Basic TravisCI configuration file to build chopBAI

[peterjc]

This pull request adds a basic .travis.yml file based on https://github.com/samtools/samtools/blob/develop/.travis.yml to compile chopBAI on both Linux and Mac.

This would address #5, results of this build here: https://travis-ci.org/peterjc/chopBAI/builds/91841166 (Initial failure visible in TravisCI build history from #7 resolved)

You would need to log into https://travis-ci.org/ as DecodeGenetics using your GitHub account, then enable testing for https://github.com/DecodeGenetics/chopBAI/ before this would be available from your repository.

[pmelsted]

The Makefile now has a make test but it depends on samtools being in the path. Do you know if it's feasible to install the dependency before running the test?

[peterjc]

Yes. The simplest route would be to add sudo apt-get install samtools to the .travis.yml recipe, but that has two downsides. First, using sudo excludes the preferred TravsisCI infrastructure https://docs.travis-ci.com/user/workers/container-based-infrastructure/ (note to self, I should update my pull request to do that, and make the same proposal to samtools [Update: Done, see https://github.com/samtools/samtools/pull/492 for samtools]). Second, it will likely get a very old version of samtools.

Alternatively one can download and compile samtools within the .travis.yml file, or for least overhead download a pre-compiled version (e.g. something like the collection from the Galaxy project used for their dependencies: https://depot.galaxyproject.org/package/linux/x86_64/samtools/ ), and put it on the local $PATH.

Which version of samtools do you need/recommend? I can try the later.

[pmelsted]

The only thing we need is the samtools view command so any old version will do. I agree with that it's nicer to use the container based one.

[peterjc]

Following the samtools example, we can get TravisCI to test under both gcc and clang on both 64 bit Linux and Mac OS X. The later means rules out downloading just one pre-compiled binary, hence the if statements in this revised version of the .travis.yml file where I download samtools.

Working now after a few false starts: https://travis-ci.org/peterjc/chopBAI/builds/92945368

[cmdcolin]

You can install certain apt packages from their whitelist under the container infrastructure. They have a "whitelist" of packages here https://github.com/travis-ci/apt-package-whitelist/blob/master/ubuntu-precise https://docs.travis-ci.com/user/apt/

Perhaps something like this might work

addons:
  apt:
    packages:
    - samtools

[peterjc]

Good point - I forgot I asked them to whitelist samtools a while back, travis-ci/travis-ci#3599

I'm not sure what would be best practise here to continue to test under Mac OS X though, I presume the apt packages for TravisCI only apply to the Linux build targets?