transferring Trapnell et al programs into a one user instance of Galaxy

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transferring Trapnell et al programs into a one user instance of Galaxy

Elwood Linney
Hello again,
I guess I now realize why there is so much traffic on the user list about tools, and I also can guess that while the online directions for dealing with them are written well for those individuals familiar with administration a  server or doing full time bioinformatics, but there are some of us computer numbskulls  that need something like a Galaxy transfer booklet for computer idiots (biologists) to transfer what we want into a single user or single lab setup.
I am hoping there is someone out there like myself who worked through the problem of transferring the Trapnell et al series of programs into a Mac Pro desktop, namely
NGS: RNA Analysis
1)  Tophat for Illumina
tophat (1.3.3-1.4.0) with bowtie + bowtie indexes
2)  Cufflinks
cufflinks (1.3.0-2.1.1)
3)  Cuffcompare
cufflinks (1.3.0-2.1.1)
4)  Cuffmerge
cuffmerge (1.3.0-2.1.1)
5)  Cuffdiff
cuffdiff (2.1.0-2.1.1)
I have transferred the galaxy framework in a work/galaxy-dist   pathway unto a solid state drive of a 64gb ram mac that has 3 other 2tb drives and have gotten some valuable advice for transferring large datasets from the same computer via admin.  For the next year at least my needs with be just the RNA analysis tools above.
Any help will be greatly appreciated.
My intention here is remove my contribution to the traffic on the online Galaxy, so some people should consider it a worthy cause

Sincerely,
Elwood Linney
Professor of Molecular Genetics and Microbiology
Duke University Medical Cener


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Re: transferring Trapnell et al programs into a one user instance of Galaxy

Jeremy Goecks
Elwood,

It's not clear what steps you're having problems with, so it's difficult to offer help. Here's the outline that I use to RNA-seq running with Galaxy:

*download Samtools, Bowtie2, Tophat2, and the Cufflinks tool suite and add them to my galaxy user's path;
*download the iGenomes data package for your genomes:


*configure Galaxy to point to particular data files in iGenomes—specifically, add entries to bowtie2_indices.loc and sam_fa_indices.loc

This page will help with this last step: <a href="http://wiki.galaxyproject.org/Admin/NGS Local Setup">http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

Let us know if you run into problems.

Best,
J.


On Jun 14, 2013, at 10:31 AM, Elwood Linney wrote:

Hello again,
I guess I now realize why there is so much traffic on the user list about tools, and I also can guess that while the online directions for dealing with them are written well for those individuals familiar with administration a  server or doing full time bioinformatics, but there are some of us computer numbskulls  that need something like a Galaxy transfer booklet for computer idiots (biologists) to transfer what we want into a single user or single lab setup.
I am hoping there is someone out there like myself who worked through the problem of transferring the Trapnell et al series of programs into a Mac Pro desktop, namely
NGS: RNA Analysis
1)  Tophat for Illumina
tophat (1.3.3-1.4.0) with bowtie + bowtie indexes
2)  Cufflinks
cufflinks (1.3.0-2.1.1)
3)  Cuffcompare
cufflinks (1.3.0-2.1.1)
4)  Cuffmerge
cuffmerge (1.3.0-2.1.1)
5)  Cuffdiff
cuffdiff (2.1.0-2.1.1)
I have transferred the galaxy framework in a work/galaxy-dist   pathway unto a solid state drive of a 64gb ram mac that has 3 other 2tb drives and have gotten some valuable advice for transferring large datasets from the same computer via admin.  For the next year at least my needs with be just the RNA analysis tools above.
Any help will be greatly appreciated.
My intention here is remove my contribution to the traffic on the online Galaxy, so some people should consider it a worthy cause

Sincerely,
Elwood Linney
Professor of Molecular Genetics and Microbiology
Duke University Medical Cener

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/