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muppetjones/setup_local_linux.sh

Last active August 29, 2015 14:25
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Perform a local install of a variety of useful (e.g., necessary) softwares
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setup_local_linux.sh
#!/bin/bash
# Perform a local install of a variety of useful (e.g., necessary) softwares
#
# Ever had to use a server and found yourself frustrated due to lack of
# root access or simply not being able/allowed to modify the setup?
# Never fear!
#
# This script does the following:
# * Modifies *.vimrc to include line numbers and set tabs to four spaces
# * Install gcc-4.5.4 (and other required)
# * Install python-3.4 (also: venv called 'py3', activate replacement called 'start')
# * Install bowtie2
# * Install R-3.2.1
# * Adds path/local/(lib|bin) to path via ~/.bash_profile (or ~/.profile)
#
# Also installs:
# * kSNP3.0
# * jellyfish-2.2.3
# * MUMmer 3.23
# * phylip-3.696
#
# To do:
# * velvet, hisat
# * test using CDPATH
# export CDPATH=${root_prefix}:${local_prefix}
# * finish moving download location to 'local/build' ($build_prefix)
# -- can't yet...still testing on local machine, which has half in 'dev'.
#
# Sets up the following directory structure:
# given/path/
# dev/
# local/
# bin/
# lib/
# venv/
# exit on error!
set -e
set +x
#------------------------------------------------------------------------------
# Functions
pause(){
read -n1 -rsp $'Press any key to continue or Ctrl+C to exit...\n'
}
speak() { echo -e "${NC}$*${NC}"; }
yell() { echo -e "\n$0: $*" >&2; }
die() { yell "ERROR: $*"; exit 111; }
try() { "$@" || die "cannot $*"; }
announce() {
speak "${NC}------------------------------------------------------"
speak $*
pause
}
accept() {
read -n1 -rsp $'Press \'y\' to continue or any key to exit: \n' response
if [[ $response != 'y' ]]; then
die "Cancelled by user"
fi
}
check_if_line_exists()
{
# grep wont care if one or both files dont exist.
grep -qsFx "$LINE_TO_ADD" $FILE_ADD_TO
}
add_line_to_file()
{
# profile=~/.profile
# [ -w "$profile" ] || profile=~/.bash_profile
echo "$LINE_TO_ADD" >> $FILE_ADD_TO
}
#------------------------------------------------------------------------------
# Cleanup!!
function finish {
echo "Cleaning up..."
for i in ${CLEANUP_FILES[@]}
do
echo "Removing file ${i}"
rm -f "${i}"
done
for i in ${CLEANUP_DIRS[@]}
do
echo "Removing dir ${i}"
rm -rf "${i}"
done
}
trap finish EXIT
CLEANUP_FILES=()
CLEANUP_DIRS=()
function DO_NOT_CLEAN {
keep="$1"
CLEANUP_DIRS=( "${CLEANUP_DIRS[@]/%$keep}" )
CLEANUP_FILES=( "${CLEANUP_FILES[@]/%$keep}" )
}
#------------------------------------------------------------------------------
# Colors
BLACK='\033[0;30m'
DARK_GRAY='\033[1;30m'
RED='\033[0;31m'
LIGHT_RED='\033[1;31m'
GREEN='\033[0;32m'
LIGHT_GREEN='\033[1;32m'
BROWN_ORANGE='\033[0;33m'
YELLOW='\033[1;33m'
BLUE='\033[0;34m'
LIGHT_BLUE='\033[1;34m'
PURPLE='\033[0;35m'
LIGHT_PURPLE='\033[1;35m'
CYAN='\033[0;36m'
LIGHT_CYAN='\033[1;36m'
LIGHT_GRAY='\033[0;37m'
WHITE='\033[1;37m'
NC='\033[0m' # No Color
CY=${CYAN} # highlight
GR=${GREEN} # files / directories
PU=${PURPLE} # executables
BO=${BROWN_ORANGE} # misc
#------------------------------------------------------------------------------
# Setup
# set profile file
if [[ ! -s "$HOME/.bash_profile" && -s "$HOME/.profile" ]] ; then
profile_file="$HOME/.profile"
else
profile_file="$HOME/.bash_profile"
fi
# get the main install directory
root_prefix="/data/sbush"
if [ -z $1 ]; then
if [ -d "$(pwd)/dev" ]; then
root_prefix="$(pwd)"
else # ask the user
speak "${NC}------------------------------------------------------"
speak "Type the root directory and hit [ENTER]:${BROWN_ORANGE}"
read root_prefix
root_prefix="${root_prefix%%/}" # remove trailing slash
fi
fi
local_prefix="${root_prefix}/local"
share_prefix="${root_prefix}/share"
dev_prefix="${root_prefix}/dev"
venv_prefix="${root_prefix}/venv"
bin_prefix="${local_prefix}/bin"
lib_prefix="${local_prefix}/lib"
build_prefix="${local_prefix}/build"
# Alert the user
nl="\n ${GR}"
speak "------------------------------------------------------"
speak "Software will be downloaded and compiled in:${nl}${build_prefix}"
speak "Virtual environments will be created in:${nl}${venv_prefix}"
speak "Binaries will be placed in:${nl}${bin_prefix}"
speak "Libraries will be place in:${nl}${lib_prefix}"
speak "* NOTE: Some software downloads to:${nl}${dev_prefix}"
speak "** PATH will be updated via ${profile_file}"
speak "------------------------------------------------------"
accept
mkdir -p "${dev_prefix}"
mkdir -p "${venv_prefix}"
mkdir -p "${bin_prefix}"
mkdir -p "${lib_prefix}"
mkdir -p "${build_prefix}"
mkdir -p "${share_prefix}"
