Running RUFUS on a file system shared across machines

jandrewrfarrell / RUFUS

RUFUS k-mer based genomic variant detection

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Running RUFUS on a file system shared across machines #10

Open jbsysadmin opened 5 years ago

jbsysadmin commented 5 years ago

Is there a way to run RUFUS (runTest.sh, clean.sh, plus anything else a standard user would do) with directed output?

In this scenario, RUFUS lives on an NFS share. But things like runtime outputs would go to /tmp or some sandbox location. (Users aren't allowed to write to the NFS share holding such builds.)

Are there environment variables that could be set to define a master output area? In our setting, users can't just cd to RUFUS-1.0 or subdirectories with the expecation of write access.

jandrewrfarrell commented 5 years ago

I have been dealing with such situations so far by just soft linking the bams I want to use into a run directory. I create a directory in a place I write access, use "ln -s" to create soft links of the bams I want to use, and just run rufus normally. Will that work for you? At the moment RUFUS just appends its output files to the name of the -s file, I realize this could be an issue and RUFUS could use a separate out flag but I haven't added that yet.