueuePool limit of size 40 overflow 50 reached, connection timed out, timeout 30 }}} These limits are not reached for regular (non-workflow) galaxy jobs. Any help on optimum values for these settings or performance tuning for workflow runs would be appreciated. Version Info: CentOS 5.7, PostgreSQL 8.4.9, Python 2.6.6, Galaxy revision 26920e20157f. -- Thanks, Shantanu

2 1

Hidden output files
by Frank Sørensen 18 Apr '12

18 Apr '12

Hi, I seem to have some problems with the visibility of tool outputs in my workflows. When I flag any given output as visible, Galaxy sometimes decides to hide it in the resulting history anyway. I can't find any systematic behavior though. It seems to be rather arbitrary weather Galaxy decides that the file should be hidden or not. I would estimate the random hiding to occur on about 50% of my outputs. Has anyone seen this before? Regards - Frank -- Frank Sørensen, B.Sc., Programmer Molecular Diagnostic Laboratory (MDL) Molekylær Medicinsk Afdeling (MOMA) Århus Universitetshospital Skejby, Brendstrupgårdsvej, 8200 Århus N Tlf. +45 7845 5363

2 5

How to specify RUM output dir?
by Dorset, Daniel C 18 Apr '12

18 Apr '12

I'm currently writing a Galaxy wrapper for RUM (RNA-seq Unified Mapper). RUM is a tool that generates many output files. It is run from the command line using the following syntax: RUM_runner.pl <config file> <reads file(s)> <output dir> <num chunks> <name> [options] I'm good with everything except the <output dir>. I can't figure out how to pass that directory information from Galaxy to the RUM_runner.pl in such a way that Galaxy will be able to subsequently capture the data. Does anybody have any advice, or can someone point me towards an existing wrapper that does something similar? Thanks! Dan

2 1

Exporting worflow to local instal
by Muehlschlegel, Jochen D.,M.D. 18 Apr '12

18 Apr '12

Hi, I would like to download/export my workflows from the Galaxy main to a local install at my institution. When I use the URL method, I get the following error message: Data at 'http://main.g2.bx.psu.edu/u/muehlsch12/w/imported-tophat---cuffdiff-paired-… ' does not appear to be a Galaxy workflow Message: No JSON object could be decoded: line 1 column 0 (char 0) When I want to download a workflow to my local machine, I get a server error (Duplicate headers received from server). The local install does not recognize publicly published workflows, so that step won't work either. Thanks for your help, Danny The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

2 1

How do you connect existing EBS volumes to a fresh EC2 instance?
by Mohammad Heydarian 18 Apr '12

18 Apr '12

Hello, How do you connect existing EBS volumes to a fresh EC2 instance on Amazon? I have been starting the EC2 instance and choosing "test cluster" where the option to use EBS volume space is given (when the Galaxy cloud console starts up), since there is no place to insert my EBS volume address. This leads to Galaxy starting one 15 GB EBS volume (the other two, 10 Gb and 700 Gb, EBS volumes are not started) and I then manually tell my desired EBS volume to connect to the fresh EC2 instance. The EBS volume says it is attached to the EC2 instance, but the Galaxy cloud console shows no linkage to any "data" (in the service status row) and the disk status is "0 \ 0 (0%)". Help would greatly be appreciated. Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205

2 1

Re: [galaxy-dev] [galaxy-user] Toolshed initial upload errors out
by Paul-Michael Agapow 18 Apr '12

18 Apr '12

Picking up on this thread, I said: > As per the title, I'm trying to setup a toolshed for our local use. After creating a repo, I try to upload the initial file only to get: > > TypeError: array item must be char > > Which seems to happen repeatedly, i.e. it's not a passing error. And Greg said: > Regarding this issue, your initial problem was regarding uploading a file to a repository that you successfully created, but your > pater log does not include anything about uploading. Can you clarify what the problem is? I'll need as much context as you can > provide. For example, have you successfully created a new repository? If so, is the problem still that you cannot upload a file > to it? If this is the case, can you send me the file you are attempting to upload? What are the contents of your hgweb.config > file, which is located in you Galaxy install directory? So, to recap: * I'm testing out using a local toolshed * I install (via hg) a brand new Galaxy instance * I configure and fire up the toolshed * Create a repository * This works fine. I go to upload a file and I get: URL: http://158.119.147.40:9009/upload/upload?repository_id=529fd61ab1c6cc36 Module paste.exceptions.errormiddleware:144 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:160 in __call__ >> body = method( trans, **kwargs ) Module galaxy.web.framework:86 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.community.controllers.upload:126 in upload >> repo.commit( user=trans.user.username, text=commit_message ) Module mercurial.localrepo:1195 in commit >> ret = self.commitctx(cctx, True) Module mercurial.localrepo:1264 in commitctx >> p2.manifestnode(), (new, drop)) Module mercurial.manifest:147 in add >> arraytext = array.array('c', text) TypeError: array item must be char * This happens repeatedly on different files (tried with several different text files, pdfs etc., but not with any archives/zips), or with different repositories, and after restart. * hgweb.config looks fine I think, showing two (non-uploadable-to) repos [paths] repos/agapow/gfdfd = database/community_files/000/repo_1 repos/agapow/testrepo = database/community_files/000/repo_2 * The paster log (community_webapp.log, see http://pastebin.com/ysgnHwcz), shows the upload call failing with the "array item must be char" (lines 98, 124 and elsewhere) * Other toolshed browsing etc functions see to work fine * Running CentOS 4 Not sure where to look next. Any ideas? ---- Paul Agapow (paul-michael.agapow(a)hpa.org.uk) Bioinformatics, Health Protection Agency ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

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galaxy-dev April 2012