galaxy-dev March 2012

galaxy-dev@lists.galaxyproject.org

110 participants
202 discussions

bug with Galaxy form validation and dynamic_options population of drop-down menus where option values are integers
by Leandro Hermida 13 Mar '12

13 Mar '12

Hello, If you have a form with an input like this: <param name="input1" type="select" dynamic_options="get_options()" /> And the options dynamically generated have integers as values, e.g. options tuples like this: [ "One", 1, 1 ], [ "Two", 2, 0 ], [ "Three", 3, 0 ] When you try to submit the galaxy form you always get the validation error "An invalid option was selected, please verify". regards, Leandro

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March 12, 2012 Galaxy Development News Brief
by Jennifer Jackson 13 Mar '12

13 Mar '12

Dear Galaxy Community, The *latest Galaxy distribution* has been released: March 12, 2012 Galaxy Development News Brief <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_03_12> *Mercurial pull:* new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 40f1816d6857 *Important Upcoming Changes to Tool Organization: * The _*Emboss tools and Emboss datatypes will be eliminated from the Galaxy distribution in the NEXT release*_. Other tools currently in the Galaxy distribution will be eliminated in following releases. Those hosting local Galaxy instances should read this revised *"Migrating tools"* <http://wiki.g2.bx.psu.edu/Tool%20Shed#Migrating_tools_from_the_Galaxy_distr…> section of the Galaxy tool shed wiki to understand how this process will work: *Migrating tools from the Galaxy distribution to the Galaxy Main tool shed <http://wiki.g2.bx.psu.edu/Tool%20Shed#Migrating_tools_from_the_Galaxy_distr…>* /(Summary)/ In 2012, the Galaxy development team will begin the process of /migrating the tools that are currently available in the Galaxy distribution to the Galaxy Main tool shed/. This will enable those that host local Galaxy instances much more flexibility in choosing to provide only those specific tools in which their users are interested. Read more... <http://wiki.g2.bx.psu.edu/Tool%20Shed#Migrating_tools_from_the_Galaxy_distr…> *Release Highlights: * * *Galaxy tools:* XML configuration <http://wiki.g2.bx.psu.edu/Tool%20Shed#XML_configuration_files_used_to_popul…>, managing tool panel layout <http://wiki.g2.bx.psu.edu/Tool%20Shed#Managing_the_layout_of_your_Galaxy_to…>, and Galaxy tool versions <http://wiki.g2.bx.psu.edu/Tool%20Shed#Galaxy_Tool_Versions> * *RNA-Seq Tools:* Added *CuffMerge* <http://cufflinks.cbcb.umd.edu> version 1.0.0, Updated *TopHat* <http://tophat.cbcb.umd.edu> default parameters * *External Display Apps:* Added RViewer<http://rviewer.lbl.gov/rviewer>, Updated *IGV * <http://www.broadinstitute.org/igv/> * Visualize ENCODE<http://genome.ucsc.edu/ENCODE> "peak" datatype tracks in the Galaxy Track Browser (aka Trackster) * Multiple *Workflow* updates including enhancements to/input dataset options, display modes, and sharing * CloudMan<http://wiki.g2.bx.psu.edu/Admin/Cloud> now offers /preliminary support for OpenNebula cloud type <http://bitbucket.org/galaxy/cloudman/src/tip/cm/clouds/opennebula.py>/ and a larger default tools volume(10GB vs old 2GB) *Need help with a local instance? * * *Installation* and *Admin* Instructions: http://getgalaxy.org * *Search* with our custom google tools: * All Galaxy mailings lists <http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching>for prior Q & A * Information about deploying, developing, customizing, and administering <http://galaxyproject.org/search/getgalaxy> Galaxy * Information about using <http://galaxyproject.org/search/usegalaxy> Galaxy * *Consider* subscribing to the galaxy-dev <http://wiki.g2.bx.psu.edu/Mailing%20Lists#Subscribing_and_Unsubscribing>mailing list Thanks for using Galaxy, The Galaxy team http://usegalaxy.org http://getgalaxy.org http://galaxyproject.org http://galaxyproject.org/wiki

