galaxy-dev February 2011

galaxy-dev@lists.galaxyproject.org

63 participants
110 discussions

February 18, 2011 Galaxy Development News Brief
by Jennifer Jackson 19 Feb '11

19 Feb '11

February 18, 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 ca0c4ad2bb39 ---- What's New = galaxyproject at Twitter = Join us at Twitter for the latest updates on development projects, conferences and training, and all things Galaxy! #usegalaxy http://twitter.com/#!/search/galaxyproject = New Ways to Search Data Libraries = In addition to searching on data library names and descriptions, we have introduced the ability to search on attributes of library datasets. Two different approaches to searching library datasets are supported 1. Searching with whoosh https://bitbucket.org/mchaput/whoosh/wiki/Home 2. Searching with Apache's Lucene http://lucene.apache.org/java/docs/index.html (Contributed by Brad Chapman) The public Galaxy instances hosted at Penn State University use the whoosh implementation, while Brad Chapman's instance uses the Lucene implementation. Choose either of these implementations for your local Galaxy instances (but not both). There are two new config settings in the "Data Libraries" section of universe_wsgi.ini.sample for these implementations (again, uncomment only one of these if you choose to use this feature): # Search data libraries with whoosh #enable_whoosh_library_search = True # Whoosh indexes are stored in this directory. #whoosh_index_dir = database/whoosh_indexes # Search data libraries with lucene #enable_lucene_library_search = False # maxiumum file size to index for searching, in MB #fulltext_max_size = 500 #fulltext_noindex_filetypes=bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger # base URL of server providing search functionality using lucene #fulltext_url = http://localhost:8081 Details for searching with whoosh You will need to build indexes on a regular, timely basis for searching your library datasets. You can do this by running the following script included in the distribution: % <your galaxy install dir>/scripts/data_libraries/build_whoosh_index.sh Running this script will build whoosh indexes in the directory named by the config setting labeled whoosh_index_dir shown above. We recommend adding something like the following setting to your Galaxy server's cron settings to keep the indexes current: 0,30 * * * * cd /var/opt/galaxy/g2test/galaxy_test ; bash ./scripts/data_libraries/build_whoosh_index.sh The above setting rebuilds the indexes every 30 minutes. You may want to build them more often because search results will include only those library datasets that were indexed the last time the script was executed. In other words, if a library dataset was uploaded after the whoosh indexes were created, it will not be returned in search results even if it meets the search criteria. Using whoosh, you can search on the "name", "info", "message" and "dbkey" attributes of library datasets using the following new search box displayed at the top of the "Data Libraries" page: http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_… Clicking the "Advanced search" link below the search box allows you to search data library names and descriptions as you did in the past: http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_… Details for searching with Lucene If you use the Lucene implementation instead of whoosh, there are a few differences. You'll need to build Lucene indexes using the following script: <your galaxy install dir>/scripts/data_libraries/build_lucene_index.sh In addition to the "name", "info", "message" and "dbkey" attributes, this implementation will also index the contents of your library datasets. You should decide on the optimal values for the following config settings for your Galaxy instance: # maxiumum file size to index for searching, in MB #fulltext_max_size = 500 #fulltext_noindex_filetypes=bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger You'll also need to decide on a value for the following config setting: # base URL of server providing search functionality using lucene #fulltext_url = http://localhost:8081 = Managing disk space with Data Libraries = Adjusted the cleanup_datasets.py script to more correctly handle the lifecycle of Library Datasets. Managing library datasets is a bit complex, so here is a scenario that hopefully provides clarification. The complexities of handling library datasets is mostly contained in the delete_datasets() method in the cleanup_datasets.py script. Example of usage: 1. Assume we have 1 library dataset with LibraryDatasetDatasetAssociation -> LibraryDataset and Dataset This dataset would have the following database column values: LibraryDatasetDatasetAssociation deleted: False LibraryDataset deleted: False, purged: False Dataset deleted: False purged: False Now a user deletes the associated dataset from a data library via a UI menu option. This action results in the following database column values: LibraryDatasetDatasetAssociation deleted: False LibraryDataset deleted: True*, purged: False Dataset deleted: False, purged: False 2. After the number of days configured for the delete_datasets() method (option -6 in the cleanup_datasets.py script) have passed, execution of the delete_datasets() method results in the following database column values: LibraryDatasetDatasetAssociation deleted: True LibraryDataset deleted: True, purged: True Dataset deleted: True*, purged: False 3. After the number of days configured for the purge_datasets() method (option -3 in the cleanup_datasets.py script) have passed, execution of the purge_datasets() method results in the following database column values: LibraryDatasetDatasetAssociation deleted: True LibraryDataset deleted: True, purged: True Dataset deleted: True, purged: True (dataset file removed from disk if -r flag is used) This scenario is about as simple as it gets. Keep in mind that a Dataset object can have many HistoryDatasetAssociations and many LibraryDatasetDatasetAssociations, and a LibraryDataset can have many LibraryDatasetDatasetAssociations. Another way of stating it is: LibraryDatasetDatasetAssociation objects map LibraryDataset objects to Dataset objects, and Dataset objects may be mapped to History objects via HistoryDatasetAssociation objects. ---- Updated & Improved = Current Tools = * Update FASTX tool wrappers to handle fastqsanger formats. * The BLAST+ tools are now uncommented in the sample tool configuration. * Fix an Rpy syntax problem in the Histogram tool that was causing the tool to fail in some local installations. * Enable Cuffcompare to take an arbitrary number of input GTF files. * Add GTF sniffer to datatypes config sample file. = New Tools = * Added a Line/Word/Character counter to Text Manipulation tool group. * Extended Extract Genomic DNA tool to support GFF/GTF features and custom genomes: ** This is especially useful for extracting genomic data that correspond to transcripts in GTF format, as is produced by Cufflinks. ** Tool also now accepts sequence data from a history item, enabling the extraction of data from custom genomes. = New Community Tools Added (Tool Shed) = * Velvet, ABySS, Minimus2, Phrap, and Newbler. http://community.g2.bx.psu.edu/ = Data Libraries = * Fix a bug that included the option for a regular (non-admin) user to upload a directory of files when the config setting existed, but the user's directory did not exist. Instead of throwing an exception, an attempt to create the directory will now be made. If the attempt fails, the option to "Upload a directory of files" will not be included in the select list on the upload form for that particular user. * When browsing a data library, only display the check boxes and the actions to perform on multiple selected datasets if library datasets are displayed. * Clean up the behavior when performing an action on multiple library datasets. Instead of throwing an error and not allowing the action on any of the datasets if the user is not authorized to perform the action on one of them, all "unauthorized" datasets are now left alone and the action is performed on all datasets for which the user is authorized to perform the action. Appropriate messages detail what occurred. * Allow regular users to delete multiple datasets returned from library dataset searches based on the behavior described above. * Do not include the "Select datasets for import into selected histories" option in the actions popup menu at the data library level if the library's root folder doesn't contain any accessible datasets. Make behavior the same for folder popup menus. * Fix a bug where a regular user could never see deleted library items when toggling show / hide deleted items in a data library. * Add a purged column to the LibraryDataset table. A LibraryDataset is marked "purged" when all associated LibraryDatasetDatasetAssociations are marked "deleted". = Workflows = * Workflow steps on the "Run workflow" page are now collapsible to just the title bar with the tool name and annotation. Steps without any inputs to be set will be collapsed by default. * When running a workflow, possible values for Input Dataset