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add PhaME installation script and testing dataset
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@chienchi
chienchi committed Sep 22, 2015
1 parent c621a60 commit 7c53eaa
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354 changes: 354 additions & 0 deletions INSTALL.sh
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#!/bin/bash

rootdir=$( cd $(dirname $0) ; pwd -P )

export PATH=$rootdir/ext/bin/:$PATH;
export PERL5LIB=$rootdir/ext/lib/:$PERL5LIB;
mkdir -p bin;

done_message () {
if [ $? == 0 ]; then
if [ "x$1" != "x" ]; then
echo $1;
else
echo "done.";
fi
else
echo "Installation failed." $2
exit 1;
fi
}

download_ext () {
if [ -e $2 ]; then
echo "$2 existed. Skiping downloading $1."
return;
fi;

if hash curl 2>/dev/null; then
curl -L $1 -o $2;
else
wget -O $2 $1;
fi;

if [ -z $2 ]; then
echo "ERROR: $1 download failed."
fi;
}

if ! hash unzip 2>/dev/null; then
echo "WARNNING: Unzip not found. You might experience error in further installation.";
fi;

echo "Checking NUCMER ..."

NUCMER_VER=`nucmer --version 2>&1 | grep -Po " version \d+\.\d+" | grep -Po "\d+\.\d+"`;

if ( hash nucmer 2>/dev/null ) && ( echo $NUCMER_VER | awk '{if($_>="3.07") exit 0; else exit 1}' )

then
echo "NUCmer >=3.07 found.";
else
echo "NUCmer >=3.07 or above not found/. Trying to download from https://github.com/chienchi/MUMmer/archive/master.zip ...";
mkdir -p ext/opt;
mkdir -p ext/bin;
download_ext https://github.com/chienchi/MUMmer/archive/master.zip ext/opt/nucmer.zip;
unzip ext/opt/nucmer.zip -d ext/opt/;
cd ext/opt/MUMmer-master;
make CPPFLAGS="-O3 -DSIXTYFOURBITS";
cp nucmer $rootdir/ext/bin/.
cp show-coords $rootdir/ext/bin/.
cp show-snps $rootdir/ext/bin/.
cp mgaps $rootdir/ext/bin/.
cp delta-filter $rootdir/ext/bin/.
cd $rootdir;
fi;
done_message " Done." "";

echo "Checking BWA ..."

BWA_VER=`bwa 2>&1 | grep -Po "Version: \d+\.\d+" | grep -Po "\d+\.\d+"`;

if ( hash bwa 2>/dev/null ) && ( echo $BWA_VER | awk '{if($_>="0.7") exit 0; else exit 1}' )
then
echo "BWA >=0.7 found.";
else
echo "BWA >=0.7 or above not found. Trying to download from https://github.com/lh3/bwa/archive/master.zip ...";
mkdir -p ext/opt;
mkdir -p ext/bin;
download_ext https://github.com/lh3/bwa/archive/master.zip ext/opt/bwa.zip;
unzip ext/opt/bwa.zip -d ext/opt/;
cd ext/opt/bwa-master;
make;
cd $rootdir;
cp ext/opt/bwa-master/bwa ext/bin/;
fi;
done_message " Done." "";

echo "Checking bowtie ..."

BOWTIE_VER=`bowtie2 2>&1 | grep -Po "version \d+\.\d+\.\d+" | grep -Po "\d+\.\d+\.\d+"`;

if ( hash bowtie2 2>/dev/null ) && ( echo $BOWTIE_VER | awk '{if($_>="2.1.0") exit 0; else exit 1}' )
then
echo "bowtie2 >=2.1.0 found.";
else
echo "bowtie >=2.1.0 or above not found. Trying to download from https://github.com/BenLangmead/bowtie2/archive/master.zip ...";
mkdir -p ext/opt;
mkdir -p ext/bin;
download_ext https://github.com/BenLangmead/bowtie2/archive/master.zip ext/opt/bowtie2.zip;
unzip ext/opt/bowtie2.zip -d ext/opt/;
cd ext/opt/bowtie2-master;
make;
cp bowtie2-build* $rootdir/ext/bin/.
cp bowtie2-align* $rootdir/ext/bin/.
cp bowtie2 $rootdir/ext/bin/.
cd $rootdir;
fi;
done_message " Done." "";

echo "Checking SAMtools ..."