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March 12, 2012 Galaxy Development News Brief
by Jennifer Jackson 13 Mar '12

13 Mar '12

Dear Galaxy Community, The latest Galaxy distributionhas been released: March 12, 2012 Galaxy Development News Brief <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_03_12> *Mercurial pull:* new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 40f1816d6857 Important Upcoming Changes to Tool Organization: The _*Emboss tools and Emboss datatypes will be eliminated from the Galaxy distribution in the NEXT release*_. Other tools currently in the Galaxy distribution will be eliminated in following releases. Those hosting local Galaxy instances should read this revised *"Migrating tools"* <http://wiki.g2.bx.psu.edu/Tool%20Shed#Migrating_tools_from_the_Galaxy_distr…> section of the Galaxy tool shed wiki to understand how this process will work: Migrating tools from the Galaxy distribution to the Galaxy Main tool shed <http://wiki.g2.bx.psu.edu/Tool%20Shed#Migrating_tools_from_the_Galaxy_distr…> (Summary) In 2012, the Galaxy development team will begin the process of migrating the tools that are currently available in the Galaxy distribution to the Galaxy Main tool shed. This will enable those that host local Galaxy instances much more flexibility in choosing to provide only those specific tools in which their users are interested. Read more... <http://wiki.g2.bx.psu.edu/Tool%20Shed#Migrating_tools_from_the_Galaxy_distr…> Release Highlights: * Galaxy toolsXML configuration <http://wiki.g2.bx.psu.edu/Tool%20Shed#XML_configuration_files_used_to_popul…>, managing tool panel layout <http://wiki.g2.bx.psu.edu/Tool%20Shed#Managing_the_layout_of_your_Galaxy_to…>, and Galaxy tool versions <http://wiki.g2.bx.psu.edu/Tool%20Shed#Galaxy_Tool_Versions>. * RNA-Seq Tools: Added CuffMerge <http://cufflinks.cbcb.umd.edu/>version 1.0.0, Updated TopHat <http://tophat.cbcb.umd.edu/>default parameters * External Display Apps: Added *RViewer* <http://rviewer.lbl.gov/rviewer>, Updated *IGV * <http://www.broadinstitute.org/igv/> * Visualize *ENCODE* <http://genome.ucsc.edu/ENCODE> "peak" datatype tracks in the Galaxy Track Browser(aka Trackster) * Multiple Workflowupdates including enhancements to/input dataset options, display modes, and sharing * *CloudMan* <http://wiki.g2.bx.psu.edu/Admin/Cloud> now offers /preliminary support for OpenNebula cloud type <http://bitbucket.org/galaxy/cloudman/src/tip/cm/clouds/opennebula.py>/ and a larger /default tools volume/ 10GB vs old 2GB). *Need help with a local instance? * Installation and Admin Instructions: http://getgalaxy.org Searchwith our custom google tools: * All Galaxy mailings lists <http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching>for prior Q & A * Information about deploying, developing, customizing, and administering <http://galaxyproject.org/search/getgalaxy> Galaxy * Information about using <http://galaxyproject.org/search/usegalaxy> Galaxy Consider *subscribing to the galaxy-dev* <http://wiki.g2.bx.psu.edu/Mailing%20Lists#Subscribing_and_Unsubscribing> mailing list Thanks for using Galaxy, The Galaxy team ------- http://usegalaxy.org http://getgalaxy.org http://galaxyproject.org http://galaxyproject.org/wiki

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March 12, 2012 Galaxy Development News Brief
by Jennifer Jackson 12 Mar '12

