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setting SGE arguments in galaxy (cloudman)
by Jim McCusker 14 Aug '14

14 Aug '14

I have a galaxy/cloudman cluster where I would like to pass a "-l mem_free=16G" parameter when galaxy submits the job to SGE. I've tried adding it like this: default_cluster_job_runner = drmaa://-l mem_free=16G/ (it was: default_cluster_job_runner = drmaa:/// ) but now the jobs don't even submit. Am I wiping out other important parameters? How should I do this? Thanks, Jim

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Announcing the UK Galaxy Community
by graham etherington (TSL) 14 Aug '14

14 Aug '14

Dear UK Galaxy-devs, We're delighted to announce the launch of the UK Galaxy Community. Please visit the site and have a look around: http://galaxy-community.org.uk/ The aims of Galaxy-UK are: * To bring the Galaxy community in the United Kingdom closer together * Identify and address the needs of the community * Encourage interaction and collaboration. Galaxy-UK is also an information hub for events such as: * UK based Galaxy training courses * UK based talks involving Galaxy * Information on the location of UK Galaxy servers * Anything else that might be pertinent to bring the UK Galaxy users/admins together as a community We will be organising both online meetings and physical meetings, so keep an eye on the site for these events. Best wishes, The Galaxy-UK Team.

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Question about composite blast datatypes
by Eric Rasche 14 Aug '14

14 Aug '14

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Workflow Loop
by Görkem Erdoğan 14 Aug '14

14 Aug '14

Hello All, I have a little issue. I want create workflow with loop but workflow's nodes must use different settings in each loop steps.How can i do this?

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Providing BLAST db in a data library
by Ulf Schaefer 14 Aug '14

14 Aug '14

Dear all I have several smallish BLAST databases that I would like to provide in a data library. I create them in a history with the makeblastdb tool and them try to add them to the library. I see that for each blast db there is an empty file created (like /path/dataset_12345.dat) and a folder with the same name (/path/dataset_12345_files/) that contains the actual db files (blastdb.n*). In my library the blastdb shows up empty and I cannot import it back to another history. I does not seem to be aware of the _files folder, despite it being the right data type (blastdbn). Any ideas what I am doing wrong? Thanks a lot for your help Ulf ************************************************************************** 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 Public Health England, 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 by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************

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unable to stob jobs
by Michael Mason 13 Aug '14

13 Aug '14

Hello all, I am running a Galaxy instance on slurm. I am unable to stop jobs via the admin "Manage Jobs" window. Via postgres, there are no jobs in the job table. Any thoughts? I realize this may not be dev but I am at a loss of what to do. Thanks Mike ________________________________ --CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org

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Galaxy server broken with install of latest changes
by Tony Kusalik 13 Aug '14

13 Aug '14

Hi, I installed the latest set of changes to Galaxy, and now the Galaxy server will not start up. I am hoping someone can point me to the source of the problem and/or a fix. This morning my Galaxy server was running just fine. I did a hg incoming and was told that a fair number of changes were waiting to be applied, changeset 13772 through changeset 14309. Fine. I did hg pull -u and got searching for changes adding changesets adding manifests adding file changes added 538 changesets with 1738 changes to 542 files 473 files updated, 0 files merged, 152 files removed, 0 files unresolved Fine. However, now my Galaxy server will not start up and run. On sh run.sh --daemon the server dies with the following produced in paster.log where /birl2/Galaxy/galaxy-dist is the name of the installation directory. -- begin paster.log -- Traceback (most recent call last): File "./scripts/paster.py", line 33, in <module> serve.run() File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 10 49, in run invoke(command, command_name, options, args[1:]) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 10 55, in invoke exit_code = runner.run(args) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 22 0, in run result = self.command() File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 64 3, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 374, in loadobj global_conf=global_conf) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 399, in loadcontext global_conf=global_conf) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 423, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 561, in get_context section) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 620, in _context_from_explicit value = import_string(found_expr) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 125, in import_string return pkg_resources.EntryPoint.parse("x=" + s).load(False) File "/birl2/Galaxy/galaxy-dist/lib/pkg_resources.py", line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/web/__init__.py", line 4, in <modul e> from framework import expose File "/birl2/Galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py", line 48 , in <module> eggs.require( "amqp" ) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 414, in req uire raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) ) galaxy.eggs.EggNotFetchable: ['amqp'] Removing PID file paster.pid -- end paster.log -- The above is the complete content of paster.log. Anyone have any idea what the problem is? More importantly, how do I fix the problem and get Galaxy running again?

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Problems uploading files to a data library
by Juan Vladimir de la Rosa Medina 12 Aug '14

