Merge pull request #59 from qiyunzhu/bash

DarkHorse2 automated installation script

benchmark/run_phylomizer.sh

@@ -99,7 +99,7 @@ do
 
     # report the best aa substitution model and the -log likelihood of the tree
     best_tree=$(head -n1 input.tree.phyml.rank.ml)
-    best_model=$(echo ${best_tree} | cut -f1)
+    best_model=$(echo "${best_tree}" | cut -f1)
     printf "$i\t$gene\t${best_tree}\n" >> $output_fp
 
     # copy the best tree to the gene tree directory

benchmark/utils.sh

@@ -33,7 +33,7 @@ function get_args() {
     for arg in ${args[@]}
     do
         # set undefined arguments to None
-        if [ -z "$(echo ${!arg})" ]
+        if [ -z "${!arg+x}" ]
         then
             eval $(echo $arg)=None
 

darkhorse/install_darkhorse.sh

@@ -0,0 +1,178 @@
+#!/bin/bash
+
+# ----------------------------------------------------------------------------
+# Copyright (c) 2015--, The WGS-HGT Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+# ----------------------------------------------------------------------------
+
+# automated installation script for DarkHorse2
+# this script will install:
+#   MySQL 5.7.18
+#   NCBI nr, taxdump and prot.accession2taxid (up-to-date)
+#   DarkHorse 2.0_rev07
+# the whole system (including MySQL) will run in a local directory and won't
+# affect anything outside
+# usage:
+#   bash install_darkhorse.sh /target/directory/to/install
+
+set -eu
+
+# confirm target install directory
+if [ $# -eq 0 ]
+then
+    echo "usage: bash install_darkhorse.sh /target/install/directory"
+    exit 1
+fi
+appdir=$(readlink -m $1)
+
+# download and compile MySQL source code
+mkdir -p $appdir/mysql
+url=https://dev.mysql.com/get/Downloads/MySQL-5.7/mysql-boost-5.7.18.tar.gz; wget $url || curl -O $url
+tar -zxvf mysql-boost-5.7.18.tar.gz
+cd mysql-5.7.18
+cmake -D MYSQL_DATADIR=$appdir/mysql/data \
+      -D SYSCONFDIR=$appdir/mysql/etc \
+      -D CMAKE_INSTALL_PREFIX=$appdir/mysql \
+      -D WITH_BOOST=./boost .
+make
+make install
+
+# clean up installation files
+cd ..
+rm mysql-boost-5.7.18.tar.gz
+rm -rf mysql-5.7.18
+
+# find an unused port number
+#   the default MySQL port is 3306
+#   to avoid conflict with system-wide MySQL (if any), search from 3307
+port=3307
+while true
+do
+    netstat -tlnp | grep $port && ((port++)) || break
+done
+
+# create MySQL configuration file
+mkdir -p $appdir/mysql/etc
+echo "
+[client]
+port           = $port
+socket         = $appdir/mysql/mysql.sock
+[mysqld]
+port           = $port
+socket         = $appdir/mysql/mysql.sock
+basedir        = $appdir/mysql
+datadir        = $appdir/mysql/data
+sql_mode       = NO_ENGINE_SUBSTITUTION
+[mysqld_safe]
+log-error      = $appdir/mysql/data/mysql.err
+pid-file       = $appdir/mysql/mysql.pid
+" > $appdir/mysql/etc/my.cnf
+
+export PATH=$appdir/mysql/bin:$PATH
+
+# initialize MySQL serivce
+mysqld --initialize-insecure
+sleep 60
+
+# start MySQL serivce
+mysqld &
+sleep 60
+
+# set up MySQL account
+#   username: root, password: password
+mysql -u root --skip-password -e "ALTER USER 'root'@'localhost' IDENTIFIED BY 'password';"
+
+# download NCBI database
+mkdir -p $appdir/ncbi
+cd $appdir/ncbi
+url=ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nr.gz; wget $url || curl -O $url
+url=ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz; wget $url || curl -O $url
+url=ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz; wget $url || curl -O $url
+gunzip nr.gz
+mkdir -p taxdump
+tar -zxvf taxdump.tar.gz -C taxdump
+rm taxdump.tar.gz
+gunzip prot.accession2taxid.gz
+
+# install required Perl modules
+export PERL_MM_USE_DEFAULT=1
+perl -MCPAN -e 'install App::cpanminus'
+cpanm DBI DBD::mysql
+
+# download DarkHorse 2-rev07
+dhv=rev07
+mkdir -p $appdir/darkhorse
+cd $appdir/darkhorse
+url=https://github.com/spodell/Darkhorse2/archive/$dhv.tar.gz; wget $url || curl -O $url
+tar -zxvf $dhv.tar.gz
+mv Darkhorse2-$dhv 2-$dhv
+rm $dhv.tar.gz
+
+# patch DarkHorse scripts
+#   let DarkHorse connect MySQL via a custom socket
+before='my $db_path = "DBI:$db_program:$db_name:$db_host:";'
+after1='my $db_path = "DBI:$db_program:$db_name:$db_host;mysql_socket=".$config_params{db_socket};'
+after2='my $db_path = "DBI:$db_program:$db_name:$db_host;mysql_socket=".$dh_config{db_socket};'
+cd $appdir/darkhorse/2-$dhv
+while read pl
+do
+    chmod +x $pl
+    grep -q "%config_params" $pl \
+         && sed -i "s/$before/$after1/g" $pl \
+         || sed -i "s/$before/$after2/g" $pl
+done <<< "$(find . -name '*.pl' -type f)"
+
+# create DarkHorse configuration file
+echo "
+# DarkHorse2 configuration file for the WGS-HGT pipeline
+# installation parameters
+[program_directory]=$appdir/darkhorse/2-$dhv
+[genbank_nr_fasta_path]=$appdir/ncbi/nr
+[names_dmp_path]=$appdir/ncbi/taxdump/names.dmp
+[nodes_dmp_path]=$appdir/ncbi/taxdump/nodes.dmp
+[protid_taxid_dmp_path]=$appdir/ncbi/prot.accession2taxid
+# database access parameters
+[db_name]=dh2nr
+[db_program]=mysql
+[db_host]=localhost
+[db_user]=root
+[db_user_password]=password
+[db_socket]=$appdir/mysql/mysql.sock
+[max_lines_per_packet]=4000
+[min_lineage_terms]=2
+[min_align_coverage]=0.7
+" > $appdir/darkhorse/config.txt
+
+# create DarkHorse database
+mysql -u root -ppassword -e "CREATE DATABASE dh2nr;"
+
+# run DarkHorse installation script
+perl install_darkhorse2.pl -c $appdir/darkhorse/config.txt
+
+# stop MySQL service
+mysqladmin -u root -ppassword shutdown
+
+# finish up
+echo "
+Summary:
+MySQL 5.7.18 has been installed at: $appdir/mysql.
+  user: root
+  password: password
+  port: $port
+  socket: $appdir/mysql/mysql.sock
+DarkHorse 2-$dhv has been installed at: $appdir/darkhorse.
+NCBI nr database has been downloaded at: $appdir/ncbi.
+MySQL database dh2nr has been created.
+
+To use DarkHorse, start MySQL first:
+  export PATH=$appdir/mysql/bin:\$PATH
+  mysqld &
+
+When completed, shut down MySQL:
+  mysqladmin -u root -ppassword shutdown
+
+"
+echo "Task completed."