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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
989 stars 354 forks source link

symlink issue during installation #278

Closed roryk closed 10 years ago

roryk commented 10 years ago

via twitter:

genetics_blog: @RoryKirchner @chapmanb @fiamh @winhide basically, data/tool dirs are symlinks, resolve differently depending on front-end vs compute nodes

Hm, this is a tricky one-- there are a couple of places in the installation that end up resolving the symlinks. Brad will have much more of an intuition regarding whether or not changing that behavior will be a huge mess.

As a workaround-- do the compute nodes all point to the same place? If so, is it possible to do the installation on the compute node, and then submit your bcbio_nextgen runs to the compute node so you aren't ever running anything on the head node?

stephenturner commented 10 years ago

The workaround may work, but I've had trouble with compiling on the compute nodes, some env thing I've never figured out. I'm installing now in stable mount.

roryk commented 10 years ago

Great, that should work as well. Let us know if you run into any more troubles. Thanks for writing your blog, you have connected me to tons of resources I would have missed otherwise.

stephenturner commented 10 years ago

Doing this seems to have worked. Running some tests now!