--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Roary/install_dependencies.sh	Fri May 14 20:27:06 2021 +0000
@@ -0,0 +1,248 @@
+#!/bin/bash
+
+set -x
+set -eu
+
+start_dir=$(pwd)
+ROARY_LIB_DIR="${start_dir}/lib"
+ROARY_BIN_DIR="${start_dir}/bin"
+
+PARALLEL_VERSION=${PARALLEL_VERSION:-"20160722"}
+PARALLEL_DOWNLOAD_FILENAME="parallel-${PARALLEL_VERSION}.tar.bz2" 
+PARALLEL_URL="http://ftp.gnu.org/gnu/parallel/${PARALLEL_DOWNLOAD_FILENAME}"
+
+BEDTOOLS_VERSION="2.27.1"
+BEDTOOLS_DOWNLOAD_FILENAME="bedtools-${BEDTOOLS_VERSION}.tar.gz"
+BEDTOOLS_URL="https://github.com/arq5x/bedtools2/releases/download/v${BEDTOOLS_VERSION}/${BEDTOOLS_DOWNLOAD_FILENAME}"
+
+CDHIT_SHORT_VERSION="4.6.8"
+CDHIT_LONG_VERSION="4.6.8-2017-0621"
+CDHIT_DOWNLOAD_FILENAME="cd-hit-${CDHIT_SHORT_VERSION}.tar.gz"
+CDHIT_URL="https://github.com/weizhongli/cdhit/releases/download/V${CDHIT_SHORT_VERSION}/cd-hit-v${CDHIT_LONG_VERSION}-source.tar.gz"
+
+PRANK_VERSION="0.140603"
+PRANK_DOWNLOAD_FILENAME="prank-msa-master.tar.gz"
+PRANK_URL="https://github.com/ariloytynoja/prank-msa/archive/master.tar.gz"
+
+BLAST_VERSION="2.6.0"
+BLAST_DOWNLOAD_FILENAME="ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz"
+BLAST_URL="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLAST_VERSION}/${BLAST_DOWNLOAD_FILENAME}"
+
+MCL_VERSION="14-137"
+MCL_DOWNLOAD_FILENAME="mcl-${MCL_VERSION}.tar.gz"
+MCL_URL="http://micans.org/mcl/src/mcl-${MCL_VERSION}.tar.gz"
+
+FASTTREE_VERSION="2.1.10"
+FASTTREE_DOWNLOAD_FILENAME="FastTree-${FASTTREE_VERSION}.c"
+FASTTREE_URL="http://microbesonline.org/fasttree/FastTree-${FASTTREE_VERSION}.c"
+
+MAFFT_VERSION="7.310"
+MAFFT_DOWNLOAD_FILENAME="mafft-${MAFFT_VERSION}-without-extensions-src.tgz"
+MAFFT_URL="http://mafft.cbrc.jp/alignment/software/${MAFFT_DOWNLOAD_FILENAME}"
+
+# Make an install location
+if [ ! -d 'build' ]; then
+  mkdir build
+fi
+cd build
+build_dir=$(pwd)
+
+PARALLEL_DOWNLOAD_PATH="$(pwd)/${PARALLEL_DOWNLOAD_FILENAME}"
+BEDTOOLS_DOWNLOAD_PATH="$(pwd)/${BEDTOOLS_DOWNLOAD_FILENAME}"
+CDHIT_DOWNLOAD_PATH="$(pwd)/${CDHIT_DOWNLOAD_FILENAME}"
+PRANK_DOWNLOAD_PATH="$(pwd)/${PRANK_DOWNLOAD_FILENAME}"
+BLAST_DOWNLOAD_PATH="$(pwd)/${BLAST_DOWNLOAD_FILENAME}"
+MCL_DOWNLOAD_PATH="$(pwd)/${MCL_DOWNLOAD_FILENAME}"
+FASTTREE_DOWNLOAD_PATH="$(pwd)/${FASTTREE_DOWNLOAD_FILENAME}"
+MAFFT_DOWNLOAD_PATH="$(pwd)/${MAFFT_DOWNLOAD_FILENAME}"
+
+PARALLEL_BUILD_DIR="$(pwd)/parallel-${PARALLEL_VERSION}"
+BEDTOOLS_BUILD_DIR="$(pwd)/bedtools2"
