galaxy-dev February 2014

galaxy-dev@lists.galaxyproject.org

90 participants
139 discussions

Galaxy packages for Bio-Linux - an update + Apache proxying
by Tim Booth 04 Apr '14

04 Apr '14

Hi All, As previously mentioned, I'm back working on packaging the Galaxy server as DEB packages for Bio-Linux (ie. Ubuntu 12.04 LTS) and ultimately pushing towards something that could be Debian compliant. There's a way to go in that regard, but I do now have an updated package for Bio-Linux in final testing and it also has a new trick: doing "apt-get install galaxy-server-apache-proxy" will set up just that with no further configuration needed. The galaxy server appears at http://localhost/galaxy and users log in with their regular system username and password. Uploads are enabled via regular SFTP so no special FTP server configuration is needed. It's a little hacky in parts but I'm generally pleased with the result. If anyone want to take a look I'd welcome comments. It's not in the main BL repo yet but can be found here: https://launchpad.net/~nebc/+archive/galaxy/+sourcepub/3711751/+listing-arc… Cheers, TIM -- Tim Booth <tbooth(a)ceh.ac.uk> NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705

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GCC2014 Early Registration and Abstract Submission are now OPEN!
by Dave Clements 25 Mar '14

25 Mar '14

Hello all, *We are pleased to announce that Early Registration <https://wiki.galaxyproject.org/Events/GCC2014/Register> and Talk and Poster Abstract Submission <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts> are now open for the 2014 Galaxy Community Conference (GCC2014) <https://wiki.galaxyproject.org/Events/GCC2014>.* GCC2014 <https://wiki.galaxyproject.org/Events/GCC2014> will be held at the Homewood Campus<http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewo…>of Johns Hopkins University <http://jhu.edu>, in Baltimore, Maryland<http://visitors.baltimorecity.gov/>, United States, from June 30 through July 2, 2014. GCC2014<https://wiki.galaxyproject.org/Events/GCC2014>starts with a Training Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> featuring four *five* parallel tracks, each with three, two and half hour long workshops. There are 13 different topics spanning the full Galactic spectrum of topics. Take a look!<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> *Early registration <https://wiki.galaxyproject.org/Events/GCC2014/Register>* is now open. Register early and *avoid paying 70% more for regular registration costs.* Early registration is very affordable, with combined registration (Training Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> + main meeting) starting at $140 for post-docs and students. Registration is capped this year at 250 participants, *and we expect to hit that limit*. Registering early assures you a place at the conference and also a spot in the Training Day workshops you want to attend. You can also book affordable conference housing at the same time you register. See the conference Logistics page<https://wiki.galaxyproject.org/Events/GCC2014/Logistics>for details on this and other housing options. *Abstract submission <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts>* for both oral presentations and posters is also open. Abstract submission for oral presentations closes April 4, while poster submission closes April 25. Poster authors will be notified of acceptance status within two weeks of submission, while presentation authors will be notified no later than May2. *Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about your work.* The *GigaScience <http://www.gigasciencejournal.com/>* "Galaxy: Data Intensive and Reproducible Research" series announced for the last conference has published its first papers<http://www.gigasciencejournal.com/series/Galaxy>, *and is continuing to take submissions for this year's meeting and beyond*. BGI is also continuing to cover the article processing charges until the end of the year, and for more information see their latest update<http://blogs.biomedcentral.com/gigablog/2014/02/06/rewarding-reproducibilit…>. Thanks, and hope to see you in Baltimore! The GCC2014 Organizing Committee<https://wiki.galaxyproject.org/Events/GCC2014/Organizers> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

1 1

Adding a tool with additional html/js interface to make input selection
by Saba Sehrish 20 Mar '14

20 Mar '14

Hi, We are trying to add a new tool to our local galaxy instance with the following requirements. When a user clicks on the tool in side panel from tools list, a table display should appear where the first element in each row is a clickable link. Users can click on any of the element, and then see only there selected row and another table with more options. Once user has made all the selections, then a form should appear describing that you have made the following selection, do you want to execute the tool now? And then users can submit the job. If we implement such a thing in galaxy, we need to load a page with aforementioned functionality, then map the users selection to the tool's inputs, and then run the tool. The question is, is there a way in galaxy to load an html with javascript and use it to prepare the inputs for the tool we want to run, using the xml wrapper. Thanks, Saba