#------------------------------------------------------------------------------
# DO THESE FIRST!!
cd "${dev_prefix}"
########################
# Update PATH in profile file
if ! grep -q "PATH=${bin_prefix}:${lib_prefix}" "${profile_file}"; then
announce "Adding PATH mods to ${GR}${profile_file}${NC} and sourcing..."
FILE_ADD_TO="${profile_file}"
LINE_TO_ADD="export PATH=${bin_prefix}:${lib_prefix}:\${PATH}"
check_if_line_exists || add_line_to_file
fi
########################
# Update certs
if [ ! -d "${local_prefix}/certs" ] || ! grep -q "cacert.pem" ~/.gitconfig ;
then
announce "Downloading updated certs to ${GR}${local_prefix}/certs${NC}"
certsdir="${local_prefix}/certs"
mkdir -p "${certsdir}"
curl http://curl.haxx.se/ca/cacert.pem -o "${certsdir}/cacert.pem"
gitconfig=~/.gitconfig
cat >>"${gitconfig}" <<EOL
[http]
sslCAinfo = ${certsdir}/cacert.pem
EOL
fi
#------------------------------------------------------------------------------
# INSTALLS
########################
# Vim 7.4
if [ ! -f "${bin_prefix}/vim" ]; then
announce "Downloading and setting up ${CY}vim${NC}"
yell "** There may be some issues related to VIMRUNTIME variable"
cd "${build_prefix}"
if [ ! -d "${build_prefix}/vim" ]; then
link="git@github.com:vim/vim.git"
git clone "${link}"
fi
cd vim
./configure --with-features=huge \
--enable-gui \
--enable-multibyte --enable-rubyinterp --enable-pythoninterp \
--with-python-config-dir=/usr/local/lib/python2.7/config \
--enable-perlinterp --enable-cscope \
--prefix=/data/sbush/local
# Tried creating and setting the VIMRUNTIME variable via make
# It set it, but it put everything in a 'share' directory
# based on '--prefix'. So...try making without setting it.
# ** Solution:
# If there are problems, find where the shared runtime directory is
# (typically 'something/share/vim/vim7X/), copy everything to the
# location vim *thinks* it's at (vim --version), then add the
# directory to 'rtp' via '~/.vimrc'
# mkdir -p "${share_prefix}"/vim/vim74
make
make install
fi
########################
# Vundle (vim package manager)
if [ ! -f ~/.vimrc ] || [ ! -d ~/.vim/bundle/Vundle.vim ]; then
announce "Downloading and setting up ${CY}Vundle${NC}"
link="https://github.com/gmarik/Vundle.vim.git"
dir=~/.vim/bundle/Vundle.vim
if [ ! -d "$dir" ]; then
git clone "$link" "$dir"
fi
cat >~/.vimrc <<EOL
set nocompatible " be iMproved, required
filetype off " required
" set the runtime path to include Vundle and initialize
set rtp+=~/.vim/bundle/Vundle.vim/
call vundle#begin()
" let Vundle manage Vundle, required
Plugin 'gmarik/Vundle.vim'
Plugin 'bling/vim-airline'
" Colorschemes
Plugin 'tomasr/molokai'
Plugin 'altercation/vim-colors-solarized'
Plugin 'tpope/vim-vividchalk'
Plugin 'Lokaltog/vim-distinguished'
Plugin 'ujihisa/unite-colorscheme'
Plugin 'chriskempson/vim-tomorrow-theme'
Plugin 'noahfrederick/vim-hemisu'
Plugin 'junegunn/seoul256'
" All of your Plugins must be added before the following line
call vundle#end() " required
filetype plugin indent on " required
" Brief help
" :PluginList - lists configured plugins
" :PluginInstall - installs plugins; append \`!\` to update or just :PluginUpdate
" :PluginSearch foo - searches for foo; append \`!\` to refresh local cache
" :PluginClean - confirms removal of unused plugins; append \`!\` to auto-approve removal
"
" see :h vundle for more details or wiki for FAQ
" Put your non-Plugin stuff after this line
colorscheme molokai
syntax enable " needed to enable syntax highlighting
set backspace=2 " need for mac 'delete' key to work
set number " show line numbers
set expandtab " tabs to spaces
set tabstop=4 " indent size
set laststatus=2 " always show status bar for airline
set background=dark
let g:solarized_termcolors=256 " for solarized theme in terminal (vs GUI)
" let g:airline_powerline_fonts = 1 " install the fonts first!
