October 2014 - galaxy-dev - lists.galaxyproject.org

Simple standard for API use of a global user/key that all loaded tools can draw upon?
by Dooley, Damion 02 Oct '14

02 Oct '14

Do any of you see the need to establish a way for tools to use a global (current site) API url/key combination? From a security perspective I'm assuming this is basically ok since tools run under the galaxy user anyways (and can directly read and write files to their heart's content). I understand that a particular user's API key could help limit what they have access to. My tool however wants to do some prepatory form display and post-job work on behalf of the Galaxy system in addition to working with user-centric data; I presume others have similar use-case needs. I think it would amount to having a standard GALAXY_TOOL_API_URL and GALAXY_TOOL_API_KEY managed in universe_wsgi.ini (left blank if not desired by sys admin). The key would be generated by a galaxy admin using a real admin user id. These would be available as python or shell environment variables when it came time to execute a tool's <command interpreter="python"> etc. work. The wee other detail is that I'm using <code file="versioned_data_form.py" /> in my tool xml because there is API information I have to retrieve to set up the form with. So the url and key need to be accessible in that execution environment too?!! Am I missing the boat; alternately has this already been talked about?! Thanks for advice ... Damion Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada

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Re: [galaxy-dev] Internal Server error when attemptng to use Admin Tab
by John Chilton 02 Oct '14