steps are filtered to datatypes that are valid for immediately subsequent steps, instead of just using 'data'. * Jquery1.5 workflow fixes with quotations and flagging of outputs. Workflows containing tools that are not loaded will now open in the editor instead of failing on the dictionary lookup. The offending nodes are marked as having an error state, and the workflow cannot be saved. This will enable users to at least look at and try to recover a workflow by removing (and potentially replacing) the offending steps, as well as providing a better view of what's actually wrong with the workflow. * Workflows will no longer try to run when required tools are not found. An error message is displayed with a link to the editor view (to fix the workflow). * Interval datatype now uses line estimates for large files. This fixes potential "'?' lines" seen by some users. * Removed "Annotation:" labels for a cleaner look on the run workflow page. * New History functionality now shows only the checkbox by default, displaying the input for a history name only when checked. * Tool text has been standardized to refer to datasets as such, instead of the older descriptor 'query'. * We now use the inflector utility to pluralize groupings. Fixes "Querys", etc. = Trackster = * Enhancements: ** Support large (10,000+) sets of chromosomes/contigs, as is often the case for low/non-model coverage genomes. ** Improve speed by streamlining data fetching and caching in Trackster. ** Add support for child tracks. ** UI hints for zooming out/in. ** Extend CIGAR string parsing to handle all operations (however, insertions still not fully supported). ** History dataset selection: show history name, show and order by hid in display. ** Modified interval index squish mode to display blocks and treat intervals as half-open. * Bug fixes: ** Fix CIGAR string parsing bug that prevented sequence data from being displayed correctly. ** BED files without score column or with scores that are floats can now be displayed. ** Better handling of error messages so that messages and data do not overlap. = User Interface (UI) = * Search improvements: ** Size of search box increases to show help text (column label). ** Help text is highlighted rather than hidden when user clicks on search box. ** Standard and advanced search divs are toggled correctly when moving between searches. = Galaxy Reports = * Clarify in the reports config that Galaxy reports do not support SQLite. * Add 2 new sample tracking reports and 2 new workflow reports, each of which provides the total number of items per month and the total number of items per user (per month). = Source = * Better egg version conflict resolution. Our eggs should always override dependencies installed elsewhere on sys.path. * Job runners are now loaded dynamically; changes to the source are no longer required. Existing 3rd-party runners will need to add a class to instantiate to the runner-global '__all__' list. See the provided runners for examples. * The Galaxy-side code for the LWR job runner by John Chilton is now included. Documentation in the wiki is forthcoming, to learn more see John's documentation at: http://bitbucket.org/jmchilton/lwr/ "LWR allows you to create a "cluster" out of any systems without installing specialized tightly integrated DRM software like PBS/SGE." = Bug Fixes = * Gracefully fall back to English if a client requests a locale not installed on the server. * Don't attempt to check for the python-daemon egg on Python 2.4 (it's used by an optional experimental component and is not compatible with Python 2.4). * The drmaa job runner would not always detect job completion on some systems. This change could also cause job failures to be considered successful job completions, but we have no way to test for these conditions. Please report if you discover this to be the case. * Migrating to database version 62 no longer fails for MySQL. Thanks Leandro Hermida. * Downloading eggs for offline systems works again. ---- = About Galaxy = Galaxy is supported in part by the following: NSF http://www.nsf.gov NHGRI http://www.genome.gov Huck Institutes of the Life Sciences http://www.huck.psu.edu The Institute for CyberScience at Penn State http://www.ics.psu.edu Core Team http://bitbucket.org/galaxy/galaxy-central/wiki/GalaxyTeam Use Galaxy Now! http://usegalaxy.org|Use Galaxy! Galaxy Project http://galaxyproject.org Galaxy Development Home http://bitbucket.org/galaxy/galaxy-central Follow Galaxy @ Twitter #usegalaxy http://twitter.com/#!/search/galaxyproject ---- Galaxy Project Team February 18, 2011