EOL
vim +PluginInstall +qall
fi
function get_downloaded_filename {
local link=$1
local f
# OPTION 1: Sourceforge latest download
if [[ "$link" == *sourceforge*latest*download* ]]; then
f=$(LANG=C wget "$link" 2>&1 | sed -n "s/.*- \`\(.*\)' saved.*/\1/p")
# OPTION 2: Anyplace else
else
f="$(basename "${link%%/download}")"
fi
echo "$f"
}
function get_root_compressed_directory {
zip_file="$1"
zip_cmd="$2"
bdir="$(${zip_cmd} ${zip_file} | sed -e 's@^\./@@' | sed -e 's@/.*@@' | uniq)"
echo "${bdir}"
}
function download_and_extract {
# Download file(s) from a link and extract to desired directory
local link=$1
local __bdir
cd "${build_prefix}"; # ensure we're in the build directory!
if [[ "${link}" == *.git ]]; then
__bdir="$(pwd)/$(basename "${link%%.git}")"
if [ ! -d "${__bdir}" ]; then
speak "Cloning from ${GR}${link}${NC}..."
git clone "$link"
fi
else
local zipf="$(pwd)/$(get_downloaded_filename "$link")"
if [ ! -f "${zipf}" ]; then
speak "Downloading '${GR}${zipf}${NC}'..."
wget "${link}" --no-check-certificate
fi
# determine compression type
ext=${zipf##*\.}
case "$ext" in
gz|tgz)
decomp="tar"
decomp_opt="-zxf"
decomp_list="tar -tzf"
;;
bz2|tbz2)
decomp="tar"
decomp_opt="-jxf"
decomp_list="tar -tjf"
;;
tar)
decomp="tar"
decomp_opt="-xf"
decomp_list="tar -tf"
;;
zip)
decomp="unzip"
decomp_opt=""
decomp_list="unzip -Z -1"
;;
*)
die "Unknown compression type"
;;
esac
# get the root directory
# -- IFF there is more than one directory, use the file name
__bdir="$(pwd)/$(get_root_compressed_directory "${zipf}" "${decomp_list}")"
if [[ "$(wc -l <<< "$__bdir")" > 1 ]]; then
# remove extension -- covers .tar*, .gz, .zip
__bdir="${zipf%%.[tgz]*}"
if [[ "$decomp" == tar ]]; then
decomp="${decomp} -C ${__bdir}"
else
decomp="${decomp} -d ${__bdir}"
fi
fi
# decompress
speak "Extracting '${GR}${zipf}${NC}'..."
${decomp} ${decomp_opt} "${zipf}"
# NOTE: Don't add to the cleanup list until we get to the end.
# Will prevent us from having to redownload if an error occurs
# while we're unzipping
CLEANUP_FILES+=("${zipf}")
fi
# echo "${__bdir}"; # NOTE: it's absolute path
# return the value!
eval "$2='$__bdir'"
}
function download_and_link {
# This function:
# 1. downloads a compressed file from a given link into build dir
# 2. decompresses the file and moves into the directory
# 3. runs configuration and make
# 4. links desired executables into bin dir
#
# Arguments:
# name (string): The name of the program (just for announcing)
# link (URL): URL of file download location.
# --config='<options'>: Options to pass to `./configure`
# --altdir=<str>: Provide if software extracts to a different directory.
# --link=exe,bin/exe: Comma-separated list of binaries to link to bin.
#
# NOTE: If no `--config` option is given, ALL leftover options will be
# Passed to `./configure`
# NOTE: The `--config` option MUST be
# a) surrounded by double quotes
# b) have it's options surrounded by single quotes
# *) it's easier just to not use it
# Example)
# "--config='--enable-python-binding'"
local name=$1
local link=$2
local opt="$*"
local bdir=''
cd "${build_prefix}"; # ensure we're in the build directory!
announce "Building ${CY}${name}${NC} at '${GR}$(pwd)${NC}'"
#### OPTIONAL parameters
# build directory
if [[ "${opt}" == *--renamedir* ]]; then
local renamedir="${build_prefix}/${opt##*--renamedir=}"
renamedir="${bdir%%[${IFS}]*}"
opt="${opt//--altdir=*[${IFS}]/}"
fi
# link list
# -- expects comma separated list
if [[ "${opt}" == *--link* ]]; then
local exec_link="${opt##*--link=}"
exec_link="${exec_link%%[${IFS}]*}"
opt="${opt//--link=*[${IFS}]/}"
fi
# configure options
# expects exactly `--config='<options>'`
local config
if [[ "${opt}" == *--config* ]]; then
config="${opt##*--config=\'}"
config="${config%%\'*}"
else
config=
fi
#### START downloading, etc.
# download (if we don't already have the expected directory)
download_and_extract "$link" bdir
echo "bdir: '${bdir}'"
echo "pwd: '$(pwd)'"
# link executables (if we were told to)
if [ ! -z "${exec_link}" ]; then
while IFS=',' read -ra EXEC_ARR; do
for f in "${EXEC_ARR[@]}"; do
speak "Linking ${PU}${f}${NC}..."
f="${bdir}/${f}"
if [ -f "${f}" ]; then
chmod +x "${f}"
ln -s "${f}" "${bin_prefix}"
fi
done
done <<< "$exec_link"
fi
cd ..