+CDHIT_BUILD_DIR="$(pwd)/cd-hit-v${CDHIT_LONG_VERSION}"
+PRANK_BUILD_DIR="$(pwd)/prank-msa-master"
+BLAST_BUILD_DIR="$(pwd)/ncbi-blast-${BLAST_VERSION}+"
+MCL_BUILD_DIR="$(pwd)/mcl-${MCL_VERSION}"
+FASTTREE_BUILD_DIR="$(pwd)/fasttree"
+MAFFT_BUILD_DIR="$(pwd)/mafft-${MAFFT_VERSION}-without-extensions"
+
+
+download () {
+  download_url=$1
+  download_path=$2
+  cd $build_dir
+  if [ -e "$download_path" ]; then
+    echo "Skipping download of $download_url, $download_path already exists"
+  else
+    echo "Downloading $download_url to $download_path"
+    wget $download_url -O $download_path
+    pwd
+  fi
+}
+
+untar () {
+  to_untar=$1
+  expected_directory=$2
+  if [ -d "$expected_directory" ]; then
+    rm -rf $expected_directory
+  fi
+  echo "Untarring $to_untar to $expected_directory"
+  cd $build_dir
+  tar xzvf $to_untar
+  rm $to_untar
+  pwd
+}
+
+if [ -e "$BLAST_BUILD_DIR/bin/blastp" ]; then
+  echo "blast already untarred to $BLAST_BUILD_DIR, skipping"
+else
+  download $BLAST_URL $BLAST_DOWNLOAD_PATH
+  untar $BLAST_DOWNLOAD_PATH $BLAST_BUILD_DIR
+fi
+
+# Build parallel
+if [ -e "$PARALLEL_BUILD_DIR/src/parallel" ]; then
+  echo "Parallel already built, skipping"
+else
+  download $PARALLEL_URL $PARALLEL_DOWNLOAD_PATH
+  echo "Untarring parallel to $PARALLEL_BUILD_DIR"
+  tar xjvf $PARALLEL_DOWNLOAD_PATH
+  echo "Building parallel"
+  cd $PARALLEL_BUILD_DIR
+  ./configure
+  make
+fi
+
+# Build bedtools
+if [ -e "$BEDTOOLS_BUILD_DIR/bin/bedtools" ]; then
+  echo "Bedtools already built, skipping"
+else
+
+  download $BEDTOOLS_URL $BEDTOOLS_DOWNLOAD_PATH
+  untar $BEDTOOLS_DOWNLOAD_PATH $BEDTOOLS_BUILD_DIR
+  cd $BEDTOOLS_BUILD_DIR
+  echo "Building bedtools"
+  ls -alrt
+  make
+fi
+
+# Build cd-hit
+if [ -e "$CDHIT_BUILD_DIR/cd-hit" ]; then
+  echo "cd-hit already built, skipping"
+else
+  download $CDHIT_URL $CDHIT_DOWNLOAD_PATH
+  untar $CDHIT_DOWNLOAD_PATH $CDHIT_BUILD_DIR
+  echo "Building cd-hit"
+  cd $CDHIT_BUILD_DIR
+  make
+fi
+
+# Build prank
+if [ -e "$PRANK_BUILD_DIR/src/prank" ]; then
+  echo "prank already built, skipping"
+else
+  download $PRANK_URL $PRANK_DOWNLOAD_PATH
+  untar $PRANK_DOWNLOAD_PATH $PRANK_BUILD_DIR
+  echo "Building prank"
+  cd $PRANK_BUILD_DIR
+  cd src
+  make
+fi
+
+# Build MCL
+if [ -e "$MCL_BUILD_DIR/src/shmcl/mcl" ]; then
+  echo "MCL already built, skipping"
+else
+  download $MCL_URL $MCL_DOWNLOAD_PATH
+  untar $MCL_DOWNLOAD_PATH $MCL_BUILD_DIR
+  echo "Building MCL"
+  cd $MCL_BUILD_DIR
+  ./configure
+  make
+fi
+