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Re: [galaxy-dev] dynamic select problem
by Saba Sehrish 19 Mar '14

19 Mar '14

I see the similar problem when I try to use first param_value as a filter on the second input selection and then second on the third input selection. The code works fine and makes right selections but displays the warning message “An invalid option was selected, please verify”. My select code is similar: <param name="inputmodel" type="select" size="100" label="Input Model" area="True"> <options from_file="coyote.loc"> <column name="name" index="2"/> <column name="value" index="2"/> <filter type="unique_value" column="2"/> </options> </param> <param name="inputSize" type="select" label="Box Size" selected="false"> <options from_file="coyote.loc"> <column name="name" index="3"/> <column name="value" index="3"/> <filter type="param_value" ref="inputmodel" column="2"/> <filter type="unique_value" column="3"/> </options> </param> <param name="inputRealization" type="select" label="Realization based on different seed values" selected="false"> <options from_file="coyote.loc"> <column name="name" index="4"/> <column name="value" index="4"/> <filter type="param_value" ref="inputmodel" column="2"/> <filter type="param_value" ref="inputSize" column="3"/> <filter type="unique_value" column="4"/> </options> </param> <param name="input" type="select" size="300" label="Input Snapshot" area="True" help="Choosing Input Snapshot files" selected="false"> <options from_file="coyote.loc"> <column name="name" index="6"/> <column name="value" index="6"/> <filter type="param_value" ref="inputmodel" column="2”/> <filter type="param_value" ref="inputSize" column=“3"/> <filter type="param_value" ref="inputRealization" column="4"/> </options> </param> Did you figure out where the problem is? Thanks, Saba

2 3

BugFix for dynamic_options ParamValueFilter to run IUC SnpEff in a workflow
by Jim Johnson 18 Mar '14

18 Mar '14

The current code in: lib/galaxy/tools/parameters/dynamic_options.py only searches the top layer of the dict to find the dependency value. A fix is provide in pull request: #343: Need to traverse the other_value dict to find dependencies for ParamValueFilter in<https://bitbucket.org/galaxy/galaxy-central/pull-request/343/need-to-traver…> SnpEff tool_config <inputs> <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> ... <conditional name="snpDb"> <param name="genomeSrc" type="select" label="Genome source"> <option value="cached">Locally installed reference genome</option> <option value="history">Reference genome from your history</option> <option value="named">Named on demand</option> </param> <when value="cached"> <param name="genomeVersion" type="select" label="Genome">  <options from_data_table="snpeff_genomedb"> <filter type="unique_value" column="0" /> </options> </param> <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations"> <help>These are available for only a few genomes</help> <options from_data_table="snpeff_annotations"> <filter type="param_value" ref="genomeVersion" key="genome" column="0" /> <filter type="unique_value" column="1" /> </options> </param> When running workflow: input.vcf -> SnpEff The values in ParamValueFilter filter_options function: |>>>| ||self*.*ref_name|| |'genomeVersion' ||>>>| ||other_values|| |{u'spliceSiteSize': '1', u'filterHomHet': 'no_filter', u'outputFormat': 'vcf', u'filterOut': None, u'inputFormat': 'vcf', u'filterIn': 'no_filter', u'udLength': '5000', u'generate_stats': True, u'noLog': True, u'chr': 'None', u'intervals': None, u'snpDb': {'extra_annotations': None, 'regulation': None, 'genomeVersion': 'GRCh37.71', 'genomeSrc': 'cached', '__current_case__': 0}, u'offset': '', u'input': <galaxy.tools.parameters.basic.DummyDataset object at 0x11451b8d0>, u'transcripts': None, u'annotations': ['-canon', '-lof', '-onlyReg']} || Since |||'genomeVersion' isn't in the keys of other_values, but rather in ||||||other_values['|||||||||snpDb'] this failed the assertion: |||||||||| assert self.ref_name in other_values, "Required dependency '%s' not found in incoming values" % self.ref_name Pull request |||||343: |||||<https://bitbucket.org/galaxy/galaxy-central/pull-request/343/need-to-traver…> |||||$ hg diff lib/galaxy/tools/parameters/dynamic_options.py diff -r 95517f976cca lib/galaxy/tools/parameters/dynamic_options.py --- a/lib/galaxy/tools/parameters/dynamic_options.py Thu Feb 27 16:56:25 2014 -0500 +++ b/lib/galaxy/tools/parameters/dynamic_options.py Fri Feb 28 11:37:04 2014 -0600 @@ -177,8 +177,27 @@ return self.ref_name def filter_options( self, options, trans, other_values ): if trans is not None and trans.workflow_building_mode: return [] - assert self.ref_name in other_values, "Required dependency '%s' not found in incoming values" % self.ref_name - ref = other_values.get( self.ref_name, None ) + ## Depth first traversal to find the value for a dependency + def get_dep_value(param_name, dep_name, cur_val, layer): + dep_val = cur_val + if isinstance(layer, dict ): + if dep_name in layer: + dep_val = layer[dep_name] + if param_name in layer: + return dep_val + else: + for l in layer.itervalues(): + dep_val = get_dep_value(param_name, dep_name, dep_val, l) + if dep_val: + break + elif isinstance( layer, list): + for l in layer: + dep_val = get_dep_value(param_name, dep_name, dep_val, l) + if dep_val: + break + return None + ref = get_dep_value(self.dynamic_option.tool_param.name, self.ref_name, None, other_values) + assert not ref, "Required dependency '%s' not found in incoming values" % self.ref_name for ref_attribute in self.ref_attribute: if not hasattr( ref, ref_attribute ): return [] #ref does not have attribute, so we cannot filter, return empty list -- James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota

