January 2011 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] [galaxy-user] Peep view for history elements broken on IE?
by Leandro Hermida 22 Feb '11

22 Feb '11

Hi everyone, I posted a similar thread back in August http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-August/003224.html There are a couple web UI issues with Galaxy when using IE, like as mentioned in this thread in the history pane data items the link is missing and you cannot expand them to "peep" at what's there. -Leandro On Thu, Jan 27, 2011 at 6:07 PM, Kanwei Li <kanwei(a)gmail.com> wrote: > Weird.. the proxy shouldn't be relevant. Could you open the javascript > error console and see what the error is? > > On Thu, Jan 27, 2011 at 8:57 AM, Peter <peter(a)maubp.freeserve.co.uk> > wrote: > > On Wed, Jan 26, 2011 at 7:49 PM, Kanwei Li <kanwei(a)gmail.com> wrote: > >> Hi Peter, > >> > >> Is this still an issue? The error you describe sounds like a jStore > >> problem but I tested it in IE7 and it works. > >> > >> Thanks, > >> > >> Kanwei > > > > Hi Kanwei, > > > > I just tried the public Galaxy at http://usegalaxy.org aka > > http://main.g2.bx.psu.edu/ and also ttp://test.g2.bx.psu.edu/ which > > says it tracks the galaxy-central repo, and for both the history peep > > links don't work. This is using Internet Explorer version 7.0.5730.13, > > which I believe is the current release (from back in 2007), from two > > different Windows XP machines at our institute (which are accessing > > the internet via a proxy - perhaps relevant?). > > > > Peter > > > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user >

3 9

Import files from local file system
by Steve Taylor 22 Feb '11

22 Feb '11

Hi, I noticed the recent update to Galaxy that allowed users to put data on the galaxy FTP server and then import it into their history. Would it be possible to use a similar mechanism to import data from the galaxy host file system but not use an FTP daemon? In our case we we would like to mount a volume to the galaxy file server and allow people to cp or mv data into it and then be able to import the data into their history. For example, In the context of the example at http://bitbucket.org/galaxy/galaxy-central/wiki/Config/UploadViaFTP could you set up a directory called '/home/nate/galaxy_dist/database/localfs/' instead of '/home/nate/galaxy_dist/database/ftp/' which contained email named directories and the files in these in these would be available to import via the upload UI? Or is it all tied into FTP? Thanks for any advice, Steve