12 Mar '12

Dear Galaxy Community, The latest *Galaxy distribution* has been released: March 12, 2012 Galaxy Development News Brief <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_03_12>. *Mercurial pull:* new: % hg clone http://www.bx.psu.edu/hg/galaxygalaxy-dist upgrade: % hg pull -u -r 40f1816d6857 *Important Upcoming Changes to Tool Organization*: The _*Emboss tools and Emboss datatypes**will be eliminated from the Galaxy distribution in the NEXT release*_. Other tools currently in the Galaxy distribution will be eliminated in following releases. Those hosting local Galaxy instances should read this revised*"Migrating tools" <http://wiki.g2.bx.psu.edu/Tool%20Shed#XML_configuration_files_used_to_popul…>*<http://wiki.g2.bx.psu.edu/Tool%20Shed#XML_configuration_files_used_to_popul…>section of the Galaxy tool shed wiki to understand how this process will work: Migrating tools from the Galaxy distribution to the Galaxy Main tool shed <http://wiki.g2.bx.psu.edu/Tool%20Shed#XML_configuration_files_used_to_popul…> (Summary) In 2012, the Galaxy development team will begin the process of migrating the tools that are currently available in the Galaxy distribution to the Galaxy Main tool shed. This will enable those that host local Galaxy instances much more flexibility in choosing to provide only those specific tools in which their users are interested. Read more... <http://wiki.g2.bx.psu.edu/Tool%20Shed#XML_configuration_files_used_to_popul…> *Release Highlights*: * *Galaxy tools* XML configuration <http://wiki.g2.bx.psu.edu/Tool%20Shed#XML_configuration_files_used_to_popul…>, managing tool panel layout <http://wiki.g2.bx.psu.edu/Tool%20Shed#Managing_the_layout_of_your_Galaxy_to…>, and Galaxy tool versions <http://wiki.g2.bx.psu.edu/Tool%20Shed#Galaxy_Tool_Versions>. * *RNA-Seq Tools*: Added *CuffMerge* <http://cufflinks.cbcb.umd.edu/> version 1.0.0, Updated *TopHat* <http://tophat.cbcb.umd.edu/> default parameters * *External Display Apps*: Added *RViewer <http://rviewer.lbl.gov/rviewer>*, Updated *IGV <http://www.broadinstitute.org/igv/>* * *Visualize *ENCODE <http://genome.ucsc.edu/ENCODE/> "peak" datatype tracks in the *Galaxy Track Browser* (aka Trackster) * Multiple *Workflow* updates including enhancements to/input dataset options, display modes, and sharing/. * *CloudMan <http://wiki.g2.bx.psu.edu/Admin/Cloud>* now offers /preliminary support for OpenNebula cloud type <https://bitbucket.org/galaxy/cloudman/src/tip/cm/clouds/opennebula.py>/ and a /larger default tools volume /(10GB vs old 2GB). *Need help with a local instance? * *Installation and Admin Instructions*: http://getgalaxy.org *Search* with our custom google tools: * All Galaxy mailings lists <http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching> for prior Q & A * Information about deploying, developing, customizing, and administering Galax <http://galaxyproject.org/search/getgalaxy>y * Information about using Galaxy <http://galaxyproject.org/search/usegalaxy> *Consider****subscribing to the galaxy-dev *mailing list <http://wiki.g2.bx.psu.edu/Mailing%20Lists#Subscribing_and_Unsubscribing> Thanks for using Galaxy, The Galaxy team ------- http://usegalaxy.org http://getgalaxy.org http://galaxyproject.org http://galaxyproject.org/wiki

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Re: [galaxy-dev] [galaxy-user] Metagenomics
by Peter Cock 12 Mar '12

12 Mar '12

On Mon, Mar 12, 2012 at 6:28 PM, John Major <john.e.major.jr(a)gmail.com> wrote: > A small warning re-the current cloud-Blast+ config. > > To properly use the metagenomic tools, if you use the blast+ galaxy tool, > make sure to export in blast.XML, then you'll need a script to parse out the > readID and the Hit_def (as the hit ID). It appears that the 'Hit_def' field > contains the correct key to the taxonomy database. Specifically, the > Hit_def field is in the format #_#, where the 'gi' id is the first #. The > tabular (normal and extended) data does not contain this info. > > I noticed this after attempting to use the tabular data, and using a trimmed > col[1] (supposed to be hit seqID), but my results always came back as a > ranked list of the most sequenced genomes in nt.... basically keying in > randomly. > > j Hi John, Can you expand on that with a specific example (ideally on the galaxy-dev list, CC'd, since BLAST+ isn't event available on the public galaxy)? Also which version of BLAST+ are you using since I recall some changes to the tabular output IDs prior to 2.2.25 (which is what the wrappers were tested on, I've not tried 2.2.26 yet). Thanks, Peter