SAMTOOLS_VER=`samtools 2>&1 | grep -Po "Version: \d+\.\d+\.\d+" | grep -Po "\d+\.\d+\.\d+"`;

if ( hash samtools 2>/dev/null ) && ( echo $SAMTOOLS_VER | awk '{if($_=="0.1.20") exit 0; else exit 1}' )
then
echo "samtools == 0.1.20 found.";
else
echo "samtools == 0.1.20 not found. Trying to download from https://github.com/samtools/samtools/archive/0.1.20.zip ...";
mkdir -p ext/opt;
mkdir -p ext/bin;
download_ext https://github.com/samtools/samtools/archive/0.1.20.zip ext/opt/samtools-0.1.20.zip;
unzip ext/opt/samtools-0.1.20.zip -d ext/opt/;
cd ext/opt/samtools-0.1.20;
make;
cd $rootdir;
cp ext/opt/samtools-0.1.20/samtools ext/bin/;
cp ext/opt/samtools-0.1.20/bcftools/bcftools ext/bin/;
cp ext/opt/samtools-0.1.20/bcftools/vcfutils.pl ext/bin/;
fi;
done_message " Done." "";

echo "Checking FastTree ..."

FASTTREE_VER=`FastTreeMP 2>&1 | grep -Po "version \d+\.\d+\.\d+" | grep -Po "\d+\.\d+\.\d+"`;

if ( hash FastTreeMP 2>/dev/null ) && ( echo $FASTTREE_VER | awk '{if($_>="2.1.8") exit 0; else exit 1}' )
then
echo "FastTree >=2.1.8 found.";
else
echo "FastTree >=2.1.8 not found. Trying to download from http://www.microbesonline.org/fasttree/FastTree.c ...";
mkdir -p ext/opt;
mkdir -p ext/bin;
download_ext http://www.microbesonline.org/fasttree/FastTree.c ext/opt/FastTree.c;
cd ext/opt/;
gcc -DOPENMP -DUSE_DOUBLE -fopenmp -O3 -finline-functions -funroll-loops -Wall -o FastTreeMP FastTree.c -lm ;
cd $rootdir;
cp ext/opt/FastTreeMP ext/bin/;
fi;
done_message " Done." "";

echo "Checking RAxML ..."

RAXML_VER=`raxmlHPC-PTHREADS -version 2>&1 | grep -Po "version \d+\.\d+\.\d+" | grep -Po "\d+\.\d+\.\d+"`;

if ( hash raxmlHPC-PTHREADS 2>/dev/null ) && ( echo $RAXML_VER | awk '{if($_>="8.0") exit 0; else exit 1}' )
then
echo "RAxML >=8.0 found.";
else
echo "RAxML >=8.0 not found. Trying to download from https://github.com/stamatak/standard-RAxML/archive/master.zip ...";
mkdir -p ext/opt;
mkdir -p ext/bin;
download_ext https://github.com/stamatak/standard-RAxML/archive/master.zip ext/opt/RAxML8.zip;
unzip ext/opt/RAxML8.zip -d ext/opt/;
cd ext/opt/standard-RAxML-master;
make -f Makefile.SSE3.PTHREADS.gcc
cd $rootdir;
cp ext/opt/standard-RAxML-master/raxmlHPC-PTHREADS-SSE3 ext/bin/raxmlHPC-PTHREADS;
fi;
done_message " Done." "";

echo "Checking MUSCLE ..."

MUSCLE_VER=`muscle -version 2>&1 | grep -Po "\d+\.\d+\.\d+"`;

if ( hash muscle 2>/dev/null ) && ( echo $MUSCLE_VER | awk '{if($_>="3.8.0") exit 0; else exit 1}' )
then
echo "MUSCLE >=3.8.0 found.";
else
echo "MUSCLE >=3.8.0 not found. Trying to download from http://www.drive5.com/muscle/downloads3.8.31/ ...";
mkdir -p ext/opt;
mkdir -p ext/bin;
#determine platform
MUSCULE_URL="http://www.drive5.com/muscle/downloads3.8.31"
FILENAME="muscle3.8.31_i86linux64"
UNAME=`uname`
UNAMEM=`uname -m`
if echo $UNAME | grep -i "linux" | grep -i "x86_64" > /dev/null; then
MUSCULE_URL="$MUSCULE_URL/${FILENAME}.tar.gz"
elif echo $UNAME | grep -i "^linux" > /dev/null; then
FILENAME="muscle3.8.31_i86linux32"
MUSCULE_URL="$MUSCULE_URL/${FILENAME}.tar.gz"
elif echo $UNAME | grep -i "darvin" | grep -i "x86_64" > /dev/null; then
FILENAME="muscle3.8.31_i86darwin64"
MUSCULE_URL="$MUSCULE_URL/${FILENAME}.tar.gz"
elif echo $UNAME | grep -i "darvin" > /dev/null; then
FILENAME="muscle3.8.31_i86darwin32"
MUSCULE_URL="$MUSCULE_URL/${FILENAME}.tar.gz"
fi;

download_ext $MUSCULE_URL ext/opt/muscle.tar.gz;
cd ext/opt/
tar xvzf muscle.tar.gz
mv $FILENAME $rootdir/ext/bin/
cd $rootdir;
fi;
done_message " Done." "";

echo "Checking MAFFT ..."