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cluster path question
by Ryan Golhar 18 Feb '11

18 Feb '11

I'm setting up Galaxy to run on my cluster using drmaa. I can see jobs getting submitted to Torque however the jobs keep failing, because the tools are in the default system path. How do I tell galaxy to append a directory to the path used by jobs? -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information.

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Torque drmaa egg
by Ryan Golhar 18 Feb '11

18 Feb '11

I'm configuring my local install of galaxy to work with my torque/maui cluster. On the Config/Cluster wiki page, there is mention about telling Galaxy where the DRMAA library is located. The example given points to libdrmaa.so. I've searched my torque installation and haven't come across that library. Does anyone know where this library comes from or where its supposed to be located for torque?

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local galaxy display problem
by Ryan Golhar 18 Feb '11

18 Feb '11

I've set up a local instance of Galaxy following the instructions in the wiki for a production instance. I'm running on CentOS with Apache, and a mysql database server. Everything looks great when viewed directly through the Galaxy web server on port 8080. I've implemented the "Serving Galaxy at a sub directory (such as /galaxy)", made the change to Apache, and the universe_wsgi.ini. When I view the page through Apache using http://server.name/galaxy, the page is garbled like something didn't take. I've restarted Apache and Galaxy but its still not work... -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information.

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Local galaxy installation problem. Please help.
by Tena Sakai 18 Feb '11

18 Feb '11

Hi I am a developer for a group. I am having a problem with local installation of galaxy. The platform I am using is: $ uname -o GNU/Linux $ uname -i x86_64 $ uname -v #1 SMP Tue Jul 22 18:01:05 EDT 2008 $ uname -r 2.6.9-78.0.1.ELsmp Here’s what I did: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist grep: http://www.bx.psu.edu/hg/galaxy: No such file or directory grep: galaxy_dist: No such file or directory I cut and pasted from your wiki page, and I assume there is no typo... $ tar xzf galaxy-dist-tip.tar.gz gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now $ gunzip galaxy-dist-tip.tar.gz gunzip: galaxy-dist-tip.tar.gz: unexpected end of file I guess there is something wrong with this gzipped tar file... $ rm galaxy-dist-tip.tar.gz $ /bin/rm -rf galaxy-dist Try it with bz2 file... $ bunzip2 galaxy-dist-tip.tar.bz2 $ tar xf galaxy-dist-tip.tar $ echo $? 0 $ cd galaxy-dist $ sh run.sh <...lots of lines here...> Fetch successful. <...more lines here...> ysam/csamtools.py", line 6, in __bootstrap__ ImportError: /home/tsakai/.python-eggs/pysam-0.1.1_kanwei_90e03180969d-py2.5-linux-x86_64-ucs2.egg-tmp/pysam/csamtools.so: undefined symbol: deflateSetHeader $ echo $? 1 So, I am lost now. Can somebody please give me a tip as to how to proceed? Many thanks. Regards, Tena Sakai tsakai(a)gallo.ucsf.edu

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Upload files from filesystem paths for non admin users
by Jean-Baptiste Denis 18 Feb '11

18 Feb '11

Hello everybody, i'm sorry for posting again. I didn't have any answer during the christmas holiday, so i take another (and last) chance :) I'm running a fresh galaxy-dist installation (changeset 4640:8729d2e29b02) on a Centos 5.5 distribution. I'm using LDAP authentication through Apache. Here is the situation. As a galaxy admin, i've created a "new data library" called "TP" through the admin interface. I've another user, called "foobar" which belongs to a group called "TP Admin" which is associated to the role "TP Admin". I've edited the permissions of the "TP" library to only associate "TP Admin" role to "add library item". No other entry is associated with any role. The "foobar" user logs into galaxy and go to "Shared Data/Data libraries". He chooses "TP" and click on "Add datasets". The problem is that the option "Upload files from filesystem paths" appears in the scrolling "upload option" list even if "foobar" is not a galaxy admin. This means that he can virtually access any file on the filesystem. The comments in the "universe_wsgi.ini" mention "Please note the security implication that this will give Galaxy Admins access to anything your Galaxy user has access to." which seems ok for Galaxy admins, but it looks like this is also the case for any galaxy user. Any advice on this behaviour? Maybe i misunderstood something. Regards, Jean-Baptiste Denis

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Creating new datatype with variable number of input files
by Kempenaar, M (med) 18 Feb '11

18 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.

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Tools to organize long histories
by Leandro Hermida 18 Feb '11

18 Feb '11

Hi everyone, Are there any capabilities or tools in Galaxy to organize long histories with many datasets? best, Leandro

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Re: [galaxy-dev] [galaxy-user] operating on, and getting at, large files in galaxy...
by Edward Kirton 17 Feb '11

