SpliceMap

A fork of Standford's SpliceMap -- Copyright (c) 2010 Kin Fai Au and John Chong Mu.

How to run from the docker

Testing the command:

The docker image comes with a small example data. You can access this and run the command on the example which will create an output folder and a temp folder in your current directory.

$ docker run -v $(pwd)/output:/Source/SpliceMap/example/output \
             -v $(pwd)/temp:/Source/SpliceMap/example/temp \
             -w /Source/SpliceMap/example \
             vacation/splicemap runSpliceMap run.cfg

Running the command on your data:

Construct a run.cfg pointing to required files within your working directory such as this one:

https://github.com/jason-weirather/SpliceMap/tree/master/example

And from within your working directory you can call splicemap on your run.cfg file like so:

$ docker run -v $(pwd):/home vacation/splicemap runSpliceMap run.cfg