Merge pull request #1 from mshakya/master

all my changes

.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

.travis.yml

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+sudo: required
+language: perl
+perl:
+  - "5.16"
+
+before_install:
+  # - eval "${MATRIX_EVAL}"
+  - sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y
+  - sudo apt-get update -qq
+  - sudo apt-get -y install -qq gcc-5 g++-5
+  - sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-5 60 --slave /usr/bin/g++ g++ /usr/bin/g++-5
+
+install:
+  - ./INSTALL.sh
+  - export PATH="$HOME/build/mshakya/PhaME-1/thirdParty/miniconda/bin:$PATH"
+
+before_script:
+  - cpanm --quiet --notest --skip-satisfied Devel::Cover::Report::Codecov
+
+script:
+  - source activate phame
+  - test/TestAll.sh
+  - cover -test
+
+after_success:
+  - cover -report codecov

Dockerfile

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+# This is the Dockefile to build PhaME
+
+############################# Base Docker Image ################################
+
+FROM ubuntu:16.04
+
+############################# MAINTAINER #######################################
+
+MAINTAINER Migun Shakya <[email protected]>
+
+############################# METADATA #######################################
+
+LABEL version="1.0"
+LABEL software="PhaME"
+LABEL description="Phylogenetic Analysis and Molecular Evolution"
+LABEL website="https://github.com/mshakya/PhaME-1"
+LABEL tags="genomics"
+
+############################# INSTALLATION #####################################
+
+RUN apt-get -y update --fix-missing
+RUN apt-get install -y wget bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 \
+	libxrender1 git curl make gcc gfortran g++ grep unzip cmake libcurl4-gnutls-dev \
+	ocl-icd-opencl-dev mpich doxygen libssl-dev
+RUN apt-get -y upgrade
+RUN apt-get clean
+RUN	git clone https://github.com/mshakya/PhaME-1.git
+WORKDIR /PhaME-1
+RUN ./INSTALL.sh
+ENV PATH="/PhaME-1/thirdParty/miniconda/bin:/PhaME-1/src:${PATH}"
+# RUN sh test/TestAll.sh
+#############################ENVIRONMENT#####################################