Create a working .travis.yml
Opened this issue · 4 comments
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....
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
Ok added at mmterpstra-patch-travis although it still won't build on travis:
https://travis-ci.org/mmterpstra/apigenome/builds
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
after some fumbeling around now the .travis.yml works. Good luck porting to yer system. Also see #3 for the code