June 2014 - galaxy-user - lists.galaxyproject.org

Galaxy-User has moved to Galaxy Biostar
by Dave Clements 06 Jun '14

06 Jun '14

Hello all, After 8+ years and more than 8100 posts, the Galaxy-User mailing list has been retired. But, don't worry, you can still get Galaxy user support at Galaxy Biostar (https://biostar.usegalaxy.org/) an online user support forum that has replaced this list. Past postings to this list are available at Galaxy Biostar. All existing archives of this list will also remain available. See the Galaxy Support page (https://wiki.galaxyproject.org/Support) and the Galaxy Mailing List page (https://wiki.galaxyproject.org/MailingLists) for all support options. Thanks for making Galaxy-User, and Galaxy Biostar, such great resources. See you online, Dave C and the Galaxy Team -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

1 0

CummeRbund on Galaxy
by Ganote, Carrie L 03 Jun '14

03 Jun '14

Hi list, Is the cummeRbund wrapper on Galaxy yet functional? I've got some replicates that I'm trying to test for a user on our local Galaxy, but I just can't get the program to behave. Using cuffdiff v2.2.0 604fa75232a2 cummeRbund version 0.0.7, 137aab1d9ac1 R 2.15.2 and 3.0.1 (tried both) Last galaxy-dist/stable changeset: 7a7985a007fb I ran cuffdiff like so: Transcripts 83: Cuffmerge on data 6, data 67, and others: merged transcripts Name control Add replicate 44: Tophat2 on data 1 and data 6: accepted_hits (ran as single-end fastq) Add replicate 54: Tophat2 on data 2 and data 6: accepted_hits (ran as single-end fastq) Name sample Add replicate 59: Tophat2 on data 3 and data 6: accepted_hits (ran as single-end fastq) Add replicate 64: Tophat2 on data 4 and data 6: accepted_hits (ran as single-end fastq) Library normalization method geometric Dispersion estimation method pooled False Discovery Rate 0.05 Min Alignment Count 10 Use multi-read correct No Perform Bias Correction No Include Read Group Datasets No Set Additional Parameters? (not recommended for paired-end reads) No Here's what I get when I run cummeRbund: (From Galaxy, with R 2.15.2) Creating database //path/job_working_directory/005/5051/galaxy_dataset_16602.dat Reading //path/dataset_files/009/dataset_9861.dat Checking samples table... Populating samples table... Writing genes table Reshaping geneData table Recasting Writing geneData table Reading //path/dataset_files/009/dataset_9861.dat Error in function (classes, fdef, mtable) : unable to find an inherited method for function 'make.db.names' for signature '"SQLiteConnection", "NULL"' Calls: readCufflinks ... make.db.names -> .valueClassTest -> is -> <Anonymous> Execution halted (From R interpreter on command line, R = 3.0.1) Reading //path/dataset_files/009/dataset_9842.dat Checking samples table... Populating samples table... Writing genes table Reshaping geneData table Recasting Writing geneData table Reading //path/dataset_files/009/dataset_9842.dat Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'make.db.names' for signature '"SQLiteConnection", "NULL"' In addition: Warning message: attributes are not identical across measure variables; they will be dropped I tried changing the group names in cuffdiff but no luck. No spaces or funny characters. Thanks for any insight, Carrie Ganote

3 2

June 2, 2014 Galaxy Distribution
by Jennifer Jackson 02 Jun '14

02 Jun '14

June 2, 2014 Galaxy Distribution <http://wiki.galaxyproject.org/News/2014_06_02_Galaxy_Distribution> *News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2014_06_02>**Highlights:* * Dataset Collections introduced * Changes to database build (dbkey) organization * Enhancements to Tool configuration and Workflow options * Trackster, User Interface, and Admin panel upgrades * Significant updates to Admin and Job functionality * Tool Shed repository and API additions * Data updates plus new Security features and Bug fixes * new*: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable *upgrade*: $ hg pull $ hg update latest_2014.06.02 getgalaxy.org <http://wiki.galaxyproject.org/Admin/Get%20Galaxy> galaxy-dist.readthedocs.org <http://galaxy-dist.readthedocs.org/> bitbucket.org/galaxy/galaxy-dist <http://bitbucket.org/galaxy/galaxy-dist>* * /Thanks for using Galaxy!/ The Galaxy Team <http://wiki.galaxyproject.org/GalaxyTeam>

1 0

(no subject)
by Ianiri, Giuseppe 02 Jun '14

02 Jun '14

Hi, I uploaded some file that resulted to be too big and my history showed that that was not more space available. Now I deleted few file, and I should have 80 GB available, but my history shows still that I have no more space available for analysis. Can anyone from the Galaxy team check this for me? Giuseppe

2 1

Galaxy User List Being Retired on June 6, 2014.
by Dave Clements 02 Jun '14

02 Jun '14

Hello all, In case you didn't see this it the June Galaxy Newsletter <http://bit.ly/SX3MuS> that went out today: Galaxy-User Being Retired June 6 [image: Galaxy Biostar] <https://biostar.usegalaxy.org/> Join the conversation! Learn how here <https://wiki.galaxyproject.org/Support/Biostar>. The *Galaxy Biostar <https://biostar.usegalaxy.org/>* online forum was launched April 23 as a replacement for the Galaxy-User mailing list <https://wiki.galaxyproject.org/MailingLists>. During the past 5 weeks, Galaxy Biostar has been wildly successful with over 125 active threads, *more than 5 times the number of active threads on Galaxy-user in the 5 weeks before the switch.* Galaxy-User has remained open during the transition, but now it's time to retire it. All new posting to Galaxy-User will be stopped on Friday, June 6, *some 101 months, and 8,100 postings* after it was launched. All those postings will remain available both in Galaxy Biostar (where they have been imported), and in the online list archives <http://user.list.galaxyproject.org/>. Thanks for making Galaxy Biostar, and Galaxy-User before it, such a great resource. Thanks again, Dave C -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

2 1