CummeRbund on Galaxy
by Ganote, Carrie L
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
7 years, 1 month
(no subject)
by Ianiri, Giuseppe
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
7 years, 1 month
Galaxy User List Being Retired on June 6, 2014.
by Dave Clements
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
--
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7 years, 1 month