+# Build FastTree
+if [ -e "$FASTTREE_BUILD_DIR/FastTree" ]; then
+  echo "FastTree already built, skipping"
+else
+  download $FASTTREE_URL $FASTTREE_DOWNLOAD_PATH
+  mkdir -p $FASTTREE_BUILD_DIR
+  mv $FASTTREE_DOWNLOAD_FILENAME $FASTTREE_BUILD_DIR
+  cd $FASTTREE_BUILD_DIR
+  echo "Building FastTree"
+  gcc -o FastTree FastTree-${FASTTREE_VERSION}.c -lm
+fi
+
+export MAFFT_INSTALL_DIR="${MAFFT_BUILD_DIR}/build"
+# Build MAFFT
+if [ -e "$MAFFT_BUILD_DIR/build/mafft" ]; then
+  echo "MAFFT already built, skipping"
+else
+  download $MAFFT_URL $MAFFT_DOWNLOAD_PATH
+  untar $MAFFT_DOWNLOAD_PATH $MAFFT_BUILD_DIR
+  echo "Building MAFFT"
+  cd $MAFFT_BUILD_DIR
+  mkdir -p $MAFFT_INSTALL_DIR
+  cd core
+  sed -i '1s!.*!PREFIX = $(MAFFT_INSTALL_DIR)!' Makefile
+  make
+  make install
+fi
+
+
+# Add things to PATH
+update_path () {
+  new_dir=$1
+  if [[ ! "$PATH" =~ (^|:)"${new_dir}"(:|$) ]]; then
+	echo "export PATH=${new_dir}:${PATH}"
+    export PATH=${new_dir}:${PATH}
+  fi
+}
+
+export PATH
+PARALLEL_BIN_DIR="$PARALLEL_BUILD_DIR/src"
+update_path $PARALLEL_BIN_DIR
+BEDTOOLS_BIN_DIR="$BEDTOOLS_BUILD_DIR/bin"
+update_path $BEDTOOLS_BIN_DIR
+CDHIT_BIN_DIR="$CDHIT_BUILD_DIR"
+update_path $CDHIT_BIN_DIR
+PRANK_BIN_DIR="$PRANK_BUILD_DIR/src"
+update_path $PRANK_BIN_DIR
+
+BLAST_BIN_DIR="$BLAST_BUILD_DIR/bin"
+update_path $BLAST_BIN_DIR
+
+MCL_BIN_DIR="$MCL_BUILD_DIR/src/shmcl"
+update_path $MCL_BIN_DIR
+MCL_BIN_DIR_2="$MCL_BUILD_DIR/src/alien/oxygen/src"
+update_path $MCL_BIN_DIR_2
+
+FASTTREE_BIN_DIR=$FASTTREE_BUILD_DIR
+update_path $FASTTREE_BIN_DIR
+MAFFT_BIN_DIR="$MAFFT_INSTALL_DIR/bin"
+update_path $MAFFT_BIN_DIR
+
+update_perl_path () {
+  new_dir=$1
+  PERL5LIB=${PERL5LIB-$new_dir}
+  if [[ ! "$PERL5LIB" =~ (^|:)"${new_dir}"(:|$) ]]; then
+	echo "export PERL5LIB=${new_dir}:${PERL5LIB}"
+    export PERL5LIB=${new_dir}:${PERL5LIB}
+  fi
+}
+
+BEDTOOLS_LIB_DIR="$BEDTOOLS_BUILD_DIR/lib"
+update_perl_path $BEDTOOLS_LIB_DIR
+
+cd $start_dir
+cpanm --notest Dist::Zilla 
+dzil authordeps --missing | cpanm --notest
+dzil listdeps --missing | cpanm --notest
+
+cd $start_dir
+
+echo "Add the following lines to one of these files ~/.bashrc or ~/.bash_profile or ~/.profile"
+echo "export PATH=${ROARY_BIN_DIR}:${PARALLEL_BIN_DIR}:${BEDTOOLS_BIN_DIR}:${CDHIT_BIN_DIR}:${PRANK_BIN_DIR}:${BLAST_BIN_DIR}:${MCL_BIN_DIR}:${MCL_BIN_DIR_2}:${FASTTREE_BIN_DIR}:${MAFFT_BIN_DIR}:${PATH}"
+echo "export PERL5LIB=${ROARY_LIB_DIR}:${BEDTOOLS_LIB_DIR}:${PERL5LIB}"
+
+set +eu
+set +x