}
function download_and_compile {
# This function:
# 1. downloads a compressed file from a given link into build dir
# 2. decompresses the file and moves into the directory
# 3. runs configuration and make
# 4. links desired executables into bin dir
#
# Arguments:
# name (string): The name of the program (just for announcing)
# link (URL): URL of file download location.
# --config='<options'>: Options to pass to `./configure`
# --altdir=<str>: Provide if software extracts to a different directory.
# --link=exe,bin/exe: Comma-separated list of binaries to link to bin.
#
# NOTE: If no `--config` option is given, ALL leftover options will be
# Passed to `./configure`
# NOTE: The `--config` option MUST be
# a) surrounded by double quotes
# b) have it's options surrounded by single quotes
# *) it's easier just to not use it
# Example)
# "--config='--enable-python-binding'"
local name=$1
local link=$2
local opt="$*"
local bdir=''
cd "${build_prefix}"; # ensure we're in the build directory!
announce "Building ${CY}${name}${NC} at '${GR}$(pwd)${NC}'"
#### OPTIONAL parameters
# build directory
if [[ "${opt}" == *--renamedir* ]]; then
local renamedir="${build_prefix}/${opt##*--renamedir=}"
renamedir="${bdir%%[${IFS}]*}"
opt="${opt//--altdir=*[${IFS}]/}"
fi
# link list
# -- expects comma separated list
if [[ "${opt}" == *--link* ]]; then
local exec_link="${opt##*--link=}"
exec_link="${exec_link%%[${IFS}]*}"
opt="${opt//--link=*[${IFS}]/}"
fi
# configure options
# expects exactly `--config='<options>'`
local config
if [[ "${opt}" == *--config* ]]; then
config="${opt##*--config=\'}"
config="${config%%\'*}"
else
config=
fi
#### START downloading, etc.
# download (if we don't already have the expected directory)
download_and_extract "$link" bdir
echo "bdir: '${bdir}'"
echo "pwd: '$(pwd)'"
# rename downloaded directory if given
if [ ! -z "${renamedir}" ]; then
speak "Renaming '${GR}$(basename ${bdir})${NC}' to '${GR}${renamedir}${NC}"
mv "${bdir}" "$(dirname "${bdir}")/${renamedir}"
bdir="$(dirname "${bdir}")/${renamedir}"
fi
# configure and make (IFF we find a configure file)
speak "Descending into ${GR}${bdir}${NC}"
cd "${bdir}"
if [ -f "${bdir}/configure" ]; then
speak "Configuring and making..."
./configure --prefix="${local_prefix}" --exec_prefix="${local_prefix}" ${config}
make
make install
else
speak "Making..."
make
fi
# link executables (if we were told to)
if [ ! -z "${exec_link}" ]; then
while IFS=',' read -ra EXEC_ARR; do
for f in "${EXEC_ARR[@]}"; do
speak "Linking ${PU}${f}${NC}..."
f="${bdir}/${f}"
if [ -f "${f}" ]; then
chmod +x "${f}"
ln -s "${f}" "${bin_prefix}"
fi
done
done <<< "$exec_link"
fi
cd ..
}
## SIMPLE BUILD!
function build_from_tar_file() {
cd "${build_prefix}"
link="$1"
tarfile="${build_prefix}/$(basename "$link")"
dir="${tarfile%%.tar*}"
CLEANUP_FILES+=("${tarfile}")
wget "$link"
tar zxvf "${tarfile}"
cd "${dir}"
# remove the first positional param ($link)
shift
./configure --prefix="${local_prefix}" "$@"
make
make install
cd "${build_prefix}"
}
########################
# g++ (into local!!)
if [ ! -f "${local_prefix}/gcc-4.5.4/bin/gcc" ]; then
cd "${local_prefix}"
gmp="gmp-4.3.2"
mpfr="mpfr-2.4.2"
mpc="mpc-0.8.1"
gcc="gcc-4.5.4"
announce "Downloading and installing ${CY}${gcc}${NC}"
yell "-- thanks to solar via http://openwall.info/wiki/internal/gcc-local-build"
gmpdir="${local_prefix}/${gmp}"
mpfrdir="${local_prefix}/${mpfr}"
mpcdir="${local_prefix}/${mpc}"
gccdir="${local_prefix}/${gcc}"
mkdir -p "${gmpdir}"
mkdir -p "${mpfrdir}"
mkdir -p "${mpcdir}"
mkdir -p "${gccdir}"
speak "--- Downloading required tarballs into ${build_prefix}"
cd "${build_prefix}"
infrastlink="ftp://gcc.gnu.org/pub/gcc/infrastructure"
releaselink="ftp://gcc.gnu.org/pub/gcc/releases/${gcc}"
if [ ! -d "${gmpdir}/include" ]; then
speak "--- ${CY}${gmp}${NC}"
cd "${build_prefix}"
wget "${infrastlink}/${gmp}.tar.bz2"
tar xjf ${gmp}.tar.bz2
cd ${gmp}
./configure --prefix="${gmpdir}" --enable-cxx
nice -n 19 time make -j8
make install
make check
echo $?
