The computational pipeline is contained in a docker image. We strongly recommend using it for your analyses. Follow the official docs for: MacOS, Linux, or Windows.
Next, choose one of the following:
A. Pull from DockerHub
docker pull octant/octopus
B. Build it yourself
git clone https://github.com/octantbio/octopus.git
cd octopus
docker build .
It is possible to run OCTOPUS without docker, but not recommended. If you insist, see the dockerfile for help.
Clone this repository
git clone https://github.com/octantbio/octopus.git
For optimal performance, we recommend deploying on a machine with at least 32 GB of RAM and 16 cores. We use GNU Parallel to distribute tasks where possible, and empirically, the RAM requirements seems to scale with the number of cores (e.g. 64 GB of RAM for 64 cores). The compute times (for 384 wells) scale asymptotically, suggesting a potential disk bottleneck.
64 cores -> 64 GB RAM -> 13 Mins
32 cores -> 32 GB RAM -> 15 Mins
24 cores -> 24 GB RAM -> 20 Mins
16 cores -> 16 GB RAM -> 25 Mins
8 cores -> 8 GB RAM -> 45 Mins
We performed all trials on two Intel(R) Xeon(R) Gold 6130 CPUs @ 2.10GHz, limiting the cores through the docker --cpuset-cpus=N flag, and estimated peak RAM usage with /bin/free.