5 10

Problems with run_functional_tests.sh and history?
by Peter 21 Feb '11

21 Feb '11

Hi all, I'm having trouble with the Galaxy functional tests. On our Linux server things seem to work, but I'm having trouble on my Mac. This affects multiple tests. For example, using a test for my own tool wrapper, on Linux my test passes. On my Mac, the tool is missing the required binary so I expect the test to fail with error level 127 and a message to stderr. However, I get the following cryptic error: $ ./run_functional_tests.sh -id tmhmm2 ... functional_tests.py INFO 2010-10-28 11:57:01,129 Embedded web server started functional_tests.py INFO 2010-10-28 11:57:01,185 Functional tests will be run against localhost:8980 nose.plugins.manager DEBUG 2010-10-28 11:57:01,210 DefaultPluginManager load plugin sqlalchemy = sqlalchemy.test.noseplugin:NoseSQLAlchemy nose.plugins.manager DEBUG 2010-10-28 11:57:01,215 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML TMHMM 2.0 ( tmhmm2 ) > Test-1 ... Error - <type 'exceptions.TypeError'>: 'NoneType' object is not callable URL: http://localhost:8980/history File '/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Paste-1.7.2-py2.5.egg/paste/exceptions/errormiddleware.py', line 144 in __call__ app_iter = self.application(environ, sr_checker) File '/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Paste-1.7.2-py2.5.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Paste-1.7.2-py2.5.egg/paste/httpexceptions.py', line 636 in __call__ return self.application(environ, start_response) File '/Users/xxx/repositories/galaxy-central/lib/galaxy/web/framework/base.py', line 154 in __call__ return body( environ, start_response ) File '/Users/xxx/repositories/galaxy-central/lib/galaxy/web/framework/__init__.py', line 668 in render template.render_context( context ) File '/Users/xxx/repositories/galaxy-central/eggs/Mako-0.2.5-py2.5.egg/mako/template.py', line 146 in render_context runtime._render_context(self, self.callable_, context, *args, **kwargs) File '/Users/xxx/repositories/galaxy-central/eggs/Mako-0.2.5-py2.5.egg/mako/runtime.py', line 381 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/Users/xxx/repositories/galaxy-central/eggs/Mako-0.2.5-py2.5.egg/mako/runtime.py', line 414 in _exec_template callable_(context, *args, **kwargs) File '/Users/xxx/repositories/galaxy-central/database/compiled_templates/root/history.mako.py', line 55 in render_body __M_writer(u'\n<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\n\n<html>\n\n<head>\n<title>') File '/Users/xxx/repositories/galaxy-central/lib/galaxy/web/framework/__init__.py', line 665 in write response_write( d.encode( 'utf-8' ) ) TypeError: 'NoneType' object is not callable CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT: 'text/html; */*' HTTP_ACCEPT_ENCODING: 'identity' HTTP_CONNECTION: 'close' HTTP_COOKIE: '$Version=1; galaxysession=eb142648ac45b770a711a07bbd8189c4a80d9868f9ceff96f0635391728a47dfe5161bca180a2aae; $Path="/"' HTTP_HOST: 'localhost:8980' PATH_INFO: '/history' REMOTE_ADDR: '127.0.0.1' REQUEST_METHOD: 'GET' SERVER_NAME: '127.0.0.1' SERVER_PORT: '8980' SERVER_PROTOCOL: 'HTTP/1.1' Configuration ------------- static_enabled: False use_translogger: False WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0xbfd2e10> paste.cookies: (<SimpleCookie: galaxysession='eb142648ac45b770a711a07bbd8189c4a80d9868f9ceff96f0635391728a47dfe5161bca180a2aae'>, '$Version=1; galaxysession=eb142648ac45b770a711a07bbd8189c4a80d9868f9ceff96f0635391728a47dfe5161bca180a2aae; $Path="/"') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0xbfd3110> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0xccf1f10> 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.throw_errors: True webob._parsed_query_vars: (MultiDict([]), '') wsgi process: 'Multithreaded' ------------------------------------------------------------ ERROR ====================================================================== ERROR: TMHMM 2.0 ( tmhmm2 ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/xxx/repositories/galaxy-central/test/functional/test_toolbox.py", line 160, in test_tool