Re: [galaxy-dev] simplest way to connect RNAseq tools for a local Galaxy instance

2013-06-20 Thread Jeremy Goecks
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 your path: (a) install all tools in one directory; (b) create a "bin" directory in

Re: [galaxy-dev] simplest way to connect RNAseq tools for a local Galaxy instance

2013-06-20 Thread Jennifer Jackson
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 inst

Re: [galaxy-dev] simplest way to connect RNAseq tools for a local Galaxy instance

2013-06-20 Thread Nicholas Kline
s.bx.psu.edu > Subject: [galaxy-dev] simplest way to connect RNAseq tools for a local > Galaxy instance > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > I have: > 1) downloaded the Galaxy framework into a Mac Pro desktop with 64gb

[galaxy-dev] simplest way to connect RNAseq tools for a local Galaxy instance

2013-06-20 Thread Elwood Linney
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 gott