Merge pull request #2 from mshakya/master

Pull request #1

.gitignore

@@ -25,3 +25,4 @@ thirdParty/messages.log
 thirdParty/evolver.out
 thirdParty/errors.log
 messages.log
+*.log

.travis.yml

@@ -1,26 +1,58 @@
 sudo: required
+
+# services:
+#   - docker
+
 language: perl
 perl:
-  - "5.16"
+  - "5.22"
 
 before_install:
-  # - eval "${MATRIX_EVAL}"
+  # - 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
+  # - 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"
+  - 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
+# before_script:
+  # - cpanm --quiet --notest --skip-satisfied Devel::Cover::Report::Codecov
 
 script:
-  - source activate phame
-  - test/TestAll.sh
-  - cover -test
+  - 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
+#after_success:
+#  - cover -report codecov

Dockerfile

@@ -2,31 +2,26 @@
 
 ############################# Base Docker Image ################################
 
-FROM ubuntu:16.04
+FROM continuumio/miniconda3
 
 ############################# MAINTAINER #######################################
 
 MAINTAINER Migun Shakya <[email protected]>
 
 ############################# METADATA #######################################
 
-LABEL version="1.0"
+LABEL version="1.0.1"
 LABEL software="PhaME"
 LABEL description="Phylogenetic Analysis and Molecular Evolution"
-LABEL website="https://github.com/mshakya/PhaME-1"
+LABEL website="https://github.com/mshakya/PhaME"
 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 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#####################################

INSTALL.sh

@@ -40,7 +40,7 @@ perl_File_Path_VER=2.09
 perl_Getopt_Long_VER=2.45
 perl_IO_Handle_VER=1.28
 perl_Parllel_ForkManager_VER=1.17
-perl_Time_BaseName=2.85
+# perl_Time_BaseName=2.85
 perl_Time_HiRes=1.9726
 perl_Statistics_Distributions_VER=1.02
 perl_Test_Exception_VER=0.43