I am testing out the process of setting up a local galaxy host - for analysis of clinical exome samples. Basic install is fine and runs ok. But I am having issues building local reference genomes.
I have trying to use the Bowtie Index builder (rev. 5515ee3559f0). This works fine for SacCer2, but when I attempt the build on hg19 it fails.
The builder does not return any apparent error messages. However, when I attempt to use the reference (hg19) in Bowtie2 it returns an error due to no index being present. When I check the tool_data file it appears that the files have not transferred from the working directory (the files appear to form correctly there during the builder run).
I am running on OSX, using SQLite. The computer is a 2012 Macbook Pro with 8Gb of ram and over 500Gb of hard drive space - so should be ok?
Has anyone encountered a similar problem and identified a solution?