self.do_it( td ) File "/Users/xxx/repositories/galaxy-central/test/functional/test_toolbox.py", line 24, in do_it self.new_history() File "/Users/xxx/repositories/galaxy-central/test/base/twilltestcase.py", line 291, in new_history self.check_history_for_string('Your history is empty') File "/Users/xxx/repositories/galaxy-central/test/base/twilltestcase.py", line 215, in check_history_for_string self.visit_page( "history" ) File "/Users/xxx/repositories/galaxy-central/test/base/twilltestcase.py", line 1040, in visit_page tc.code( 200 ) File "/Users/xxx/repositories/galaxy-central/eggs/twill-0.9-py2.5.egg/twill/commands.py", line 133, in code should_be)) TwillAssertionError: code is 500 != 200 ---------------------------------------------------------------------- Ran 1 test in 0.824s FAILED (errors=1) functional_tests.py INFO 2010-10-28 11:57:02,079 Shutting down functional_tests.py INFO 2010-10-28 11:57:02,079 Shutting down embedded web server ... ############################################################################### Here is my suggested fix: diff -r 82743fcbf23c lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Thu Oct 28 11:41:18 2010 +0100 +++ b/lib/galaxy/web/framework/__init__.py Thu Oct 28 11:56:16 2010 +0100 @@ -660,6 +660,9 @@ ## return template.render( **data ) def render( environ, start_response ): response_write = start_response( self.response.wsgi_status(), self.response.wsgi_headeritems() ) + if response_write is None: + log.error( "Error: this request returned None from start_response: %s" % self.request.browser_url ) + return [] class StreamBuffer( object ): def write( self, d ): response_write( d.encode( 'utf-8' ) ) ############################################################################### With the patch, I get: $ ./run_functional_tests.sh -id tmhmm2 ... functional_tests.py INFO 2010-10-28 11:52:37,742 Embedded web server started functional_tests.py INFO 2010-10-28 11:52:37,800 Functional tests will be run against localhost:9383 nose.plugins.manager DEBUG 2010-10-28 11:52:37,825 DefaultPluginManager load plugin sqlalchemy = sqlalchemy.test.noseplugin:NoseSQLAlchemy nose.plugins.manager DEBUG 2010-10-28 11:52:37,829 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML TMHMM 2.0 ( tmhmm2 ) > Test-1 ... galaxy.web.framework ERROR 2010-10-28 11:52:38,685 Error: this request returned None from start_response: http://localhost:9383/history ERROR ====================================================================== ERROR: TMHMM 2.0 ( tmhmm2 ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/xxx/repositories/galaxy-central/test/functional/test_toolbox.py", line 160, in test_tool self.do_it( td ) File "/Users/xxx/repositories/galaxy-central/test/functional/test_toolbox.py", line 24, in do_it self.new_history() File "/Users/xxx/repositories/galaxy-central/test/base/twilltestcase.py", line 291, in new_history self.check_history_for_string('Your history is empty') File "/Users/xxx/repositories/galaxy-central/test/base/twilltestcase.py", line 217, in check_history_for_string tc.find(subpatt) File "/Users/xxx/repositories/galaxy-central/eggs/twill-0.9-py2.5.egg/twill/commands.py", line 239, in find raise TwillAssertionError("no match to '%s'" % (what,)) TwillAssertionError: no match to 'Your' -------------------- >> begin captured logging << -------------------- galaxy.web.framework: ERROR: Error: this request returned None from start_response: http://localhost:9383/history --------------------- >> end captured logging << --------------------- ---------------------------------------------------------------------- Ran 1 test in 0.821s FAILED (errors=1) functional_tests.py INFO 2010-10-28 11:52:38,691 Shutting down functional_tests.py INFO 2010-10-28 11:52:38,691 Shutting down embedded web server ... ############################################################################### I'm still puzzled about what is going wrong - this affects other Galaxy tests as well - not just mine. Is there something obvious wrong with the setup on this machine? Actually using Galaxy running on this Mac seems to work. Thanks, Peter