02 Oct '14

Thanks for the additional details - I am responding on list for people who may encounter similar problems in the future. The job running code will provide both core tools and tool shed tools with the same PYTHONPATH - but some tools might setup a Python virtualenv for instance which would replace the PYTHONPATH completely I believe. Since gsummary is not in the tool shed - it will not be able to find any of the tool shed dependencies. These rpy issues are tough ones. It should be possible to hack something together if you change the requirements in gsummary to be package requirements for R and Rpy and then find working env.sh files in tool_dependency_dir and copy them to tool_dependency_dir/R/2.11/env.sh and tool_dependency_dir/Rpy/1.0.3/env.sh respectively. The tool shed is suppose to solve all of these pesky dependency problems - but not all the tools have been migrated and fixed yet. Thanks for your patience and for using Galaxy! -John On Wed, Oct 1, 2014 at 1:36 PM, David Bernick <dbernick(a)soe.ucsc.edu> wrote: > Hi John - > > Yes, we are using MySQL. This event happened as a result of attempting to add/delete tools from our instance (Rpy_1_0_3 and R_2_11). > We ended up reloading the database from our nightly backup, and that got us going again. > > The issue I was trying to solve when I "broke" the database was Summary_statistics not being able to find its Rpy module. I now have R and Rpy installed, such that tool-shed tools are happy with it, but gsummary.py is still unable to find Rpy. We are attempting to solve this, but are as yet without a fix. In the meantime, I have installed datamash, and that is working, It seems that tool-shed tools have a different PYTHONPATH than galaxy-dist tools? > > As it happens, we also had a few cases with multiple instances of tool-shed tools being installed. Since this server is brand new, it was fine to delete them. I suppose that maybe we are now fitting in MySQL BLOBs now?? > > thanks again - > David > > > > On Oct 1, 2014, at 9:44 AM, John Chilton <jmchilton(a)gmail.com> wrote: > >> Hello David, >> >> We don't have a workaround yet - but we (Dan did most of the >> investigating) understand the problem I think. You are using a MySQL >> database I assume? (Ignore the rest of this e-mail if not). I think >> MySQL has lower limits on the size of BLOBs that can be stored in the >> database than postgres - and we think the tool shed is tried to >> storing a really large blob of metadata in the database and it got >> truncated and now Galaxy is failing because it cannot load that entry >> as JSON. >> >> The work around would be something like trying to find the truncated >> column in the tool_repositories table - deleting it and references - >> changing that column to a LONGBLOB and reinstalling that tool. >> >> I have created a Trello card for this bug report. >> >> https://trello.com/c/RbW6pOd2 >> >> It is said a lot but we strongly encourage not using MySQL. >> >> It might be worth trying this patch >> (https://bitbucket.org/galaxy/galaxy-central/pull-request/511/allow-model-ob…) >> from Dan as well. I am not sure what the tool shed would do if it >> cannot find the metadata though. >> >> -John >> >> On Mon, Sep 29, 2014 at 11:41 AM, David Bernick <dbernick(a)soe.ucsc.edu> wrote: >>> Good morning - >>> >>> I have acquired an Internal server error on our local galaxy install. It >>> seems to be an unterminated string. How do I resolve this? >>> thanks in advance - >>> David Bernick >>> UCSC >>> >>> Here is the relevant portion of the log (I hope). >>> >>> Error - <type 'exceptions.ValueError'>: Unterminated string starting at: >>> line 1 column 65528 (char 65528) >>> URL: http://campusrocks.cse.ucsc.edu:8080/admin/index >>> File >>> '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', >>> line 149 in __call__ >>> app_iter = self.application(environ, sr_checker) >>> File >>> '/projects/galaxy/bin/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', >>> line 84 in __call__ >>> return self.application(environ, start_response) >>> File >>> '/projects/galaxy/bin/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', >>> line 633 in __call__ >>> return self.application(environ, start_response) >>> File '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/framework/base.py', >>> line 132 in __call__ >>> return self.handle_request( environ, start_response ) >>> File '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/framework/base.py', >>> line 190 in handle_request >>> body = method( trans, **kwargs ) >>> File >>> '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/framework/__init__.py', >>> line 383 in decorator >>> return func( self, trans, *args, **kwargs ) >>> File >>> '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/base/controllers/admin.py', >>> line 34 in index >>> installing_repository_ids = >>> suc.get_ids_of_tool_shed_repositories_being_installed( trans.app, >>> as_string=True ) >>> File >>> '/projects/galaxy/bin/galaxy-dist/lib/tool_shed/util/shed_util_common.py', >>> line 277 in get_ids_of_tool_shed_repositories_being_installed >>> app.install_model.ToolShedRepository.status == loading_datatypes_status ) >>> ): >>> File >>> '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py', >>> line 2348 in instances >>> File >>> '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', >>> line 2120 in _instance >>> File >>> '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', >>> line 1974 in populate_state >>> File >>> '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py', >>> line 150 in fetch_col >>> File >>> '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/types.py', >>> line 658 in process >>> File '/projects/galaxy/bin/galaxy-dist/lib/galaxy/model/custom_types.py', >>> line 52 in process_result_value >>> return json_decoder.decode( str( _sniffnfix_pg9_hex(value) ) ) >>> File '/usr/lib64/python2.6/json/decoder.py', line 319 in decode >>> obj, end = self.raw_decode(s, idx=_w(s, 0).end()) >>> File '/usr/lib64/python2.6/json/decoder.py', line 336 in raw_decode >>> obj, end = self._scanner.iterscan(s, **kw).next() >>> File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan >>> rval, next_pos = action(m, context) >>> File '/usr/lib64/python2.6/json/decoder.py', line 183 in JSONObject >>> value, end = iterscan(s, idx=end, context=context).next() >>> File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan >>> rval, next_pos = action(m, context) >>> File '/usr/lib64/python2.6/json/decoder.py', line 217 in JSONArray >>> value, end = iterscan(s, idx=end, context=context).next() >>> File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan >>> rval, next_pos = action(m, context) >>> File '/usr/lib64/python2.6/json/decoder.py', line 183 in JSONObject >>> value, end = iterscan(s, idx=end, context=context).next() >>> File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan >>> rval, next_pos = action(m, context) >>> File '/usr/lib64/python2.6/json/decoder.py', line 217 in JSONArray >>> value, end = iterscan(s, idx=end, context=context).next() >>> File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan >>> rval, next_pos = action(m, context) >>> File '/usr/lib64/python2.6/json/decoder.py', line 183 in JSONObject >>> value, end = iterscan(s, idx=end, context=context).next() >>> File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan >>> rval, next_pos = action(m, context) >>> File '/usr/lib64/python2.6/json/decoder.py', line 217 in JSONArray >>> value, end = iterscan(s, idx=end, context=context).next() >>> File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan >>> rval, next_pos = action(m, context) >>> File '/usr/lib64/python2.6/json/decoder.py', line 217 in JSONArray >>> value, end = iterscan(s, idx=end, context=context).next() >>> File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan >>> rval, next_pos = action(m, context) >>> File '/usr/lib64/python2.6/json/decoder.py', line 155 in JSONString >>> return scanstring(match.string, match.end(), encoding, strict) >>> ValueError: Unterminated string starting at: line 1 column 65528 (char >>> 65528) >>> >>> >>> ___________________________________________________________ >>> 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/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >

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'KeyError' in workflow extraction when using newer tool version
by Peter Briggs 02 Oct '14

