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.travis.yml
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.travis.yml
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# 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
dist: trusty
group: edge
python:
- "3.6"
perl:
- "5.24"
addons:
apt:
packages:
- libspatialindex-dev
- bedtools
env:
matrix:
- TESTENV=docs
- TESTENV=code
- TESTENV=pylint
#create folders for installation
before_install:
- sudo apt-get install gawk
- chmod +x ./tests/run_tests.sh
- mkdir -p ${HOME}/bin
- mkdir -p ${HOME}/lib
- export PATH="${HOME}/bin:$PATH"
- cd ${HOME}/lib
# install hicup
- wget https://www.bioinformatics.babraham.ac.uk/projects/hicup/hicup_v0.6.1.tar.gz
- tar -xzf hicup_v0.6.1.tar.gz
- cd hicup_v0.6.1
- chmod a+x *
# install bwa
- cd ${HOME}/lib
- wget https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.17.tar.bz2
- bzip2 -d bwa-0.7.17.tar.bz2
- tar -xf bwa-0.7.17.tar
- cd bwa-0.7.17
- make
# install bowtie2
- cd ${HOME}/lib
- wget --max-redirect 1 https://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.4/bowtie2-2.3.4-linux-x86_64.zip
- unzip bowtie2-2.3.4-linux-x86_64.zip
#install htslib
- cd ${HOME}/lib
- git clone https://github.com/samtools/htslib.git
- cd htslib
- autoheader
- autoconf
- ./configure --prefix=${HOME}/lib/htslib
- make
- make install
# install samtools
- cd ${HOME}/lib
- git clone https://github.com/samtools/samtools.git
- cd samtools
- autoheader
- autoconf -Wno-syntax
- ./configure --prefix=${HOME}/lib/samtools
- make
- make install
#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
- sudo apt-get install r-base-core
- sudo apt-get install python-rpy2
#Get chicago preprocessing scripts
- cd ${HOME}/build/Multiscale-Genomics/pyCHiC/CHiC/tool/scripts/
- wget https://bitbucket.org/chicagoTeam/chicago/raw/e288015f75d36c5367d1595e0ac8099f2ce82aa1/chicagoTools/runChicago.R
- wget https://bitbucket.org/chicagoTeam/chicago/raw/e288015f75d36c5367d1595e0ac8099f2ce82aa1/chicagoTools/bam2chicago.sh
- wget https://bitbucket.org/chicagoTeam/chicago/raw/e288015f75d36c5367d1595e0ac8099f2ce82aa1/chicagoTools/makeDesignFiles.py
- chmod +x bam2chicago.sh
#installing chicago
- sudo apt-get install libtbb-dev
- sudo apt-get install libssl-dev
- cd ${HOME}/build/Multiscale-Genomics/pyCHiC/
- sudo chmod +x CHiC/tool/scripts/travis/docs_harness.sh
- sudo chmod +x CHiC/tool/scripts/travis/pylint_harness.sh
- sudo Rscript CHiC/tool/scripts/install_packages.R
- cd ${HOME}/build/Multiscale-Genomics/pyCHiC/
# command to install dependencies
install:
- pip install --upgrade setuptools pip
- pip install --upgrade -e .
- pip install -r requirements.txt
- if [[ "$TESTENV" == "docs" ]]; then pip install sphinx;fi
- if [[ "$TESTENV" == "pylint" ]]; then pip install pylint;fi
before_script:
- cd ${HOME}/bin
- ln -s ${HOME}/lib/bedtools2/bin/* .
- ln -s ${HOME}/lib/hicup_v0.6.1/* ${HOME}/bin/
- ln -s ${HOME}/lib/bwa-0.7.17/bwa ${HOME}/bin/
- ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2
- ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2-align-l
- ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2-align-l-debug
- ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2-align-s
- ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2-align-s-debug
- ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2-build
- ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2-build-l
- ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2-build-l-debug
- ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2-build-s
- ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2-build-s-debug
- ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2-inspect
- ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2-inspect-l
- ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2-inspect-l-debug
- ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2-inspect-s
- ln -s ${HOME}/lib/bowtie2-2.3.4-linux-x86_64/bowtie2-inspect-s-debug
- 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
# command to run tests
script:
- cd ${HOME}/build/Multiscale-Genomics/pyCHiC
- if [[ "$TESTENV" == "code" ]]; then python tests/test_toolchains.py; fi
- if [[ "$TESTENV" == "docs" ]]; then CHiC/tool/scripts/travis/docs_harness.sh; fi
- if [[ "$TESTENV" == "pylint" ]]; then CHiC/tool/scripts/travis/pylint_harness.sh; fi