I've been running some RNA seq data through the Cufflinks tools on Galaxy this week. I noticed today that some of my post processing didn't work right. After digging deeper, I see that some of my samples ran through cufflinks 1.0.3 and others say 1.3.0. Did Cufflinks get updated this week? Is there a place to see when these updates take place? The twitter feed mentions other tools and the Wiki doesn't list these as being updated.
I've asked some questions about sharing an instance but it doesn't
seem to be working the way I'm expecting (Unfortunately I'm also new
to Amazon EC2/S3 so that may be part of my difficulty). I'm thinking
maybe if I can explain what I'm trying to do, you guys could tell me
the best way to do it:
My End Goal:
So I want to install a bioinformatics program* (and it's dependencies
e.g., R, samtools, biopython, etc) that will use SGE provided by
Then once everything is configured and installed, I want to share it
with other researchers.
I'm envisioning them launching Cloudman via
http://biocloudcentral.herokuapp.com, having some method to get at my
customizations, loading their own data via SCP and then running it.
What I've Tried So Far:
I created an instance of CloudMan,
I chose the data cluster option on the first dialog.
Then I ssh'd in and installed stuff on /mnt/galaxyData
Then I clicked the share icon on the cloudman front page.
(But when I look in S3 I don't think I'm seeing the programs I
installed, and I'm not sure how my /mnt/galaxyData volume can be
shared with the sharestring.)
Let me know your thoughts.
Thanks again for the help,
* I'm also hoping for an easy way to update the program while keeping it shared.
When I first go to my cloudman page at <public dns>/cloud I get a
dialog asking for some settings.
What does the Galaxy Cluster choice do? What does the Data Cluster
choice do? Why can't I choose both? How much space should I
Text of dialog:
Galaxy Cluster: Galaxy application, available tools, reference
datasets, SGE job manager, and a data volume. Specify the initial
storage size (in Gigabytes):
Share-an-Instance Cluster: derive your cluster form someone else's
cluster. Specify the provided cluster share-string (for example,
Data Cluster: a persistent data volume and SGE. Specify the initial
storage size (in Gigabytes):
Test Cluster: SGE only. No persistent storage is created.
I was wondering if anyone had any experience using the program DIAL to call snps without a reference genome.
Jeremy C. Andersen
Department of Environmental Science,
Policy & Management
Office: Room 310 Wellman Hall
We're a bit confused about exactly how the adaptor clipping tool works. Is there some documentation that describes how it does the clipping? In the clipping example given on the Galaxy page for "Clip adapter sequences" (the adaptor is CTGTAGGCACCATCATTATTTATATAA ):
* How large a substring of the sequence must the adaptor be in order for it to be clipped? E.g., if the sequence is ATGGACTCTG, it seems to clip the terminal CTG, but it doesn't clip if CTG appears somewhere in the middle of a sequence.
* Does it clip if, say, the middle part of the adaptor appears somewhere in the middle of a sequence, and if so, how long must it be before it clips?
Francisc Raul Kantor