02 Oct '14

Dear all One of my users has encountered a problem with extracting a workflow from a history in our local Galaxy installation (tag latest_2014.08.11, changeset 14342:db520d154716). The history was created with a version of a local tool which has since been updated, and the extraction page warns that the newer version of the tool will be used for those datasets i.e.: Dataset was created with tool version "0.0.4", but workflow extraction will use version "0.0.7". However when the extraction is run it fails immediately: the user sees the "Internal Server Error" page, and in the log I see: ===== Error - <type 'exceptions.KeyError'>: 'platform' URL: https://galaxy.ls.manchester.ac.uk/workflow/build_from_current_history File '/home/galaxy/production/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/home/galaxy/production/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/galaxy/production/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/galaxy/production/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/home/galaxy/production/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/home/galaxy/production/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 1220 in build_from_current_history workflow_name=workflow_name File '/home/galaxy/production/galaxy-dist/lib/galaxy/workflow/extract.py', line 30 in extract_workflow steps = extract_steps( trans, history=history, job_ids=job_ids, dataset_ids=dataset_ids, dataset_collection_ids=dataset_collection_ids ) File '/home/galaxy/production/galaxy-dist/lib/galaxy/workflow/extract.py', line 104 in extract_steps tool_inputs, associations = step_inputs( trans, job ) File '/home/galaxy/production/galaxy-dist/lib/galaxy/workflow/extract.py', line 271 in step_inputs associations = __cleanup_param_values( tool.inputs, param_values ) File '/home/galaxy/production/galaxy-dist/lib/galaxy/workflow/extract.py', line 330 in __cleanup_param_values cleanup( "", inputs, values ) File '/home/galaxy/production/galaxy-dist/lib/galaxy/workflow/extract.py', line 327 in cleanup group_values = values[input.name] KeyError: 'platform' ===== 'platform' is a conditional parameter that was introduced into the tool between the two versions. It looks like when tying to use the newer verison of the new tool, that the new parameter is not getting picked up. Is this expected behaviour? (Btw I've seen a similar issue i.e. the "KeyError: 'platform' exception when I have the two versions of this tool installed from a local toolshed, and try switching between to the newer one from the older one.) Any help or suggestions are greatly appreciated. Many thanks Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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please subscribe
by Ioana Cristina Chintauan-Marquier 02 Oct '14

02 Oct '14

thank you! -- Dr. Ioana C. Chintauan-Marquier Muséum National d'Histoire Naturelle Institut de SYstématique Evolution Biodiversité (ISYEB) UMR MNHN/CNRS/UPMC/EPHE 7205 57 Rue Cuvier, CP50 (Entomologie, équipe Phylevo) F-75231 PARIS cedex 05 France Tel: +33 (0)1 40 79 34 15/+33 (0)6 02 27 32 41 Email: imarquier(a)mnhn.fr, icchintauan.marquier(a)gmail.com <icchintauan.marquier(a)gmail.com>

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Vagrant-Galaxy for development purposes
by Kandalaft, Iyad 01 Oct '14

01 Oct '14

Hi Everyone I wanted to share some code with the galaxy community and I am looking for opinions on the following approach. Overview: We want to create a standardized galaxy tool development environment to address specific problems we faced in the past while minimizing training and hand-holding efforts associated with galaxy development. Problems encountered: Getting start with Galaxy tool development is complicated as it requires an understanding of the whole system (not just Galaxy and the tool shed). Devs accidentally use the latest galaxy release to develop their tools instead of the in-house production server release. Dev's environment is tainted with system-wide installed software -> tool-dependencies can't be verified because the system installed binaries are on the path regardless. Dev's environment is substantially different from production server environment -> tool dependencies work in dev but not in prod. Several other issues that I can't quite remember Solution and outcomes: Use provisioning software such as vagrant to standardize the dev environment. · Reduce time and training required on getting galaxy/toolshed installed and started · Provides ability to easily blow away the dev environment and re-instantiate it · Provides a clean dev environment every time that isn't tainted with system-wide installations of software · Provides a more similar environment to the production server (assuming it runs the same OS) I hope that this is useful for other galaxy tool devs. I am open to collaboration to improve this initiative and I am looking for insight on some problems we are facing. The repo is on github: https://github.com/AAFC-MBB/vagrant-galaxy Forked from the Smithsonian/vagrant-galaxy repo Regards, Iyad Kandalaft Bioinformatics Application Developer, Science and Technology Branch Agriculture and Agri-Food Canada / Government of Canada Iyad.Kandalaft(a)Agr.gc.ca / Tel: 613-759-1228 / TTY: 613-773-2600 Développeur de logiciels bioinformatique, Direction Général de Science et Technology Agriculture et Agroalimentaire Canada / Gouvernement du Canada Iyad.Kandalaft(a)Agr.gc.ca / Tél. : 613-759-1228 / ATS: 613-773-2600

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Login with a system user
by Daniel Ruiz Molina 01 Oct '14

01 Oct '14

Hello, I have configured Galaxy, but I would be very interested in configure it with PAM or /etc/passwd (/etc/shadow) instead of creating a user in the web interface. How can I configure Galaxy for authenticating with system files? Thanks.