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Error when installing toolshed tool
by Anthonius deBoer 12 Mar '12

12 Mar '12

I'm getting this error when I try to install the NGS Java toolkit toolshed... Version information for the tools included in the java_genomics_toolkit repository is missing. Reset all of this repository's metadata in the tool shed, then set the installed tool versions from the installed repository's Repository Actions menu. Installed 1 repository and all tools were loaded into tool panel section NGS: Toolkit: Installed repositories: java_genomics_toolkit. Any idea why the version number stuff is not correctly inserted in the database? Bug? Thanks Thon

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Re: [galaxy-dev] bacterial genomes missing?
by Jennifer Jackson 12 Mar '12

12 Mar '12

Hi Alex, This particular issue didn't involve a correction to any code, just to the processing (our mistake). However, we do frequently make changes to code, mostly as general improvements but also in response to bugs found. These are available in the galaxy-central repository immediately, go to the public server at the next update (timing can vary), and can be tracked in the changelog at bitbucket here: http://bitbucket.org/galaxy/galaxy-central/changesets Hopefully this helps! Best, Jen Galaxy team On 3/12/12 9:50 AM, Oleksandr Moskalenko wrote: > > On Mar 10, 2012, at 12:14 AM, Jennifer Jackson wrote: > >> Hello, >> >> Yes, this was noticed but it took a few days to track down and correct the problem. As of this afternoon, the genome builds list was restored to the original content plus a few new additions. >> >> If you notice any genome missing that was previously present, we would definitely like to know. >> >> Very sorry for the inconvenience! >> >> Best, >> >> Jen >> Galaxy team > > > Hi Jen, > > I keep wondering from time to time how wonderful it would be to have the Public Galaxy changelog somewhere people like myself who are running local Galaxy instances could reach to avoid re-inventing the bicycle and spending time figuring out the same problems the illustrious Galaxy team already successfully solved. Has anything like that been ever discussed? > > Cheers, > > Alex -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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Bug in "Export to File"
by Jerzy Dyczkowski 12 Mar '12

12 Mar '12

Hello, I am new here. I am running Galaxy at http://main.g2.bx.psu.edu/ using Mozilla Firefox 10.0.1 I try using "Export to File" tool on different files and workflows, and every time the report is: "Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) " I don't know what to do, and I cannot find the option "turn debug on". best regards, :) Jerzy

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Bugs in FASTQ Quality Trimmer (version 1.0.0) on-line window
by "Штратникова Виктория" 12 Mar '12

12 Mar '12

1. Where you are using Galaxy (Main, local or cloud instance, etc.). Site http://main.g2.bx.psu.edu/, on-line. # The date/time the bug was detected 11-12.03.2012 # Exact steps to reproduce the issue FASTQ Quality Trimmer (version 1.0.0). No posiibility to upload fastq file for treat. Pulldone for uploading does not work. Used browsers -Mozilla Firefox 3.6.6 and IE. OS - Linux Mandiva. # What troubleshooting steps (if any) you have tested out Using of Windows and Debian browsers. Uploading fastq file to Galaxy witn another application and using FASTQ Groomer on uploading file. # Request for private communication/discussion (as needed) If problem on my side. -- Shratnikova Viktoriya, s.r. CIT BAS RAS, vtosha(a)itcbas.ru, 8-499-132-56-94, 8-903-524-57-30.

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bacterial genomes missing?
by Langhorst, Brad 10 Mar '12

10 Mar '12

It seems that the bacterial genomes that used to come from ucsc via update_ucsc.sh are now gone... Has anybody else observed this? Fixed it? Brad -- Brad Langhorst langhorst(a)neb.com<mailto:langhorst@neb.com> 978-380-7564

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galaxy-dev March 2012