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:
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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