2 6

Creating new datatype with variable number of input files
by Kempenaar, M (med) 17 Feb '11

17 Feb '11

Hello, This is the first question I ask on this list, please let me know if I'm 'doing it wrong'. Currently I'm trying to implement a workflow that uses a sort of microarray data which consists of one CSV file for each experiment done. The first step in the workflow is to preprocess the data and merge all files into a single CSV file (using an R script). Now my question is, is it possible to supply the user a Galaxy 'upload file' interface where he/she can: - enter the number of experiments done (thus number of files to upload) - depending on the above, present one 'select file' button and a new metavalue used for naming the experiment - directly execute an R script after pressing the 'Execute' button. - add the single resulting file from this R script to the users history pane (an intermediate composite datatype holding all uploaded files and manually executing the script is fine as well) If this is possible, could you please add a hint in the right direction, that would be very helpful! Also, just giving an example of a Galaxy workflow that does any of the mentioned would be great too! However if this seems to be impossible to do, what are the alternatives? Maybe create my own webtool that does the above and link that to my Galaxy? Thanks in advance for any replies. - Marcel De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

2 1

python2.6 UserWarning: Unbuilt egg for pytz
by Vipin TS 11 Feb '11

11 Feb '11

Hi all, Last day we upgraded our galaxy service computing cluster nodes operating system from Ubuntu hadry to lucid 10.4. We updated python eggs and now getting an Warning message, it apparently kills the galaxy jobs. Warning message as follows: /home/abc/galaxy/lib/galaxy/eggs/__init__.py:332: UserWarning: Unbuilt egg for pytz [unknown version] (/usr/lib/python2.6/dist-packages) env = pkg_resources.Environment( platform=pkg_resources.get_platform() ) >From the warning message I can see that the problem with unbuilt egg for pytz module. Before approaching you I googled the same and got a good thread which explains similar kind of issues ( https://bugs.launchpad.net/ubuntu/+source/distribute/+bug/576434) I followed #9 from TJ and made a work around and unfortunately no luck. Does anyone had a problem with this before, if yes I like to hear from you that how do u managed to get rid of the warning message. Many thanks, Vipin T S Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany

2 1

New Remote Job Runner
by John Chilton 11 Feb '11

11 Feb '11

Hello, We are looking at integrating some tools into Galaxy for a domain where many of the existing programs are Windows only. My desire is to write tool files and have the certain jobs run remotely on a Windows host (our Galaxy servers are Linux). It wasn't clear how to do this with the existing job runners since they all seem to require a shared file system and absolute file paths that are the same on the Galaxy server as they are on the remote execution hosts. I developed a new job runner that allows for the remote execution of jobs that also rewrites paths and stages files as part of the job execution. There is a server application that needs to be running on the remote machine (*nix or Windows). This application is likely easier to setup/configure than SGE/PBS/etc... because it is a simple Python paste application, with just a few configuration options. There may be valid use cases for this approach for non-Windows applications as well - if you would like a lighter weight server component on the remote system, if shared file systems are impossible/impractical, etc.... The path rewrites are not going to cover every possible way an absolute path can sneak into the execution, so this is only useful for a subset of tools. But it does handle normal file inputs and outputs, config files, and scripts in the tool definition directory. I welcome input/advice on this approach or the implementation. If there is any way I can improve the code base to the point where it can be included in galaxy-central I would be more than happy to make the desired changes. If not, it is out there for people to use if they have a similar use case. The server application as well as a patch to add the runner/client to a galaxy-central installation can be found at: https://bitbucket.org/jmchilton/lwr/src Thanks for your time, John ------------------------------------------------ John Chilton Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 E-Mail: chilton(a)msi.umn.edu

2 1

How can I execute one module with different input parameters in several nodes ?
by 조수안 07 Feb '11

07 Feb '11

Hi, How can I execute a module with different input parameters in several nodes ? For example, there is a module that calculates chromosome length, and a input file that contains 25 chromosome sequences. When I execute the module for the input file, I want to execute the module in 25 nodes with each chromosome sequence. In this situation, when I make a workflow, can I place the module once in the workflow ? not placing the module 25 times. Thanks Suan cho

2 1

Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?
by Peter 01 Feb '11

01 Feb '11

On Wed, Oct 13, 2010 at 10:22 AM, Peter <peter(a)maubp.freeserve.co.uk> wrote: > On Wed, Oct 13, 2010 at 12:58 AM, Kanwei Li <kanwei(a)gmail.com> wrote: >> >> Hi Peter, >> >> The BLAST+ branch has been transplanted into galaxy-central. Thank you! >> >> Kanwei > > Wow. Thanks :) There are another few change sets on this follow up branch, http://bitbucket.org/peterjc/galaxy-central/src/blastplus2 These are: Include BLAST-XML to tabular in tool_conf.xml.sample http://bitbucket.org/peterjc/galaxy-central/changeset/629448f1a17b Workaround Issue 397 using 'if' in Cheetah template to avoid hidden parameters http://bitbucket.org/peterjc/galaxy-central/changeset/02ce0b68936a Ignore Unix editor backup files ending with tilde (not BLAST+ specific): http://bitbucket.org/peterjc/galaxy-central/changeset/708816ffd451 Ignore # lines in BLAST tabular output in my filter script http://bitbucket.org/peterjc/galaxy-central/changeset/b2dcd6b8d434 And a capitalisation fix in my XML caption: http://bitbucket.org/peterjc/galaxy-central/changeset/6efadbea0cfc > > I mentioned it needs tests: > I've worked out how to add unit tests to the XML wrapper (that is well documented) and run them via run_functional_tests.sh - so adding some BLAST+ tests should be possible now. Peter

