Hi, Sofie - yes, that's right - third party tools are not 'bundled' with our source distribution and must be obtained from the tool authors and installed where they are needed - we just provide wrappers to make them work inside Galaxy. Same goes for the large genomic data and indexes needed by some tools such as bwa.
The Galaxy distribution includes code for some of the inbuilt tools like the fastq groomer, but most of the distribution tool wrappers rely on popular third party packages such as cufflinks, bwa, FastQC, R/BioC packages and so on. There's a list of third party dependencies at http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies - they have to be available on the computational nodes for Galaxy jobs requiring them to run.
On Tue, Oct 4, 2011 at 10:50 AM, Sofia Robb sofia2341@gmail.com wrote:
I have installed the local galaxy distribution on my MacBook Pro Mac OS X Version 10.7.1 using hg as described on get galaxy.org hg clone https://bitbucket.org/galaxy/galaxy-dist/ the run.sh script runs, and i am able to open localhost:8080 and i am able to upload data files. I have not tested many applications but it seems that the applications are not installed, or at least bwa and bowtie are not installed from the error I receive. An error occurred running this job: Error indexing reference sequence /bin/sh: bowtie-build: command not found -and- An error occurred running this job: Could not determine BWA version Error indexing reference sequence. /bin/sh: bwa: command not found Are the applications not installed? I searched for them but could not find them within /galaxy-dist (find /galaxy-dist -name "*bwa*" ). I find wrappers but no apps. Where should they be located? Thanks, Sofia ___________________________________________________________ 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: