Add dependency installation

.gitignore

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+install.log
+test/results/
+test/.DS_Store
+test/contigs_list.txt
+test/fasta_list.txt
+test/working_list.txt
+src/.DS_Store
+.DS_Store
+test/workdirs/ebola_comp_contigs_pread/
+test/workdirs/
+2NG.dN
+2NG.dS
+2NG.t
+4fold.nuc
+PhaME-1.sublime-project
+PhaME-1.sublime-workspace
+lnf
+rst
+rst1
+rub
+sftp-config.json
+thirdParty/miniconda/
+thirdParty/hyphy-2.3.11/
+thirdParty/messages.log
+thirdParty/evolver.out
+thirdParty/errors.log
+messages.log
+*.log
+docs/_build/*
+.vscode/

.travis.yml

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+sudo: required
+
+# services:
+#   - docker
+
+language: perl
+perl:
+  - "5.22"
+
+before_install:
+  # - docker pull migun/phame-1 
+  - sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y
+  - sudo apt-get update -qq
+  # - sudo apt-get -y install -qq gcc-5 g++-5
+  # - sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-5 60 --slave /usr/bin/g++ g++ /usr/bin/g++-5
+
+install:
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+  - chmod +x miniconda.sh
+  - ./miniconda.sh -b -f
+  - export PATH="/home/travis/miniconda3/bin:$PATH"
+  - conda update --yes -n base conda
+  - conda config --add channels r
+  - conda config --add channels defaults
+  - conda config --add channels conda-forge
+  - conda config --add channels bioconda
+  - conda create --yes -n phame_env
+  - conda install --yes -c bioconda phame -n phame_env
+  # - conda install --yes -c bioconda samtools>=1.7
+  # - conda install --yes -c bioconda bbmap>=37.62
+  # - conda install --yes -c bioconda bowtie2=2.3.0
+  # - conda install --yes -c bioconda perl-app-cpanminus=1.7039
+  # - conda install --yes -c bioconda bcftools
+  # - conda install --yes -c bioconda bwa
+  # - conda install --yes -c bioconda fasttree
+  # - conda install --yes -c bioconda bbmap
+  # - conda install --yes -c bioconda raxml
+  # - cpanm Getopt::[email protected]
+  # - cpanm Test::[email protected]
+  # - cpanm Statistics::[email protected]
+  # - cpanm File::[email protected]
+  # - cpanm File::[email protected]
+  # - cpanm File::[email protected]
+  # - cpanm Parallel::[email protected]
+  # - export PATH="$HOME/build/mshakya/PhaME-1/src:$HOME/build/mshakya/PhaME-1/thirdParty/miniconda/bin:$PATH"
+
+# before_script:
+  # - cpanm --quiet --notest --skip-satisfied Devel::Cover::Report::Codecov
+
+script:
+  - source activate phame_env
+  - test/TestAll.sh 2
+  - test/TestAll.sh 7
+  # - cover -test
+  # - docker run --rm migun/phame-1 sh test/TestAll.sh 
+
+#after_success:
+#  - cover -report codecov

Dockerfile

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+# This is the Dockefile to build PhaME
+
+############################# Base Docker Image ################################
+
+FROM continuumio/miniconda3
+
+############################# MAINTAINER #######################################
+
+MAINTAINER Migun Shakya <[email protected]>
+
+############################# METADATA #######################################
+
+LABEL version="1.0.1"
+LABEL software="PhaME"
+LABEL description="Phylogenetic Analysis and Molecular Evolution"
+LABEL website="https://github.com/mshakya/PhaME"
+LABEL tags="genomics"
+
+############################# INSTALLATION #####################################
+
+RUN conda config --add channels r
+RUN conda config --add channels defaults
+RUN conda config --add channels conda-forge
+RUN conda config --add channels bioconda
+RUN conda install -c bioconda phame 
+# RUN sh test/TestAll.sh
+#############################ENVIRONMENT#####################################