Hi Elwood,
It sounds like you are getting closer, and that the instructions a few
days ago from Jeremy are helping:
http://dev.list.galaxyproject.org/transferring-Trapnell-et-al-programs-into-a-one-user-instance-of-Galaxy-tc4660245.html#none
For each of these tools in #2, you will need to install them according
to the instructions that comes with them from the source. However, there
is one change I can mention. Symbolic links pointing from
bowtie->bowtie2 and tophat->tophat2 are likely to be present in the
default installation. You will want to remove those. Galaxy makes a
clear distinction between the versions of the tools.
So, you have added tool's as required following the instructions in this
wiki:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
And, in #3, you say that you have started to follow the instructions in
this wiki:
http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
Jeremy also sent you the links about how to obtain and set up the
genomes and indexes.
Some of this does require limited unix-command line actions and file
editing. The instructions are detailed, and some have command lines,
because not all, as the exact thing to type can vary. If the
line-command is entirely new, I wonder if there is someone locally with
unix experience at your site that you can get help from? This last part
should not take very long.
Best,
Jen
Galaxy team
On 6/20/13 8:45 AM, Elwood Linney wrote:
I have:
1) downloaded the Galaxy framework into a Mac Pro desktop with 64gb ram
2) downloaded Mac OS versions of Tophat2, Bowtie2, and the Cufflink
suite to the mac
3) have looked at the Galaxy wiki on connecting these
[http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies]
4) I have gotten some useful advice from Dannon Baker on how to
introduce my large datasets on the some computer into Galaxy through
Admin changing some permissions
but my minimal knowledge of unix commands and tricks has me stymied
Question:
If my primary purpose is to use this local instance for the analysis
of RNAseq data within my lab, what is the simplest way of connecting
the programs to the Galaxy framework?
While from reviewing info on the Galaxy website I am only guessing
that adding them to $PATH might be the easiest way for me to do this
(but I am not exactly sure what this means or specifically how I would
do it in my case). However, I do initiate the running of Galaxy by sh
run.sh on my terminal and visualizing things via my localhost port.
There is some indication from the wiki I found that this might not be
good for a system initiated by sh run.sh .
[http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies] under
"Local Jobs"
I would appreciate any specific advice on this.
Sincerely,
Elwood Linney
DUMC
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Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
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