2 2

FTP password and web interface password
by Yec'han Laizet 17 Mar '14

17 Mar '14

Hello, I set up a FTP server with SFTP support on my galaxy instance. I have a strange behavior when trying to connect by SFTP. Some users cannot authentify (access denied) whereas other can. As all users can login to the web interface with their credentials, I wanted to check if the length of the password could be the problem with SFTP. To do so, I went to the admin interface to reset the password of a user who could connect by SFTP. Then, this user can connect to the galaxy web interface with the new password but not by SFTP ; if we use the old password, it still works for SFTP authenfication as if both passwords are independent. Could you help me to solve the problem? Yec'han ================================================ Dr. Yec'han LAIZET Ingenieur Bioinformatique Tel: +33 (0)5 57 12 27 75 _________________________________ INRA-UMR BIOGECO 1202 Equipe Genetique 69 route d'Arcachon 33612 CESTAS ================================================

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upload error
by ruiwang.sz 14 Mar '14

14 Mar '14

Hi Guys, Our galaxy instance has been in use for a couple years but since Feb 2014 it started to show us some weird behavior. Recently the upload function suddenly stopped working properly. We are getting messages like the following. I'm not sure if this only happens to us. If someone has seen this before, please give me some hints. P.S., I searched online and many says that this is because the browser does not wait till all the data from the server is received and closes the socket. However it happens both in firefox and chrome. I'm wondering if it is because galaxy has any change recently but when I do 'hg update stable' it reported that it is up to date. Thanks! Rui Error messages: Exception happened during processing of request from ('127.0.0.1'---------------------------------------- Exception happened during processing of request from (, 52259'127.0.0.1', 52260) Traceback (most recent call last): ) Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread ---------------------------------------- Exception happened during processing of request from (---------------------------------------- File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread Exception happened during processing of request from'127.0.0.1' , ('127.0.0.1'52264, 52262---------------------------------------- ) Exception happened during processing of request from ('127.0.0.1'---------------------------------------- , ) Traceback (most recent call last): Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread Exception happened during processing of request from 52261('127.0.0.1', ---------------------------------------- )Exception happened during processing of request from Traceback (most recent call last): 52263('127.0.0.1') File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread Traceback (most recent call last): , 52265) File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request self.finish_request(request, client_address) self.finish_request(request, client_address) self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request 127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:27.0) Gecko/20100101 Firefox/27.0" self.RequestHandlerClass(request, client_address, self) self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ self.RequestHandlerClass(request, client_address, self) self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ self.finish() self.RequestHandlerClass(request, client_address, self) self.finish() self.RequestHandlerClass(request, client_address, self) self.finish() File "/usr/lib/python2.7/SocketServer.py", line 693, in finish File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ File "/usr/lib/python2.7/SocketServer.py", line 693, in finish File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 693, in finish File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ self.finish() self.finish() File "/usr/lib/python2.7/SocketServer.py", line 693, in finish self.wfile.flush() self.wfile.flush() File "/usr/lib/python2.7/SocketServer.py", line 693, in finish self.wfile.flush() self.finish() File "/usr/lib/python2.7/SocketServer.py", line 693, in finish File "/usr/lib/python2.7/socket.py", line 303, in flush File "/usr/lib/python2.7/socket.py", line 303, in flush self.wfile.flush() self.finish() self.wfile.flush() File "/usr/lib/python2.7/socket.py", line 303, in flush self.wfile.flush() File "/usr/lib/python2.7/SocketServer.py", line 693, in finish File "/usr/lib/python2.7/socket.py", line 303, in flush File "/usr/lib/python2.7/socket.py", line 303, in flush File "/usr/lib/python2.7/socket.py", line 303, in flush self.wfile.flush() File "/usr/lib/python2.7/socket.py", line 303, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) self._sock.sendall(view[write_offset:write_offset+buffer_size]) self._sock.sendall(view[write_offset:write_offset+buffer_size]) self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe error: [Errno 32] Broken pipe self._sock.sendall(view[write_offset:write_offset+buffer_size]) ---------------------------------------- self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe error: [Errno 32] Broken pipe error: [Errno 32] Broken pipe ---------------------------------------- self._sock.sendall(view[write_offset:write_offset+buffer_size]) ---------------------------------------- error: [Errno 32] Broken pipe ---------------------------------------- ---------------------------------------- error: [Errno 32] Broken pipe ----------------------------------------