5 29

Data Library - upload files from filesystem paths
by Nicki Gray 01 Feb '11

01 Feb '11

Hi As an admin I have created a data library on our local instance of galaxy, created folders in that library and added datasets using 'upload files from filesystem paths' option, choosing not to copy the data into Galaxy, which then loads all the files in the given directory into the data library. Is there a way to refresh this list automatically? so that if a new file is added into that directory it will appear in the data library? or do I have to add new files in that directory manually, giving the path to the new file? I am also having a problem with creating sub folders - I choose to create sub folder from the drop down list and it reports that the sub folder has been created but I cant see it, and I cant click on the blue triangles to the left of the folders either. Does anyone else have this problem? Any help would be appreciated, Thanks, Nicki --------------------- Nicki Gray MRC Molecular Haematology Unit 01865 222434

2 4

January 31, 2011 Galaxy Development News Brief
by Jennifer Jackson 31 Jan '11

31 Jan '11

January 31, 2011 Galaxy Development News Brief http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_… ---- Get Galaxy! http://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy * new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist * upgrade: % hg pull -u -r 95d65755ac69 ---- What's New = Workflow Additions= 1) Usability improvements for workflow annotations * Workflow annotation is now shown at the top of the page. * Step annotations are shown in the step header rather than at the bottom. example: Annotation http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_… 2) Easier to move workflows directly from one Galaxy instance to another * Workflow download/export page now provides URL that can be used to directly import a workflow from one instance to another. example: URL import http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_… 3) New Parameter settings for global application or specific actions * Workflow parameters are a new feature we've added to simplify reuse of workflows, and to allow for easier variation of parameters when re-running a workflow. * Instead of filling in explicit values when building a workflow, you can now use flexible parameters. To specify a workflow parameter, simply use a tag like ${my_variable_name} in any tool input field or in a rename dataset action field. * The workflow shown below has two parameters, as shown in the Workflow Parameters display in the top right of the editor window. You can see the ${filter_condition} parameter in the right panel in both the tool input and the rename action. ** Note that while this ${filter_condition} is only used in a single step in this simple demo workflow, variables can be used across steps. example: Parameters http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_… *As the inputs are filled in the Workflow Parameters box, seen in the runtime example below, the new values will be reflected in all workflow steps and will be used when the workflow is executed. example: Runtime display http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_… 4) General workflow tuning * HideDataset Action will no longer show in the workflow editor. The ability to manually create one of these actions has been deprecated in favor of the workflow outputs approach. * Workflow run results can now be sent to a new history instead of the current one. * Ordering of workflow steps is now sorted based on the layout in the workflow editor, arranged based on distance from top left corner of the editor. This won't affect existing workflows until re-saved. * Workflows that contain steps expecting tools that are unavailable (as might be the case for a workflow imported from another Galaxy instance) will now have problem nodes marked with an error state. The workflow cannot be saved until the steps are removed or the tools are added to the current Galaxy instance. = Deferred Jobs & Managed Transfers = These components are under rapid development and interfaces should be considered experimental. They can be enabled by setting 'enable_beta_job_managers = True' in universe_wsgi.ini. 1) Deferred Jobs * A generic method for creating a dependency on an event before executing arbitrary code has now been defined in: galaxy-dist/lib/galaxy/job/deferred/__init__.py * The deferred job runner loads plugins found in the same directory which implement the necessary methods check_job() and run_job(). check_job() returns a state which informs the deferred job runner whether it is