CLEANUP_FILES+=("${build_prefix}/${gmp}.tar.bz2")
fi
if [ ! -d "${mpfrdir}/include" ]; then
speak "--- ${CY}${mpfr}${NC}"
cd "${build_prefix}"
wget "${infrastlink}/${mpfr}.tar.bz2"
tar xjf ${mpfr}.tar.bz2
cd ${mpfr}
./configure --prefix="${mpfrdir}" --with-gmp="${gmpdir}"
nice -n 19 time make -j8
make install
CLEANUP_FILES+=("${build_prefix}/${mpfr}.tar.bz2")
fi
if [ ! -d "${mpcdir}/include" ]; then
speak "--- ${CY}${mpc}${NC}"
cd "${build_prefix}"
wget "${infrastlink}/${mpc}.tar.gz"
tar xzf ${mpc}.tar.gz
cd ${mpc}
LD_LIBRARY_PATH=${gmpdir}/lib:${mpfrdir}/lib ./configure --prefix=${mpcdir} --with-gmp=${gmpdir} --with-mpfr=${mpfrdir}
LD_LIBRARY_PATH=${gmpdir}/lib:${mpfrdir}/lib nice -n 19 time make -j8
make install
CLEANUP_FILES+=("${build_prefix}/${mpc}.tar.gz")
fi
if [ ! -d "${gccdir}/include" ]; then
speak "--- ${CY}${gcc}${NC}"
cd "${build_prefix}"
if [ ! -d "${build_prefix}/${gcc}" ]; then
wget "${releaselink}/${gcc}.tar.bz2"
tar xjf ${gcc}.tar.bz2
fi
cd "${build_prefix}/${gcc}"
LD_LIBRARY_PATH=${gmpdir}/lib:${mpfrdir}/lib:${mpcdir}/lib ./configure --prefix=${gccdir} --with-gmp=${gmpdir} --with-mpfr=${mpfrdir} --with-mpc=${mpcdir} --host=x86_64-redhat-linux --enable-languages=c,c++,fortran --disable-multilib --enable-threads=posix
LD_LIBRARY_PATH=${gmpdir}/lib:${mpfrdir}/lib:${mpcdir}/lib nice -n 19 time make -j8
make install
CLEANUP_FILES+=("${build_prefix}/${gcc}.tar.bz2")
fi
FILE_ADD_TO="${profile_file}"
LINE_TO_ADD="export LD_LIBRARY_PATH=${gmpdir}/lib:${mpfrdir}/lib:${mpcdir}/lib:${gccdir}/lib64:\${LD_LIBRARY_PATH}"
check_if_line_exists || add_line_to_file
LINE_TO_ADD="export PATH=${gccdir}/bin:\$PATH"
check_if_line_exists || add_line_to_file
fi
########################
# autotools -- autconf and automake
# NOTE: current system has m4 vX.XX, which works fine
if [ ! -f "${bin_prefix}/autoconf" ] || [ ! -f "${bin_prefix}/automake" ];
then
if [ ! -f "${bin_prefix}/pkg-config" ]; then
announce "Downloading and compiling ${CY}pkg-config${NC}"
link="http://pkgconfig.freedesktop.org/releases/pkg-config-0.28.tar.gz"
build_from_tar_file "$link"
hash pkg-config
fi
if [ ! -f "${bin_prefix}/m4" ]; then
announce "Downloading and compiling ${CY}m4${NC}"
link="http://ftp.gnu.org/gnu/m4/m4-latest.tar.gz"
link="http://ftp.gnu.org/gnu/m4/m4-1.4.17.tar.gz"
# NOTE: The change in CPPFLAGS is necessary for older systems
build_from_tar_file "$link" CPPFLAGS="-fgnu89-inline"
hash m4
fi
if [ ! -f "${bin_prefix}/libtool" ]; then
announce "Downloading and compiling ${CY}libtool${NC}"
link="http://ftp.gnu.org/gnu/libtool/libtool-latest.tar.gz"
link="http://ftp.gnu.org/gnu/libtool/libtool-2.4.6.tar.gz"
build_from_tar_file "$link"
hash libtool
hash libtoolize
fi
if [ ! -f "${bin_prefix}/autoconf" ]; then
announce "Downloading and compiling ${CY}autoconf${NC}"
link="http://ftp.gnu.org/gnu/autoconf/autoconf-latest.tar.gz"
link="http://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.gz"
link="http://ftp.gnu.org/gnu/autoconf/autoconf-2.65.tar.gz"
build_from_tar_file "$link"
hash autoconf
hash autoreconf
hash autoheader
hash autom4te
hash autoscan
hash autoupdate
fi
if [ ! -f "${bin_prefix}/automake" ]; then
announce "Downloading and compiling ${CY}automake${NC}"
link="http://ftp.gnu.org/gnu/automake/automake-latest.tar.gz"
link="http://ftp.gnu.org/gnu/automake/automake-1.15.tar.gz"
build_from_tar_file "$link"
hash automake
hash aclocal
fi
fi
########################
# python3
if [ ! -f "${bin_prefix}/python3" ]; then
announce "Setting up ${CY}Python-3.4.3${NC}..."
