.travis.yml

# See the NOTICE file distributed with this work for additional information
# regarding copyright ownership.

# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at

#     http://www.apache.org/licenses/LICENSE-2.0

# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

language: python

os: linux

python:
    - "2.7"
    - "3.6"

cache:
    directories:
        - $HOME/.cache/pip
        - ${HOME}/lib

before_cache:
    - rm -f $HOME/.cache/pip/log/debug.log

env:
    matrix:
        - TESTENV=docs
        - TESTENV=pylint
        - TESTENV=code
        - TESTENV=wgbs_code_1
        - TESTENV=wgbs_code_2

addons:
    apt:
        packages:
            #system environment
            - make
            - python-dev
            - build-essential
            - libssl-dev
            - zlib1g-dev
            - libbz2-dev
            - libreadline-dev
            - libsqlite3-dev
            - libtiff5-dev
            - libjpeg8-dev
            - libfreetype6-dev
            - liblcms2-dev
            - libwebp-dev
            - tcl8.6-dev
            - tk8.6-dev
            - python-tk
            - wget
            - curl
            - llvm
            - libncurses5-dev
            - libncursesw5-dev
            - xz-utils
            - tk-dev
            - mcl
            - libgtk2.0-dev
            - libcurl4-gnutls-dev
            - unzip
            - liblzma-dev
            - libtool
            - pigz
            - tree
            - libblas-dev
            - liblapack-dev

# env:
#   - COVERALLS=false

before_install:
    - pwd
    - ls /usr/lib/
    - mkdir -p ${HOME}/bin
    - mkdir -p ${HOME}/lib
    - mkdir -p ${HOME}/code
    - mkdir -p ${HOME}/R
    - lsb_release -a

    # Install the latest version of R
    - sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
    - echo "deb http://cran.r-project.org/bin/linux/ubuntu trusty/" | sudo tee -a /etc/apt/sources.list
    - sudo apt-get update -qq

    - cd ${HOME}/build/Multiscale-Genomics/mg-process-fastq
    - sudo chmod +x scripts/travis/includeMAC2.sh
    - sudo chmod +x scripts/travis/includeTADbit.sh
    - sudo chmod +x scripts/travis/install_wgbs_code.sh

    - if [[ "$TESTENV" == "code" ]]; then sudo apt-get install r-base-core; fi
    - if [[ "$TESTENV" == "code" ]]; then sudo apt-get install python-rpy2; fi
    - if [[ "$TESTENV" == "code" ]]; then sudo ./scripts/travis/install_code_test_dependencies.sh; fi
    - if [[ "$TESTENV" == "code" ]]; then pip install Cython; fi
    - if [[ "$TESTENV" == "code" ]]; then ./scripts/travis/includeMAC2.sh; fi
    - if [[ "$TESTENV" == "code" ]]; then ./scripts/travis/includeTADbit.sh; fi
    - if [[ "$TESTENV" == "wgbs_code_1" ]]; then sudo ./scripts/travis/install_wgbs_code.sh; fi
    - if [[ "$TESTENV" == "wgbs_code_2" ]]; then sudo ./scripts/travis/install_wgbs_code.sh; fi
    - if [[ "$TESTENV" == "pylint" ]]; then ./scripts/travis/includeMAC2.sh; fi
    - if [[ "$TESTENV" == "pylint" ]]; then ./scripts/travis/includeTADbit.sh; fi

services:
    - docker

install:
    # libtbb-dev did not seem to be installing correctly without using sudo
    - sudo apt-get install libtbb-dev

    # Install APIs and Pipelines
    - cd ${HOME}/build/Multiscale-Genomics/mg-process-fastq
    - git status
    - pip install --upgrade -e .
    - pip install -r requirements.txt

    - if [[ "$TESTENV" == "code" ]]; then pip install cutadapt; fi
    - if [[ "$TESTENV" == "docs" ]]; then pip install sphinx; fi
    # Fixed version so that it matches the numpy version required by h5py
    - if [[ "$TESTENV" == "docs" ]]; then pip install --upgrade numpy==1.14; fi
    - if [[ "$TESTENV" == "pylint" ]]; then pip install pylint; fi

    # Install BSseeker
    - cd ${HOME}/lib
    - if [[ ! -d "BSseeker2" ]]; then git clone https://github.com/BSSeeker/BSseeker2.git; fi

    - cd ${HOME}/build/Multiscale-Genomics/mg-process-fastq
    - ln -s ${HOME}/lib/BSseeker2/bs_align bs_align
    - ln -s ${HOME}/lib/BSseeker2/bs_index bs_index
    - ln -s ${HOME}/lib/BSseeker2/bs_utils bs_utils
    - ln -s ${HOME}/lib/BSseeker2/FilterReads.py FilterReads.py

before_script:
    - cd ${HOME}/bin

    - ln -s ${HOME}/lib/FastQC/fastqc
    - ln -s ${HOME}/lib/TrimGalore-0.5.0/trim_galore trim_galore

    - ln -s ${HOME}/lib/bedtools2/bin/bedtools bedtools

    - ln -s ${HOME}/lib/bedToBigBed bedToBigBed
    - ln -s ${HOME}/lib/wigToBigWig wigToBigWig
    - ln -s ${HOME}/lib/faToTwoBit faToTwoBit
    - ln -s ${HOME}/lib/twoBitInfo twoBitInfo
    - ln -s ${HOME}/lib/kallisto_linux-v0.43.1/kallisto kallisto

    - ln -s ${HOME}/build/Multiscale-Genomics/mg-process-fastq/scripts/iNPS iNPS

    - ln -s ${HOME}/lib/bwa/bwa bwa

    - ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2 bowtie2
    - ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2-align-s bowtie2-align-s
    - ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2-align-l bowtie2-align-l
    - ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2-build bowtie2-build
    - ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2-build-s bowtie2-build-s
    - ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2-build-l bowtie2-build-l
    - ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2-inspect bowtie2-inspect
    - ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2-inspect-s bowtie2-inspect-s
    - ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2-inspect-l bowtie2-inspect-l

    - ln -s ${HOME}/lib/gemtools-1.7.1-core2/bin/gem-2-bed gem-2-bed
    - ln -s ${HOME}/lib/gemtools-1.7.1-core2/bin/gem-2-gem gem-2-gem
    - ln -s ${HOME}/lib/gemtools-1.7.1-core2/bin/gem-2-sam gem-2-sam
    - ln -s ${HOME}/lib/gemtools-1.7.1-core2/bin/gem-2-wig gem-2-wig
    - ln -s ${HOME}/lib/gemtools-1.7.1-core2/bin/gem-indexer gem-indexer
    - ln -s ${HOME}/lib/gemtools-1.7.1-core2/bin/gem-indexer_bwt-dna gem-indexer_bwt-dna
    - ln -s ${HOME}/lib/gemtools-1.7.1-core2/bin/gem-indexer_fasta2meta+cont gem-indexer_fasta2meta+cont
    - ln -s ${HOME}/lib/gemtools-1.7.1-core2/bin/gem-indexer_generate gem-indexer_generate
    - ln -s ${HOME}/lib/gemtools-1.7.1-core2/bin/gem-info gem-info
    - ln -s ${HOME}/lib/gemtools-1.7.1-core2/bin/gem-mapper gem-mapper
    - ln -s ${HOME}/lib/gemtools-1.7.1-core2/bin/gemtools gemtools

    - ln -s ${HOME}/lib/htslib/bin/bgzip bgzip
    - ln -s ${HOME}/lib/htslib/bin/htsfile htsfile
    - ln -s ${HOME}/lib/htslib/bin/tabix tabix

    - ln -s ${HOME}/lib/samtools/bin/ace2sam ace2sam
    - ln -s ${HOME}/lib/samtools/bin/blast2sam.pl blast2sam.pl
    - ln -s ${HOME}/lib/samtools/bin/bowtie2sam.pl bowtie2sam.pl
    - ln -s ${HOME}/lib/samtools/bin/export2sam.pl export2sam.pl
    - ln -s ${HOME}/lib/samtools/bin/interpolate_sam.pl interpolate_sam.pl
    - ln -s ${HOME}/lib/samtools/bin/maq2sam-long maq2sam-long
    - ln -s ${HOME}/lib/samtools/bin/maq2sam-short maq2sam-short
    - ln -s ${HOME}/lib/samtools/bin/md5fa md5fa
    - ln -s ${HOME}/lib/samtools/bin/md5sum-lite md5sum-lite
    - ln -s ${HOME}/lib/samtools/bin/novo2sam.pl novo2sam.pl
    - ln -s ${HOME}/lib/samtools/bin/plot-bamstats plot-bamstats
    - ln -s ${HOME}/lib/samtools/bin/psl2sam.pl psl2sam.pl
    - ln -s ${HOME}/lib/samtools/bin/sam2vcf.pl sam2vcf.pl
    - ln -s ${HOME}/lib/samtools/bin/samtools samtools
    - ln -s ${HOME}/lib/samtools/bin/samtools.pl samtools.pl
    - ln -s ${HOME}/lib/samtools/bin/seq_cache_populate.pl seq_cache_populate.pl
    - ln -s ${HOME}/lib/samtools/bin/soap2sam.pl soap2sam.pl
    - ln -s ${HOME}/lib/samtools/bin/varfilter.py varfilter.py
    - ln -s ${HOME}/lib/samtools/bin/wgsim wgsim
    - ln -s ${HOME}/lib/samtools/bin/wgsim_eval.pl wgsim_eval.pl
    - ln -s ${HOME}/lib/samtools/bin/zoom2sam.pl zoom2sam.pl

    - cd ${HOME}/build/Multiscale-Genomics/mg-process-fastq

    # - echo "R_LIB=${HOME}/R" > ${HOME}/.Renviron
    # - echo "options(repos = c(CRAN = 'http://mirrors.ebi.ac.uk/CRAN/'))" > ${HOME}/.Rprofile
    # - echo ".libPaths('~/R')" >> ${HOME}/.Rprofile
    # - echo 'message("Using library:", .libPaths()[1])' >> ${HOME}/.Rprofile
    # - Rscript scripts/install_packages.R


    - cd ${HOME}/build/Multiscale-Genomics/mg-process-fastq
    - docker run -p 80:80 --name biobambamcontainer multiscalegenomics/mgprocessfastqbbb:latest
    - pwd

    - cd ${HOME}/build/Multiscale-Genomics/mg-process-fastq
    - chmod +x shims/*
    - export PATH="$PWD/shims:$PATH"
    - docker ps -a

    - cd ${HOME}/build/Multiscale-Genomics/mg-process-fastq
    - chmod +x scripts/travis/harness.sh
    - chmod +x scripts/travis/wgbs_harness.sh
    - chmod +x scripts/travis/docs_harness.sh
    - chmod +x scripts/travis/pylint_harness.sh
    - ls tests/data/
    - git status

    - export PATH="${HOME}/bin:$PATH"

script:
    - if [[ "$TESTENV" == "code" ]]; then ./scripts/travis/harness.sh; fi
    - if [[ "$TESTENV" == "wgbs_code_1" ]]; then ./scripts/travis/wgbs_harness.sh; fi
    - if [[ "$TESTENV" == "wgbs_code_2" ]]; then ./scripts/travis/wgbs_harness.sh; fi
    - if [[ "$TESTENV" == "docs" ]]; then ./scripts/travis/docs_harness.sh; fi
    - if [[ "$TESTENV" == "pylint" ]]; then ./scripts/travis/pylint_harness.sh; fi