okay to execute the run_job() method. * The deferred job runner is independent from the regular tool-related job runner and is not coupled with tools, nor does it have any integrated cluster support. * No documentation is provided for the format of a plugin at this time, but a sample plugin will be included at a later date. 2) Transfer Manager * Galaxy can now spawn persistent transfers of (unauthenticated) http and https URLs via the code in: galaxy-dist/lib/galaxy/job/transfer_manager.py * The transfer manager is accessible in-application at app.transfer_manager. * Transfers are daemonized and thus not influenced by Galaxy restarts, although a loss of database connection (restarting the database server) will cause transfers to fail. * A transfer can be polled for progress via JSON-RPC requests to its socket. An interface for this request is available in the transfer_manager class. * Future enhancements will allow for authenticated http/https and scp. ---- Updated & Improved = Data Content = * New "Get Data" source: modENCODE modMine server. * New Genomes: format: Genome [dbkey] ** //Pseudomonas aeruginos (str. PA7) [16720] ** Pseudomonas aeruginos (str. PAO1) [pseuAeru] ** Pseudomonas aeruginos (str. UCBPP-PA14) [386] ** Silkworm (Bombyx mori str. p50T) [Bombyx_mori_p50T_2.0] ** Rice pathogen: Xanthomonas oryzae (str. KACC10331) [12931] ** Rice pathogen: Xanthomonas oryzae (str. MAFF 311018) [16297] ** Rice pathogen: Xanthomonas oryzae (str. PXO99A) [Xanthomonas_oryzae_PXO99A] ** Little Brown Bat (Myotis lucifugus) [myoluc2] = Current Tools = * Optional 'min' and 'max' attributes for tool integer and float parameters. * Add --max and --un options to Bowtie. * Validators enforce min/max values and generated error messages for invalid values. * Add Standard deviation operation to grouping tool. * Enhance histogram tool to allow plotting as frequency/counts. * Allow fastx_toolkit clipper wrapper to work on fastqsanger formatted files. * SAM metadata detection and setting sped up dramatically upon import. * Wig-to-bigWig converter tool default parameters now same as UCSC's. * Cufflinks tool suite updates: ** Update Cufflinks tool suite wrappers to support v0.9.3. ** Add support for bias correction to Cufflinks and Cuffdiff; bias correction improves transcript quantitation results (FPKM values). ** Enable Cuffcompare to use sequence data so that it can generate data for use by Cuffdiff. Cuffcompare uses sam_fa_indices.loc to find locally cached genome sequence data and indices that are needed for this option. ** Add normalization support to Cufflinks and Cuffdiff and replicate support for cuffdiff. = New Tools = * BED-to-bigBed converter tool now under "Convert Formats". ** Converts sorted BED files into UCSC's bigBed format. ** Requires bedToBigBed in PATH. * BLAST+ tools are now commented in tool_conf.xml.sample. ** Not in Galaxy main, for local instance use. ** If you run the BLAST+ tools at your site, please be sure to uncomment them if updating to the latest tool_conf.xml.sample (will be default at next update). * Add SAMtools flagstat tool. * Add CCAT ChIP-seq peak/region caller. * Add BWA wrapper for SOLiD. = Histories = * Estimated size is now displayed for very large text-based (non-binary) datasets. * Always show Galaxy masthead and enable Saved Histories to work with and without panels. * New "Copy Datasets" link added under History Options dropdown. ** Dataset and history IDs are now encoded. ** JS dropdown used to change source history, so you no longer have to switch desired source history to be "active". ** Remove link in "edit attributes" of datasets. ** Simplified destination interface by using a single select box by default, but also providing a link to show checkboxes for multiple destination histories. ** Use newly imported Inflector library to get correct plural/singular nouns on actions. ** Added arrow between source and destination. ** Removed checkbox for copying to a new history. Instead, create new history if new history field is not blank. = Data Libraries= * Creating job information (stdout/stderr) is now available on the library item info page, which is helpful when library uploads fail. = Trackster = * Add bigWig display to trackster. Automatically converts wig to bigwig if needed (NOTE: datatypes_conf.xml.sample has been edited to add the new converter, you must update datatypes_conf.xml to use it). The converter requires that wigToBigWig be in the PATH, but no other tools are needed to view bigwig files as they are provided by bx_python. * Tuning ** Fix track preferences not being applied ** Fix chroms not being