Michael,
(I'm CCing galaxy-dev because this has to do with a local installation, not our public server.)
There is a wiki page discussing how to install several of the NGS tools, including Bowtie: https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup . Note that this page is slightly out-of-date regarding working with the loc files. We have introduced data tables since the page was written and it hasn't yet been updated. There is a basic page on data tables: https://bitbucket.org/galaxy/galaxy-central/wiki/DataTables. TopHat and Cufflinks are not detailed on that page, but the process should be very similar to Bowtie.
Let us know if you have further questions.
Regards, Kelly
On Dec 16, 2010, at 4:12 PM, Weiner, Michael wrote:
I have been asked by a research fellow to setup a local instance of Galaxy. In addition, he would like the latest versions of packages like bowtie, cufflinks, tophat, etc to be installed and available through that instance. Being a newbie to Galaxy, and just a systems administrator responsible for building this environment, I am unsure how exactly to go about doing this.
I have an instance running, and worked my way through the fastx- toolkit installation/update but I cannot seem to find a similar how-to for the other packages. Could someone point me in the right direction please?
Thank you in advance Michael Weiner UNIX Systems Administrator Lerner Research Institute Cleveland Clinic
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