10 24

Pick-you-own columns in BLAST+ tabular output
by Peter Cock 14 Mar '14

14 Mar '14

Hello all, I've mentioned before that a forthcoming update to the BLAST+ Galaxy wrappers would be adding a most customisable output option with pick-your-own columns. This is available to test now from the Test Tool Shed, along with other enhancements like more masking tools and an update to BLAST+ 2.2.29: http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus (This will be released as the ncbi_blast_plus wrappers v0.1.0, and includes recent contributions from Jim Johnson and Björn Grüning - thank you both): Previously (for tabular output) we've only offered the standard 12 column output (-outfmt 6), and an extended set which has grown to currently include 25 columns. The new custom column mode offers the 12 standard columns, and the extended set (making 25 columns), plus other (to me less interesting) identifiers, some other miscellaneous columns, and the taxonomy columns (44 columns in all): [image: Inline image 1] [image: Inline image 2] As previously discussed, the list of columns has been grouped - the first two groups reflect the standard 12 columns and the columns used in Galaxy's (default) 25 column extended tabular output. The remaining columns I have split into three groups (assorted identifiers, miscellaneous, and taxonomy) which I hope is self explanatory. Note that this does *not* allow you pick the column order - they will be produced in the order shown. The underlying BLAST+ tools would support this, but the Galaxy GUI would I feel be too complicated. Some community testing/comments would be appreciated. Thanks, Peter

2 3

Re: [galaxy-dev] Local Galaxy web layout
by sam guerler 13 Mar '14

13 Mar '14

Hi Shenwiyn, Can you specify what is not working? Did you find the file? Thanks, Sam On Wed, Feb 19, 2014 at 1:42 AM, shenwiyn(a)gmail.com <shenwiyn(a)gmail.com>wrote: > Hi Sam and Hans-Rudolf， > Thank you very much for your help.It seems that the > static/scripts/galaxy.menu.js fail to work in my local Galaxy.As a > result,would you please show me some more details about this? > > Regards, Shenwiyn > > > *From:* sam guerler <aysam.guerler(a)gmail.com> > *Date:* 2014-02-18 01:20 > *To:* Hans-Rudolf Hotz <hrh(a)fmi.ch> > *CC:* shenwiyn(a)gmail.com; galaxy-dev <galaxy-dev(a)lists.bx.psu.edu> > *Subject:* Re: [galaxy-dev] Local Galaxy web layout > Hi Shenwiyn, > > This has changed recently. Please take a look at: > > static/scripts/galaxy.menu.js > > Using that file, you can add/remove/change labels and their position. It > is recommended to run pack_scripts.py after changing the source file. > > Regards, Sam > > > On Mon, Feb 17, 2014 at 11:33 AM, Hans-Rudolf Hotz <hrh(a)fmi.ch> wrote: > >> Hi Shenwiyn >> >> >> Have a look at: >> >> ~/galaxy_dist/database/compiled_templates/base_panels.mako.py >> >> >> Regards, Hans-Rudolf >> >> >> >> >> On 02/17/2014 08:04 AM, shenwiyn(a)gmail.com wrote: >> >>> Galaxy developers: >>> I want to change my local Galaxy web layout,for example,delete the top >>> button of "Visualization" and "Cloud" or change their positions.Could >>> anyone show me some details about this? >>> Thank you very much. >>> >>> ------------------------------------------------------------------------ >>> shenwiyn(a)gmail.com >>> >>> >>> ___________________________________________________________ >>> 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/ >>> >>> ___________________________________________________________ >> 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/ >> > >