cd "${build_prefix}"
link="https://www.python.org/ftp/python/3.4.3/Python-3.4.3.tgz"
pytar="$(basename ${link})"
pydir="${build_prefix}/$(basename ${link%%.tgz})"
CLEANUP_DIRS+=("${pydir}")
CLEANUP_FILES+=("${pytar}")
CLEANUP_DIRS+=("${venv_prefix}/py3")
CLEANUP_FILES+=("${bin_prefix}/python3")
CLEANUP_FILES+=("${bin_prefix}/pip3")
CLEANUP_FILES+=("${bin_prefix}/pyvenv")
speak "Downloading and compiling ${GR}${pytar}${NC}..."
wget ${link} --no-check-certificate
tar zxvf Python-3.4.3.tgz
cd Python-3.4.3
./configure --prefix="${local_prefix}" --exec_prefix="${local_prefix}"
make
make altinstall
# links
speak "Linking ${PU}python3${NC}, ${PU}pip3${NC}, ${PU}pyenv${NC}"
ln -s "${bin_prefix}/python3.4" "${bin_prefix}/python3"
ln -s "${bin_prefix}/pip3.4" "${bin_prefix}/pip3"
ln -s "${bin_prefix}/pyvenv-3.4" "${bin_prefix}/pyvenv"
# venv start script
speak "Creating virtual environment script ${PU}start${NC}"
scriptfile="${bin_prefix}/start"
cat >"${scriptfile}" <<EOL
#!/bin/bash
# A replacement for activate, based (shamelessly copied) on 'inve'
# -- thanks to datagrok via https://gist.github.com/datagrok/2199506
# Improvements (modifications?) for 'deactivate' and .bashrc from muppetjones
# NOTE: If you add to the front of your path in your .bashrc
# or .bash_profile, it will overwrite these settings.
# Consider using a conditional setup for VIRTUAL_ENV.
# if [ -z "$VIRTUAL_ENV" ]; then
# export PATH=/mypath/bin:${PATH}
# else
# alias deactivate='exit'
# export PATH=${PATH}:/mypath/bin:${lib_path}
# fi
# NOTE: To include prompt replacement, add the following to your .bashrc, etc:
# __venv_ps1() {
# if [ ! -z $VIRTUAL_ENV ]; then
# printf -- "(%s) " "$(basename ${VIRTUAL_ENV})"
# fi
# }
# PS1='$(declare -F __venv_ps1 &>/dev/null && __venv_ps1)$PS1'
export VIRTUAL_ENV="${venv_prefix}/\$1"
export PATH="$VIRTUAL_ENV/bin:$PATH"
unset PYTHONHOME
exec "$SHELL"
# Just to keep with tradition, allow the use of 'deactivate'
# NOTE: You must set "alias deactivate='exit'" in your .bashrc
# or .bash_profile, preferably conditionally defined
# within [ ! -z ${VIRTUAL_ENV} ] (see above example)
unalias deactivate
EOL
chmod +x "${scriptfile}"
speak "Creating virtual env ${BO}py3${NC} in ${GR}${venv_prefix}${NC}"
cd "${venv_prefix}"
pyvenv py3
DO_NOT_CLEAN "${dev_prefix}/Python-3.4.3"
DO_NOT_CLEAN "${venv_prefix}/py3"
DO_NOT_CLEAN "${dev_prefix}/Python-3.4.3.tgz"
DO_NOT_CLEAN "${bin_prefix}/python3"
DO_NOT_CLEAN "${bin_prefix}/pip3"
DO_NOT_CLEAN "${bin_prefix}/pyvenv"
cd "${dev_prefix}"
fi
########################
# Perl local::lib
if [ ! -f "${lib_prefix}/perl5/lib/perl5" ]; then
link="https://cpan.metacpan.org/authors/id/H/HA/HAARG/local-lib-2.000015.tar.gz"
local bdir=''
download_and_extract "$link" bdir
cd "$bdir"
local perl_lib="${lib_prefix}"/perl5
perl Makefile.PL --bootstrap="${perl_lib}"
make
make install
FILE_ADD_TO="${profile_file}"
LINE_TO_ADD="[ $SHLVL -eq 1 ] && eval \"$(perl -I${perl_lib}/lib/perl5 -Mlocal::lib=${perl_lib})\""
check_if_line_exists || add_line_to_file
fi
########################
# bowtie2
if [ ! -f "${bin_prefix}/bowtie2" ]; then
name="bowtie2"
link="git@github.com:BenLangmead/bowtie2.git"
bin_list="bowtie2,bowtie2-build,bowtie2-inspect"
download_and_compile $name $link --link=$bin_list
fi
########################
# R
if [ ! -f "${bin_prefix}/R" ]; then
name="R"
link="https://cran.r-project.org/src/base/R-3/R-3.2.1.tar.gz"
# NOTE: R requires gcc to be compiled for fortran
download_and_compile $name $link
fi
########################
# fastqc
if [ ! -f "${bin_prefix}/fastqc" ]; then
name="FastQC"