12 Aug '14

Hi everyone,I recently have installed a local instance of galaxy in my computer, everything worked fine until I changed the path for library_import_dir in the universe_wsgi.ini file, to upload files to data libraries.I followed the Galaxy documentation to setup this feature:This is the path in the universe_wsgi.ini filelibrary_import_dir = /media/New/Vladimir/My_RNA-seq/The steps I followed are: Admin > Data Library > Create new data library > Add datasets > Upload directory of files file format was set to auto-detect server Directory was /media/New/Vladimir/My_RNA-seq/ and we chose the option to link to files instead of copying themWhen I try to upload files, galaxy displays the following error:Error Traceback:⇝ AttributeError: 'NoneType' object has no attribute 'new_state'<?xml version="1.0" ?><traceback> <sysinfo> <language version="2.7.3">Python</language> </sysinfo> <stack> <frame> <module>weberror.evalexception.middleware</module> <filename>/home/labinmunologiaulpgc/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py</filename> <line>364</line> <function>respond</function> <operation>app_iter = self.application(environ, detect_start_response)</operation> <operation_context> try: __traceback_supplement__ = errormiddleware.Supplement, self, environ app_iter = self.application(environ, detect_start_response) try: return_iter = list(app_iter)</operation_context> </frame> <frame> <module>paste.recursive</module> <filename>/home/labinmunologiaulpgc/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py</filename> <line>84</line> <function>__call__</function> <operation>return self.application(environ, start_response)</operation> <operation_context> environ['paste.recursive.script_name'] = my_script_name try: return self.application(environ, start_response) except ForwardRequestException, e: middleware = CheckForRecursionMiddleware(</operation_context> </frame> <frame> <module>paste.httpexceptions</module> <filename>/home/labinmunologiaulpgc/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py</filename> <line>633</line> <function>__call__</function> <operation>return self.application(environ, start_response)</operation> <operation_context> []).append(HTTPException) try: return self.application(environ, start_response) except HTTPException, exc: return exc(environ, start_response)</operation_context> </frame> <frame> <module>galaxy.web.framework.base</module> <filename>/home/labinmunologiaulpgc/galaxy-dist/lib/galaxy/web/framework/base.py</filename> <line>132</line> <function>__call__</function> <operation>return self.handle_request( environ, start_response )</operation> <operation_context> self.trace( message="Starting request" ) try: return self.handle_request( environ, start_response ) finally: self.trace( message="Handle request finished" )</operation_context> </frame> <frame> <module>galaxy.web.framework.base</module> <filename>/home/labinmunologiaulpgc/galaxy-dist/lib/galaxy/web/framework/base.py</filename> <line>190</line> <function>handle_request</function> <operation>body = method( trans, **kwargs )</operation> <operation_context> kwargs.pop( '_', None ) try: body = method( trans, **kwargs ) except Exception, e: body = self.handle_controller_exception( e, trans, **kwargs )</operation_context> </frame> <frame> <module>galaxy.webapps.galaxy.controllers.library_common</module> <filename>/home/labinmunologiaulpgc/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/library_common.py</filename> <line>927</line> <function>upload_library_dataset</function> <operation>**kwd )</operation> <operation_context> widgets=widgets, replace_dataset=replace_dataset, **kwd ) if created_outputs_dict: if cntrller == 'api':</operation_context> </frame> <frame> <module>galaxy.webapps.galaxy.controllers.library_common</module> <filename>/home/labinmunologiaulpgc/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/library_common.py</filename> <line>1049</line> <function>upload_dataset</function> <operation>state = tool.new_state( trans )</operation> <operation_context> tool_id = 'upload1' tool = trans.app.toolbox.get_tool( tool_id ) state = tool.new_state( trans ) errors = tool.update_state( trans, tool.inputs_by_page[0], state.inputs, kwd ) tool_params = state.inputs</operation_context> </frame> </stack> <exception> <type>AttributeError</type> <value>'NoneType' object has no attribute 'new_state'</value> </exception></traceback> I have been looking for a solution to fix this problem on the web without success. thank you very much

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Installed tool invisible in Galaxy
by Peter van Heusden 12 Aug '14

12 Aug '14

Hi there I updated a tool of mine recently, committed to the local toolshed, did the update from within the Admin panel and then got this error: Error - <type 'exceptions.AttributeError'>: 'Tool' object has no attribute 'citations' A restart of Galaxy seemed to fix the problem, but since then the tool could not be found - it is not in any of the Tool categories. Deleting and re-installing the tool does not fix this problem - and on installation time I never get asked what group to add it to. It seems as if it is somehow "stuck" in an incorrect state. Any ideas where to go poking? Presumably there is somewhere in the database to go poking to "reset" things. Thanks, Peter P.S. this is with the latest Galaxy from galaxy-central.

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Determining datatype inheritance in tool XML Cheetah
by Peter Cock 12 Aug '14

12 Aug '14

Hi all, I've just uploaded a simple sequence composition tool to the Test Tool Shed: https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_composition https://github.com/peterjc/pico_galaxy/commit/45669446f5a14fd90a8a0d9d74304… This accepts multiple input in FASTA, FASTQ, or SFF format - and allows a mixture of these: <inputs> <param name="input_file" type="data" format="fasta,fastq,sff" multiple="true" label="Sequence file" help="FASTA, FASTQ, or SFF format." /> </inputs> In order to build the command line string, I am currently using this for loop: <command interpreter="python"> seq_composition.py -o "$output_file" ##For loop over inputs #for i in $input_file --$i.ext "${i}" #end for </command> This results in things like this being run: seq_composition.py -o XXX.dat --fastqsanger XXX.dat --sff XXX.dat This works, but means my Python script has to know about not just the core data types that I specified in my input parameter XML (fasta,fastq,sff) but also any subclasses (e.g. fastqsanger). It seems what I want/need would be something along these lines in pseudo-code to map any datatype which is a subclass for fastq to use a single command line option: <command interpreter="python"> seq_composition.py -o "$output_file" ##For loop over inputs #for i in $input_file #if isinstance($i.datatype, fastq): --fastq "${i}" #else --$i.ext "${i}" #end if #end for </command> This mock example borrows from the Python isinstance function, but of course some Galaxy datatypes are defined as subclasses at the XML level rather than literally at the Python class level. This should result in getting the following regardless of which flavour of FASTQ the input dataset had assigned: seq_composition.py -o XXX.dat --fastq XXX.dat --sff XXX.dat Does anyone have any Tool XML examples probing an input file's datatype in this way? Peter

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