3 2

Re: [galaxy-dev] Plugins
by Michael E. Cotterell 12 Mar '14

12 Mar '14

Over next couple days, I'll take a look at what's in lib/galaxy/web/base/pluginframework.py and see if there is a way to refactor it with my stuff in order to get a general plugin framework (galaxy.pluginframework) as proposed by James. Sorry for the delay. Teaching a math class this semester is really eating up my time. Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA & TA, University of Georgia Department Liaison, CS Graduate Student Association, University of Georgia mepcotterell(a)gmail.com (mailto:mepcotterell@gmail.com) mepcott(a)uga.edu (mailto:mepcott@uga.edu) mec(a)cs.uga.edu (mailto:mec@cs.uga.edu) http://michaelcotterell.com/ On Tuesday, September 3, 2013 at 12:45 PM, Carl Eberhard wrote: > It is web-specific and only handles the mako/static serving cases. I think the only areas we were generalizing at this point were the directory structures and main configuration. > > Agreed on more generalization and the hook system. Michael's stuff is a good direction to move in. > > I know John was looking to use it for dynamic job destinations and dynamic toolbox filters. I'd like to see some lab/community discussion on (even broad stroke) functional requirements and use cases. > > > On Tue, Sep 3, 2013 at 12:27 PM, James Taylor <james(a)jamestaylor.org (mailto:james@jamestaylor.org)> wrote: > > Carl, is what you have now totally web specific? It would be great to > > have a general plugin framework (galaxy.pluginframework) which the web > > stuff could perhaps extend? > > > > > > On Tue, Sep 3, 2013 at 10:56 AM, Carl Eberhard <carlfeberhard(a)gmail.com (mailto:carlfeberhard@gmail.com)> wrote: > > > Heya, Michael > > > > > > Right now our only plugin code is located in > > > lib/galaxy/web/base/pluginframework.py. It's only purpose so far is to: > > > - allow locally modified/created code to serve mako templates and static > > > pages/resources from paste. > > > - serve as a super class for the visualization framework. > > > > > > I think your git repo has some great ideas. > > > > > > Carl > > > > > > > > > On Fri, Aug 30, 2013 at 2:25 PM, Michael Cotterell <mepcotterell(a)gmail.com (mailto:mepcotterell@gmail.com)> > > > wrote: > > > > > > > > Is this plugin code hosted anywhere (like in central)? > > > > > > > > > > > > On Monday, August 26, 2013, James Taylor wrote: > > > > > > > > > > Michael, > > > > > > > > > > Carl has been working on a plugin framework for Galaxy, and John > > > > > Chilton has made some improvements. It would be great if you could > > > > > look over what each other has done and come up with some suggestions. > > > > > I personally am in favor of a very generic hook system where a hook > > > > > can be defined anywhere in the code and then the user can provide any > > > > > callable. > > > > > > > > > > I'm fond of the way sup implemented hooks, see the use of HookManager > > > > > here: https://github.com/sup-heliotrope/sup/blob/develop/lib/sup/time.rb > > > > > > > > > > Your approach is quite similar and I like it. > > > > > > > > > > This makes it easy to have a script that can list all available hooks > > > > > with their documentation. > > > > > > > > > > > > > > > -- > > > > > James Taylor, Assistant Professor, Biology/CS, Emory University > > > > > > > > > > > > > > > On Fri, Aug 23, 2013 at 10:29 AM, Michael E. Cotterell > > > > > <mepcotterell(a)gmail.com (mailto:mepcotterell@gmail.com)> wrote: > > > > > > James, > > > > > > > > > > > > Has there been any more talk about this? I'd be willing to work in my > > > > > > reference implementation into central as a pull request, but I don't want to > > > > > > do that unless there is an agreed upon roadmap or something. > > > > > > > > > > > > Thanks! > > > > > > > > > > > > Sincerely, > > > > > > Michael E. Cotterell > > > > > > > > > > > > Ph.D. Student in Computer Science, University