selectable when a new track browser is created ** Fix ReferenceTrack not working with filters ** Fix visual analytics error when tool configuration has changed ** Fix visualization saving on Chrome by using $.each instead of for loop ** Fix shared visualizations ** Fix tracks fetching from data provider when indexer returned None, and when ** Fix BAM reads without cigar string. = Sample Tracking = * Additions and tuning to improve tracking (complete documentation will be available soon). = User Interface (UI) = *Version info is now printed in history item for Bowtie, BWA, Lastz, TopHat, Samtools, Cuffdif, Cufflinks, Cuffcompare, BFAST, and PerM. * Turn off web browser auto-complete for tool search (includes workflows). * Grid changes resulting in better readability: ** Better page number display. ** Use "~" instead of "about" example: "about 2 hours ago" -> "~ 2 hours ago". ** Cell padding decreased. ** Added new "nowrap" parameter to prevent text from being wrapped. Currently only used for tags to prevent "X tags" from wrapping in the middle. = Application Programming Interface (API) = * Still 'alpha', but: Initial pass completed for forms, request_type, users and roles. See README and examples in source. = Source = * Galaxy now runs with system python on 64-bit mac kernel. * Enhance select parameter wrapper objects to provide access to additional fields by name for dynamically generated select lists (i.e. dynamic_options). example: use ${param.fields.path} to access a path field * Updated the XML in filter specification for output files. The closing filter tag can now be on separate line to use as an # actual filter. * Implemented 'from_work_dir' attribute for tool outputs. Using this attribute matches a file in the working directory to a tool output/HDA; when a tool finishes, the file in the working directory is automatically copied to the HDA. Hence, it's no longer necessary for tool wrapper scripts to manually copy tool output files to HDA files. * More programmatic control of page numbers on grid (custom UI). * Many formerly undocumented options have been added to the universe_wsgi.ini.sample file. Please compare your working copy with the new .sample and determine whether any of the options are relevant to your environment. *The "welcome page" found at static/welcome.html, has been renamed to static/welcome.html.sample. * The UCSC Genome Browser now supports loading data via https. If you implemented this former Galaxy URLs from https->http method in Apache as per the wiki documentation you will also need to remove it there, and allow the browser through your authentication scheme over https. * Explicitly convert autocomplete dropdown values on refresh_on_change. * Adjust image links in tools to work with a proxy prefix (thanks Brad Chapman). = Bug Fixes = * Ensembl GTF files are recognized correctly. * Make Tophat wrapper compatible with python 2.4 by removing try-catch-finally. * Fix unicode error for dataset peeks. * Sanitize tool links in tool menu so that they can be searched. Use only lowercase letters, numbers, and underscores in links to ensure cross-browser functionality. * Fix for building form element for boolean tool parameter when default state is configured as checked in tool configuration, but user provided value is non-checked. Fixes an issue seen in workflows that prevents saving the unchecked state under described conditions. * Fix typo in BFAST. * Trackster: fix BAM display bugs, Dense display bug, better dataset selection. * Add validator to Tophat's segment mismatches parameter. * Turn off web browser autocomplete for tool search in workflows. * Fix Trackster's BAM display bugs, Dense display bug, better dataset selection. * Add validator to Tophat's segment mismatches parameter. * Added the ctypes egg so the DRMAA egg will now work under Python 2.4. * Bug fixes to the Mac OS X launcher in the galaxy-dist/contrib/ folder (from Florent Angly). * Python reports the wrong platform when running a 32-bit Python on 64-bit Linux, so Galaxy now forces the correct platform in this environment (thanks David Hoover). * Fix Chrome not auto-saving changes to workflow checkboxes. ---- About Galaxy Galaxy is supported in part by NSF, NHGRI, the Huck Institutes of the Life Sciences, and The Institute for CyberScience at Penn State. Core Team http://bitbucket.org/galaxy/galaxy-central/wiki/GalaxyTeam Use Galaxy! http://usegalaxy.org GalaxyProject.org http://galaxyproject.org|GalaxyProject.org Development Home http://bitbucket.org/galaxy/galaxy-central ---- Galaxy Team January 31, 2011

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