link="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.3.zip"
altdir="FastQC"
bin_list="fastqc"
download_and_compile $name $link --link=$bin_list
fi
########################
# TagDust
if [ ! -f "${bin_prefix}/tagdust" ]; then
name="TagDust"
link="http://sourceforge.net/projects/tagdust/files/tagdust-2.31.tar.gz/download"
bin_list="tagdust2"
download_and_compile $name $link --link=$bin_list
fi
########################
# Skewer
if [ ! -f "${bin_prefix}/skewer" ]; then
name="Skewer"
link="http://sourceforge.net/projects/skewer/files/Binaries/skewer-0.1.127-linux-x86_64/download"
bin_list="skewer"
cd "${bin_prefix}"
wget "${link}"
ln -s "${bin_prefix}/skewer-0.1.127-linux-x86_64" "skewer"
chmod +x skewer*
fi
########################
# GNU scientific library
if [ ! -f "${bin_prefix}/gsl-1.6"* ]; then
name="GSL"
link="http://gnu.mirror.vexxhost.com/gsl/gsl-1.16.tar.gz"
download_and_compile $name $link
FILE_ADD_TO="${profile_file}"
LINE_TO_ADD="export LD_LIBRARY_PATH=${lib_prefix}:${lib_prefix}64:\${LD_LIBRARY_PATH}"
check_if_line_exists || add_line_to_file
FILE_ADD_TO="${profile_file}"
LINE_TO_ADD="export CPATH=${local_prefix}/include:\${CPATH}"
check_if_line_exists || add_line_to_file
fi
########################
# EA-utils
if [ ! -f "${bin_prefix}/fastq-mcf" ]; then
name="EA-utils"
announce "Downloading and installing ${CY}${name}${NC}"
link="http://ea-utils.googlecode.com/svn/trunk/"
bin_list="skewer"
cd "${build_prefix}"
svn checkout http://ea-utils.googlecode.com/svn/trunk/ ea-utils-read-only
cd ea-utils-read-only/clipper
PREFIX="${local_prefix}" make install
fi
########################
# kSNP
if [ ! -f "${bin_prefix}/kSNP3" ]; then
announce "Downloading and installing ${CY}kSNP 3.0${NC}"
cd "${dev_prefix}"
link="http://sourceforge.net/projects/ksnp/files/kSNP3.0_Linux_package.zip/download"
ksnptar="$(basename $(dirname "${link}"))"
ksnpdir="${dev_prefix}/${ksnptar%%.zip}"
ksnpdir_rename="kSNP3_Linux"
CLEANUP_FILES+=("${dev_prefix}/${ksnptar}")
if [ ! -d "${ksnpdir_rename}" ]; then
wget "${link}" --no-check-certificate
unzip "${ksnptar}"
mv "${ksnpdir}" "kSNP3_Linux"
perl -pi -e "s|(set kSNP=)/usr/local/kSNP3|\1$(pwd)/kSNP3|" "${ksnpdir}/kSNP3/kSNP3"
fi
ksnpdir="${dev_prefix}/kSNP3_Linux"
cd "${ksnpdir}"
cat >"${ksnpdir}/run_me.sh" <<EOL
#!/bin/bash
# Run __prog__ in whatever folder you darn well please.
PATH=${ksnpdir}/kSNP3:$PATH
"${ksnpdir}/kSNP3/__prog__" "\$@"
EOL
function make_ksnp_command() {
prog_name=$1
script_name="${ksnpdir}/kSNP3/run_${prog_name}.sh"
cp "${ksnpdir}/run_me.sh" "${script_name}"
perl -pi -e "s/__prog__/${prog_name}/g" "${script_name}"
ln -s "${script_name}" "${bin_prefix}/${prog_name}"
chmod +x "${script_name}"
}
make_ksnp_command Kchooser
make_ksnp_command kSNP3
make_ksnp_command MakeFasta
fi
########################
# jellyfish
if [ ! -d "${dev_prefix}/jellyfish-2.2.3" ]; then
announce "Cloning and installing ${CY}Jellyfish${NC}"
cd "${build_prefix}"
# github install
# -- requires g++ >= 4.4
# link="git@github.com:gmarcais/Jellyfish.git"
# gdir="${dev_prefix}/$(basename "${gitssh%%.git}")"
# CLEANUP_DIRS+=("${gdir}")
# git clone "${link}"
# cd "${gdir}"
# autoreconf -i
# ./configure --prefix="${local_prefix}" --enable-python-binding="${lib_prefix}/python3.4"
# make
# make install
link="https://github.com/gmarcais/Jellyfish/releases/download/v2.2.3/jellyfish-2.2.3.tar.gz"
tarfile="$(basename "$link")"
dir="$(pwd)/${tarfile%%.tar.gz}"
CLEANUP_DIRS+=("${dir}")
CLEANUP_FILES+=("${build_prefix}/${tarfile}")
curl -O -L -k "${link}" # redirects to amazon s3...very frustrating
tar zxvf "${tarfile}"
cd "${dir}"