of Georgia > > > > > > Instructor of Record, Graduate RA & TA, University of Georgia > > > > > > Department Liaison, CS Graduate Student Association, University of > > > > > > Georgia > > > > > > mepcotterell(a)gmail.com (mailto:mepcotterell@gmail.com) (mailto:mepcotterell@gmail.com) > > > > > > mepcott(a)uga.edu (mailto:mepcott@uga.edu) (mailto:mepcott@uga.edu) > > > > > > mec(a)cs.uga.edu (mailto:mec@cs.uga.edu) (mailto:mec@cs.uga.edu) > > > > > > http://michaelcotterell.com/ > > > > > > > > > > > > > > > > > > On Tuesday, July 16, 2013 at 2:08 PM, Michael E. Cotterell wrote: > > > > > > > > > > > > > James, > > > > > > > > > > > > > > That's exactly what I was thinking. In my opinion, hooks are the way > > > > > > > to go (as seen in my example), but if there's a better way then I'm game for > > > > > > > that to. I just want to be able to extend Galaxy without modifying Galaxy > > > > > > > itself. > > > > > > > > > > > > > > Thanks! > > > > > > > > > > > > > > Sincerely, > > > > > > > Michael E. Cotterell > > > > > > > > > > > > > > Ph.D. Student in Computer Science, University of Georgia > > > > > > > Instructor of Record, Graduate RA & TA, University of Georgia > > > > > > > Faculty Liaison, CS Graduate Student Association, University of > > > > > > > Georgia > > > > > > > mepcotterell(a)gmail.com (mailto:mepcotterell@gmail.com) (mailto:mepcotterell@gmail.com) > > > > > > > mepcott(a)uga.edu (mailto:mepcott@uga.edu) (mailto:mepcott@uga.edu) > > > > > > > mec(a)cs.uga.edu (mailto:mec@cs.uga.edu) (mailto:mec@cs.uga.edu) > > > > > > > http://michaelcotterell.com/ > > > > > > > > > > > > > > > > > > > > > On Tuesday, July 16, 2013 at 2:05 PM, James Taylor wrote: > > > > > > > > > > > > > > > Michael, > > > > > > > > > > > > > > > > Galaxy is all about plugins! Tools, datatypes, batch systems, > > > > > > > > visualizations, et cetera. > > > > > > > > > > > > > > > > Additional ways to extend Galaxy through plugins are very welcome. > > > > > > > > We > > > > > > > > just need to make sure that whatever solution is chosen is extremely > > > > > > > > general. > > > > > > > > > > > > > > > > -- > > > > > > > > James Taylor, Assistant Professor, Biology/CS, Emory University > > > > > > > > > > > > > > > > > > > > > > > > On Tue, Jul 16, 2013 at 1:57 PM, Michael E. Cotterell > > > > > > > > <mepcotterell(a)gmail.com (mailto:mepcotterell@gmail.com) (mailto:mepcotterell@gmail.com)> wrote: > > > > > > > > > Are there any plans in the works to support plugins within Galaxy? > > > > > > > > > One of the tools I'm working on is actually more of an extension of the > > > > > > > > > workflow canvas/editor's user interface. Right now, I've minimized the > > > > > > > > > modifications required to the editor.mako file to simply adding a mako > > > > > > > > > include near the bottom of the file. However, like I just said, this > > > > > > > > > requires editing a Galaxy file. It would be a lot better if Galaxy supported > > > > > > > > > plugins with hooks, thus allowing me to extend the user interface (or any > > > > > > > > > other part of the application) by registering hooks in a plugin. > > > > > > > > > > > > > > > > > > To demonstrate how easy it would be to integrate plugins into a > > > > > > > > > python application, I've written up a simple plugin manager script (~100 > > > > > > > > > loc) an placed it in a gist: https://gist.git > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > Sincerely, > > > > Michael E. Cotterell > > > > > > > > Ph.D. Student in Computer Science, University of Georgia > > > > Graduate RA & TA, University of Georgia > > > > mepcotterell(a)gmail.com (mailto:mepcotterell@gmail.com) > > > > mepcott(a)uga.edu (mailto:mepcott@uga.edu) > > > > mec(a)cs.uga.edu (mailto:mec@cs.uga.edu) > > > > http://michaelcotterell.com/ > > > > > >

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galaxy-dev February 2014