This pull request adds a starting setup for continuous integration testing on Travis CI. You may have to make an account there and give access to your GitHub repository. The current setup takes about 18 minutes.
This pull request includes:
a .travis.yml file with settings for building and testing on the Travis server
a NanoSatellite.yml file specifying the environment for conda
an install.sh script installing the tool and dependencies using conda and R devtools. It might be better if this uses the NanoSatellite.yml file to keep the main environment clean for users, but that's currently not the case.
a test.sh script executing most of the bash and Rscript scripts of the package on data from NA19240 (Spanning_read_extractor.sh is not tested as this requires a bam file) (this could use your review)
an example.R script containing code for visualization of the results (as demonstrated in the README) (this could use your review)
a directory containing just 4 fast5 files for testing purposes (too limited?)
I believe you can "squash and merge" to turn my commits in one commit message for this pull request and avoid making a mess out of your commit history.
This pull request adds a starting setup for continuous integration testing on Travis CI. You may have to make an account there and give access to your GitHub repository. The current setup takes about 18 minutes.
This pull request includes:
Spanning_read_extractor.sh
is not tested as this requires a bam file) (this could use your review)