./configure --prefix="${local_prefix}" --enable-python-binding="${lib_prefix}/python3.4"
make
make install
DO_NOT_CLEAN "${dir}"
cd "${dev_prefix}"
fi
########################
# Parsimonator
if [ ! -f "${bin_prefix}/parsimonator" ]; then
announce "Cloning and installing ${CY}Parsimonator${NC}"
cd "${build_prefix}"
link="git@github.com:stamatak/Parsimonator-1.0.2.git"
gdir="$(pwd)/$(basename "${link%%.git}")"
git clone "${link}"
cd "${gdir}"
make -f Makefile.gcc
ln -s "${gdir}/parsimonator" "${bin_prefix}/"
fi
########################
# Mummer
if [ ! -f "${bin_prefix}/mummer" ]; then
announce "Downloading and installing ${CY}Mummer${NC}"
cd "${build_prefix}"
link="http://sourceforge.net/projects/mummer/files/latest/download"
file=$(LANG=C wget "${link}" 2>&1 | sed -n "s/.*- \`\(.*\)' saved.*/\1/p")
dir="$(pwd)/$(basename "${file%%.tar.gz*}")"
CLEANUP_FILES+=("${build_prefix}/${file}")
tar zxvf "${file}"
cd "${dir}"
make check
make install
for f in *; do
if [-f "${f}" ] && [ -x "${f}" ]; then
ln -s "$(pwd)/${f}" "${bin_prefix}/"
fi
done
fi
########################
# Primux -- already in kSNP (and a pain to get working)
# if [ ! -f "${bin_prefix}/primux" ]; then
# announce "Downloading and installing ${CY}Primux${NC}"
# # NOTE: The tar creates a 'primux' directory (no version name)
#
# cd "${build_prefix}"
# set -x
# link="http://sourceforge.net/projects/primux/files/primux_20_july_2014.tar.gz/download"
# file="$(basename $(dirname "${link}"))"
# dir="$(pwd)/${filename%%.tar*}"
# wget -O "${file}" "${link}"
#
# CLEANUP_FILES+=("${file}")
#
# tar zxvf "${file}"
# cd "${dir}"
#
# make check
# make install
# fi
########################
# Phylip
# -- kSNP uses consense, but it is finicky
if [ ! -f "${build_prefix}/phylip-3.696/exe/consense" ]; then
announce "Downloading and installing ${CY}Phylip${NC}"
cd "${build_prefix}"
link="http://evolution.gs.washington.edu/phylip/download/phylip-3.696.tar.gz"
file="$(basename "${link}")"
dir="$(pwd)/${file%%.tar*}"
CLEANUP_FILES+=("${build_prefix}/${file}")
if [ ! -d "$dir/src" ]; then
wget "$link"
tar zxvf "$file"
cd "$dir/src"
fi
if [ ! -f "$dir/exe/consense" ]; then
make -f Makefile.unx install
fi
# fix the kSNP situation
ksnplink="$(readlink -f "${bin_prefix}/kSNP3")"
ksnpdir="$(dirname "${ksnplink}")"
if [ -d "${ksnpdir}" ]; then
mkdir -p "${ksnpdir}/backup"
mv "${ksnpdir}/consense" "${ksnpdir}/backup/"
ln -s "${dir}/exe/consense" "${ksnpdir}"
fi
fi
########################
# RAST (and SEED)
# -- annotate prokaryotic genomes
# -- does NOT contain parent directory!!
if [[ ! "${PATH}" != *"/sas/bin"* ]]; then
announce "Downloading and installing ${CY}RAST${NC}"
cd "${build_prefix}"
link="http://blog.theseed.org/downloads/sas-33a23.tgz"
link="http://blog.theseed.org/downloads/sas.tgz"
file="$(basename "${link}")"
dir="$(pwd)/${file%%.tgz}"
CLEANUP_FILES+=("${dir}/${file}")
if [ ! -d "$dir/modules" ]; then
mkdir -p "${dir}"
cd "${dir}"
wget "$link"
tar zxvf "$file"
fi
cd "${dir}/modules"
./BUILD_MODULES
FILE_ADD_TO="${profile_file}"
LINE_TO_ADD="export PERL5LIB=\$PERL5LIB:${dir}/lib:${dir}/modules/lib"
check_if_line_exists || add_line_to_file
LINE_TO_ADD="export PATH=\$PATH:${dir}/bin"
check_if_line_exists || add_line_to_file
fi
#######################
# Pstat
if [ ! -f "${bin_prefix}/pstat" ]; then
cd "${build_prefix}"
link="git@github.com:muppetjones/qstat-pretty.git"
gdir="$(pwd)/$(basename "${link%%.git}")"
git clone "${link}"
cd "${gdir}"
python setup.py build
ln -s "${gdir}/pstat" "${bin_prefix}/"
fi
# source profile
source "${profile_file}"
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