Here's some specific information about what the PATH variable is for UNIX
systems and how to set it: http://kb.iu.edu/data/acar.html
Many folks do the following so that you only need to add a single directory to
(a) install all tools in one directory;
(b) create a "bin" directory in the tools directory;
(c) use symbolic linking ( http://kb.iu.edu/data/abbe.html ) to link tool
executables into the bin directory, e.g., from the bin directory:
ln -f -s ../tophat-2.0.8/tophat tophat2
(d) add the bin directory to your path.
On Jun 20, 2013, at 3:34 PM, Jennifer Jackson wrote:
> Hi Elwood,
> It sounds like you are getting closer, and that the instructions a few days
> ago from Jeremy are helping:
> 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:
> And, in #3, you say that you have started to follow the instructions in this
> Jeremy also sent you the links about how to obtain and set up the genomes and
> 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.
> 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
>> 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
>> but my minimal knowledge of unix commands and tricks has me stymied
>> 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.
>> Elwood Linney
>> Please keep all replies on the list by using "reply all"
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> Jennifer Hillman-Jackson
> Galaxy Support and Training
> 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:
> To search Galaxy mailing lists use the unified search at:
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:
To search Galaxy mailing lists use the unified search at: