Create a working .travis.yml

[mmterpstra]

Please consider updating this .travis.yml by forking this branch and then squash commits and merge into sandbox.

This will also help with my issue below:
Our cluster the install is quite a pain because new automake/autconf features.
I could spend a day or two trying to fix the possible issues or create a good starting point to fix this using travis. Me of course did the latter and this is what I got.
problems:

• no documentation needing gnuplot/R/etc...
• htslib complains about config.status: error: cannot find input file: 'htslib/Makefile.in' and htslib complains about missing HMAC library -> a (rm -r htslib && git clone https://github.com/samtools/htslib.git && cd htslib && autoheader && autoconf && ./configure && make && make install) fixes both though...
• then it crashes with a lot of undefined references which might be due to our build system....

[ghuls]

I also had problems compiling apigenome.

The instructions above helped a lot.

I only had a small problem. HTSlib is now version 1.4 and requires also libbzip2 and liblzma (and libcurl), so I guess the following line should be changed in src/Makefile.am:

bcfast_LDADD = ../htslib/libhts.a -lpthread

cramore_LDADD = ../htslib/libhts.a -lpthread -lgomp

bcfast_LDADD = ../htslib/libhts.a -lpthread -lbz2 -llzma -lcurl

cramore_LDADD = ../htslib/libhts.a -lpthread -lgomp -lbz2 -llzma -lcurl

[mmterpstra]

Ok added at mmterpstra-patch-travis although it still won't build on travis:
https://travis-ci.org/mmterpstra/apigenome/builds

[ghuls]

I think libzip-dev is not needed.

Like mentioned in #1 I still had to copy htslib/Makefile to htslib/Makefile.im.

I also ran:

autoheader
autoreconf
./configure

# For some reason ./configure generates a libtool in the current dir from Debian which is incompatible with the autoconf version I have installed.
cp /usr/bin/libtool libtool

make

[mmterpstra]

after some fumbeling around now the .travis.yml works. Good luck porting to yer system. Also see #3 for the code