17 Feb '11

Hi Nick, Yes, these nextgen reads files are huge and getting bigger every quarter! But there will be storage issues nomatter whether you use Galaxy or not. In fact, i think users are more likely to cleanup files and histories in galaxy than they are to cleanup NFS folders -- out of sight, out of mind! Firstly, I think unnecessary intermediate files are more of a problem than whether or not the file is compressed or not. Indeed, just transferring these files back and forth from the cluster takes a while, not to mention the delay in waiting to be rescheduled for each step. And so I created a tool which would do the job of fastq groomer, end-trimmer, process pairs, and a few other simple tasks -- all in one shot. I haven't uploaded it to the toolshed yet but I will. I hate to duplicate existing tools, but i have a lot of seq data. I will also create a fastqilluminabz2 datatype as well and include it with the tool. For getting files into galaxy, I created a simple tool which would allow staff to enter NFS paths and the option to either copy or symlink if the location was considered stable. I allowed only certain folders (e.g. /home, /storage) and added a password, for security. Similarly, for getting a file out, all you need is a dinky tool for users to provide a destination path. since i've got galaxy running as a special galaxy user in a special galaxy group, file access is restricted (as it should be), so i tell users to create a dropbox folder in their homedir (and chmod 777). by creating a tool like this, you don't need to care how galaxy names the files. i deliberately try to not mess around under the hood. i can upload these to galaxy toolshed, but like i said, there isn't much to them. Ed On Wed, Feb 9, 2011 at 4:17 AM, Nick Schurch <N.Schurch(a)dundee.ac.uk> wrote: > > Hi all, > > I've recently encountered a few problems when trying to use Galaxy which > are really driving me away from using it as a bioinformatics platform for > NGS. I was wonderinf if there are any simple solutions that I've missed... > > Firstly, It seems that while there are a few solutions for getting large > files (a few GB) into a local install of galaxy without going through HTTP, > many tools that operate on these files produces multiple, uncompressed large > files which quickly eat up the disk allocation. This is particularly > significant in a workflow that has multiple processing steps which each > leave behind a large file. With no way to compress or archive files produced > by intermediate steps in a workflow, and no desire to delete them since I > may need to go back to them and they can take hours to re-run, the only two > remaining options seem to be to save them and then delete them. > > And this brings me to the second problem. Getting large files out of > Galaxy. The only way to save large files from Galaxy (that I can see) is the > save icon, which downloads the file via http. This take *ages* for a large > file and also causes big headaches for my firefox browser. I've taken a > quick peek at the Galaxy file system to see if I could just copy a file, but > its almost completely indecipherable if you want to find out what file in > the file system corresponds to a file saved from a tool. Is there some way > to get the location of a particular file on the galaxy file system, that I > can just copy? > > -- > Cheers, > > Nick Schurch > > Data Analysis Group (The Barton Group), > School of Life Sciences, > University of Dundee, > Dow St, > Dundee, > DD1 5EH, > Scotland, > UK > > Tel: +44 1382 388707 > Fax: +44 1382 345 893 > > > > -- > Cheers, > > Nick Schurch > > Data Analysis Group (The Barton Group), > School of Life Sciences, > University of Dundee, > Dow St, > Dundee, > DD1 5EH, > Scotland, > UK > > Tel: +44 1382 388707 > Fax: +44 1382 345 893 > > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user > >

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upload directory of files error
by David Hoover 17 Feb '11

17 Feb '11

This used to work. Now when I try to upload a directory of files, it gives this error: URL: https://galaxy.cit.nih.gov/library_common/ldda_info?library_id=a799d38679e9… File '/gs1/users/galaxy/pro/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/gs1/users/galaxy/pro/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/gs1/users/galaxy/pro/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/gs1/users/galaxy/pro/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/gs1/users/galaxy/pro/lib/galaxy/web/framework/middleware/remoteuser.py', line 121 in __call__ return self.app( environ, start_response ) File '/gs1/users/galaxy/pro/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/gs1/users/galaxy/pro/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/gs1/users/galaxy/pro/lib/galaxy/web/controllers/library_common.py', line 574 in ldda_info status=status ) File '/gs1/users/galaxy/pro/lib/galaxy/web/framework/__init__.py', line 645 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/gs1/users/galaxy/pro/lib/galaxy/web/framework/__init__.py', line 656 in fill_template_mako return template.render( **data ) File '/gs1/users/galaxy/pro/eggs/Mako-0.2.5-py2.6.egg/mako/template.py', line 133 in render return runtime._render(self, self.callable_, args, data) File '/gs1/users/galaxy/pro/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 364 in _render _render_context(template, callable_, context, *args, **_kwargs_for_callable(callable_, data)) File '/gs1/users/galaxy/pro/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 381 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/gs1/users/galaxy/pro/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 414 in _exec_template callable_(context, *args, **kwargs) File '/gs1/users/galaxy/pro/database/compiled_templates/base.mako.py', line 40 in render_body __M_writer(unicode(next.body())) File '/gs1/users/galaxy/pro/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 255 in <lambda> return lambda *args, **kwargs:callable_(self.context, *args, **kwargs) File '/gs1/users/galaxy/pro/database/compiled_templates/library/common/ldda_info.mako.py', line 224 in render_body if job.stdout.strip() != '': AttributeError: 'NoneType' object has no attribute 'strip' Huh? David Hoover Helix Systems Staff http://helix.nih.gov

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galaxy-dev February 2011