.travis.yml

---
language: perl
perl:
  - "5.26.0"
sudo: required

before_install:
## Install SSL
  - sudo apt-get update
  - sudo apt-get install libssl1.0.0 libssl-dev libcrypto++9 libcrypto++-dev
  - cd /lib/x86_64-linux-gnu
  - sudo ln -s libssl.so.1.0.0 libssl.so.10
  - sudo ln -s libcrypto.so.1.0.0 libcrypto.so.10
  - cd -

## Install conda
  - wget https://repo.anaconda.com/miniconda/Miniconda2-4.5.12-Linux-x86_64.sh -O miniconda.sh;
  - bash miniconda.sh -b -p $HOME/miniconda
  - source $HOME/miniconda/etc/profile.d/conda.sh
  - conda activate base
  - conda config --set always_yes yes --set changeps1 no
#  - conda update -q conda
  - conda info -a

## Download cpan libraries
## For some reason DB_File installation fails, it is not needed for the test
  - sed -i '/DB_File/d' ./definitions/cpanfile
  - cd definitions; cpanm --quiet --notest --installdeps .
  - cd -
## Set up for cpanm dependencies test
  - cpanm --notest Devel::Cover::Report::Coveralls

install:
## Test installation script and gather coverage information
  - PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl t/mip_install.test
## Generate rare disease installation script
  - PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl mip install rd_dna --bash_set_errexit --install emip epeddy eperl_5.26 epy3 etiddit --envn emip=mip_travis --snpg GRCh37.75 --skip gatk
## Install MIP rare disease
  - bash mip.sh
## Generate rna installation script
  - PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl mip install rd_rna --bash_set_errexit --install emip epy3 eperl5.26
## Install MIP rna
  - bash mip.sh

script:
## Test MIP rd_dna
  - conda activate mip_travis
  - cd /lib/x86_64-linux-gnu
  - sudo ln -s "$ROOTSYS"/lib/*so .
  - cd -
## Set-up test coverage for test directory "t"
  - PERL5OPT=-MDevel::Cover=-ignore,"^t/",+ignore,"prove",-coverage,statement,branch,condition,path,subroutine prove -lrs -j 9 t
## Set-up test coverage for mip_analyse_rd_dna.test
  - PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl t/mip_analyse_rd_dna.test
## Set-up test coverage for mip_analyse_vcf_rerun.test
  - PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl t/mip_analyse_rd_dna_vcf_rerun.test
## Set-up test coverage for mip_analyse_rna.test
  - conda activate MIP_rd_rna
  - PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl t/mip_analyse_rd_rna.test 
## Get some coverage statistics
  - cover

after_success:
## Generate report for coveralls
  - cover -report coveralls