biokepi Which tools do we expect to find on the cluster by default?

Java
gcc
cmake > 3.1
python
...?

May 13 '16 18:05 ihodes

Food for thought: might be nice to have some dummy workflow nodes for these guys so that we can make our tools explicitly depend on them. If we change our minds, this might help refactoring/bookkeeping easier.

May 13 '16 18:05 armish

Also since I'm testing #266 on gcloud with Ubuntu, here are my notes (I get everything in biokepi except GATK/mutect installed; but didn't run anything end-to-end):

Biokepi ./all_downloads test requires:

sudo apt-get install --yes openjdk-9-jre cmake r-base

And razers3 does not compile on a “small” instance:

sudo fallocate -l 2G /swapfile
sudo chmod 600 /swapfile
sudo mkswap /swapfile
sudo swapon /swapfile

Just check it worked:

free -h

             total        used        free      shared  buff/cache   available
Mem:           1.7G         83M        1.5G         20M        112M        1.5G
Swap:          2.0G          0B        2.0G

May 13 '16 18:05 smondet

This is relevant also: https://github.com/hammerlab/biokepi/issues/283

Jun 17 '16 15:06 smondet

Also relevant:

https://github.com/hammerlab/stratocumulus/blob/master/src/lib/deploy.ml#L223
https://github.com/hammerlab/stratocumulus/blob/master/src/lib/deploy.ml#L122

I've run a bunch of the tools on those Xenial GCloud boxes.

Jun 17 '16 16:06 smondet