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Internal Server error when attemptng to use Admin Tab
by David Bernick 01 Oct '14

01 Oct '14

Good morning - I have acquired an Internal server error on our local galaxy install. It seems to be an unterminated string. How do I resolve this? thanks in advance - David Bernick UCSC Here is the relevant portion of the log (I hope). Error - <type 'exceptions.ValueError'>: Unterminated string starting at: line 1 column 65528 (char 65528) URL: http://campusrocks.cse.ucsc.edu:8080/admin/index File '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/projects/galaxy/bin/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/projects/galaxy/bin/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 383 in decorator return func( self, trans, *args, **kwargs ) File '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/base/controllers/admin.py', line 34 in index installing_repository_ids = suc.get_ids_of_tool_shed_repositories_being_installed( trans.app, as_string=True ) File '/projects/galaxy/bin/galaxy-dist/lib/tool_shed/util/shed_util_common.py', line 277 in get_ids_of_tool_shed_repositories_being_installed app.install_model.ToolShedRepository.status == loading_datatypes_status ) ): File '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py', line 2348 in instances File '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 2120 in _instance File '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 1974 in populate_state File '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py', line 150 in fetch_col File '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/types.py', line 658 in process File '/projects/galaxy/bin/galaxy-dist/lib/galaxy/model/custom_types.py', line 52 in process_result_value return json_decoder.decode( str( _sniffnfix_pg9_hex(value) ) ) File '/usr/lib64/python2.6/json/decoder.py', line 319 in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File '/usr/lib64/python2.6/json/decoder.py', line 336 in raw_decode obj, end = self._scanner.iterscan(s, **kw).next() File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan rval, next_pos = action(m, context) File '/usr/lib64/python2.6/json/decoder.py', line 183 in JSONObject value, end = iterscan(s, idx=end, context=context).next() File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan rval, next_pos = action(m, context) File '/usr/lib64/python2.6/json/decoder.py', line 217 in JSONArray value, end = iterscan(s, idx=end, context=context).next() File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan rval, next_pos = action(m, context) File '/usr/lib64/python2.6/json/decoder.py', line 183 in JSONObject value, end = iterscan(s, idx=end, context=context).next() File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan rval, next_pos = action(m, context) File '/usr/lib64/python2.6/json/decoder.py', line 217 in JSONArray value, end = iterscan(s, idx=end, context=context).next() File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan rval, next_pos = action(m, context) File '/usr/lib64/python2.6/json/decoder.py', line 183 in JSONObject value, end = iterscan(s, idx=end, context=context).next() File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan rval, next_pos = action(m, context) File '/usr/lib64/python2.6/json/decoder.py', line 217 in JSONArray value, end = iterscan(s, idx=end, context=context).next() File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan rval, next_pos = action(m, context) File '/usr/lib64/python2.6/json/decoder.py', line 217 in JSONArray value, end = iterscan(s, idx=end, context=context).next() File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan rval, next_pos = action(m, context) File '/usr/lib64/python2.6/json/decoder.py', line 155 in JSONString return scanstring(match.string, match.end(), encoding, strict) ValueError: Unterminated string starting at: line 1 column 65528 (char 65528)

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bowtie_indices.loc for 'bowtie_wrappers' tool
by Peter Briggs 01 Oct '14

01 Oct '14

Dear all Am I right in thinking that, although the current 'bowtie_wrappers' package from the toolshed creates the file .../galaxy-dist/tool-data/bowtie_indices.loc no data is ever actually loaded from this file (and so any entries added to it are ignored)? Empirically, it appears only entries in the .loc file under .../galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/9ca609a2a421/ are actually used to populate the relevant menu in the "bowtie for illumina" tool. Is there a reason why the redundant file is still created? Thanks, best wishes Peter Ps this is in galaxy-dist changeset 14355:007f6a80629a -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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October 2014 Galaxy Newsletter
by Dave Clements 01 Oct '14

01 Oct '14

Hello all, A lot is happening in in the Galaxy in October, and a lot of good stuff happened in September too. Take a look at the October 2014 Galaxy Newsletter <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10> for the complete story, but here are some highlights: - *Galaxy needs your input! <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#Galaxy_Needs_Your_Inpu…>* You may even get rewarded for your input ... - IRC channel to be logged <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#IRC_Channel_Policy_Cha…>, starting this month - Slides from ECCB'14 and upcoming events <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#Events> - 71 new papers <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#New_Papers>, including 6 featured papers - Who's Hiring? <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#Who.27s_Hiring> Lots of places, that's who - Two new public Galaxy Servers <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#New_Public_Servers> - New Deployment Catalog and Log Board entries <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#Community_Galaxy_Hubs> - 36 new ToolShed repos <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#ToolShed_Contribution> - And a smattering of other news <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#Other_News> too Happy October! Dave Clements and the Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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