MAFFT_VER=`mafft -version 2>&1 | grep "MAFFT v" | grep -Po "\d+\.\d+"`;

if ( hash mafft 2>/dev/null ) && ( echo $MAFFT_VER | awk '{if($_ >= 7.221) exit 0; else exit 1}' )
then
echo "MAFFT >=7.221 found.";
else
echo "MAFFT >=7.221 not found. Trying to download from http://mafft.cbrc.jp/alignment/software/mafft-7.221-without-extensions-src.tgz ...";
mkdir -p ext/opt;
mkdir -p ext/bin;
download_ext http://mafft.cbrc.jp/alignment/software/mafft-7.221-without-extensions-src.tgz ext/opt/mafft-7.221-without-extensions-src.tgz;
cd ext/opt/
tar xvzf mafft-7.221-without-extensions-src.tgz
cd mafft-7.221-without-extensions/core;
sed -i.bak 's,PREFIX = \/usr\/local,'"PREFIX = $rootdir/ext"',' Makefile
make clean && make && make install
cd $rootdir;
fi;
done_message " Done." "";


echo "Checking PAL2NAL ..."

PAL2NAL_VER=`pal2nal.pl 2>&1 | grep "pal2nal.pl" | grep -Po "v\d+" | grep -Po "\d+"`;

if ( hash pal2nal.pl 2>/dev/null ) && ( echo $PAL2NAL_VER | awk '{if($_>="14") exit 0; else exit 1}' )
then
echo "PAL2NAL >=14 found.";
else
echo "PAL2NAL >=14 not found. Trying to download from http://www.bork.embl.de/pal2nal/distribution/pal2nal.v14.tar.gz ...";
mkdir -p ext/opt;
mkdir -p ext/bin;
download_ext http://www.bork.embl.de/pal2nal/distribution/pal2nal.v14.tar.gz ext/opt/pal2nal.v14.tar.gz;
cd ext/opt/
tar xvzf pal2nal.v14.tar.gz
cd $rootdir;
cp ext/opt/pal2nal.v14/pal2nal.pl ext/bin/;
fi;
done_message " Done." "";

echo "Checking PAML ..."

PAML_VER=`evolver \0 2>&1 | grep "version" | grep -Po "\d+\.\d+"`;

if ( hash evolver 2>/dev/null ) && ( echo $PAML_VER | awk '{if($_>=4.8) exit 0; else exit 1}' )
then
echo "PAML >=4.8 found.";
else
echo "PAML >=4.8 not found. Trying to download from http://abacus.gene.ucl.ac.uk/software/pamlX1.3.1+paml4.8a-win32.tgz ...";
mkdir -p ext/opt;
mkdir -p ext/bin;
download_ext http://abacus.gene.ucl.ac.uk/software/pamlX1.3.1+paml4.8a-win32.tgz ext/opt/pamlX1.3.1+paml4.8a-win32.tgz;
cd ext/opt/
tar xvzf pamlX1.3.1+paml4.8a-win32.tgz
cd paml4.8/;
rm bin/*.exe
cd src
make -f Makefile
cp baseml basemlg codeml evolver pamp yn00 mcmctree chi2 $rootdir/ext/bin/;
cd $rootdir
fi;
done_message " Done." "";

echo "Checking CMake the cross-platform, open-source build system. ..."

CMake_VER=`cmake -version 2>&1 | grep -Po "\d+\.\d+\.\d+"`;

if ( hash cmake 2>/dev/null ) && ( echo $CMake_VER | awk '{if($_>="3.0.0") exit 0; else exit 1}' )
then
echo "CMake >=3.0.0 found."
else
echo "CMake >=3.0.0 not found. Trying to download from https://github.com/Kitware/CMake/archive/master.zip ..."
mkdir -p ext/opt;
mkdir -p ext/bin;
download_ext https://github.com/Kitware/CMake/archive/master.zip ext/opt/CMake.zip;
unzip ext/opt/CMake.zip -d ext/opt/;
cd ext/opt/CMake-master;
./bootstrap --prefix=$rootdir/ext && make && make install
cd $rootdir
fi;
done_message " Done." "";

echo "Checking HyPhy ..."

HyPhy_VER=`echo -e "1\n2\n3" | HYPHYMP 2>&1 | grep HYPHY | grep -Po "\d+\.\d+"`;

if ( hash HYPHYMP 2>/dev/null ) && ( echo $HyPhy_VER | awk '{if($_>="2.2") exit 0; else exit 1}' )
then
echo "HyPhy >=2.2 found.";
else
echo "HyPhy >=2.2 not found. Trying to download from https://github.com/veg/hyphy/archive/master.zip ...";
mkdir -p ext/opt;
mkdir -p ext/bin;
download_ext https://github.com/veg/hyphy/archive/master.zip ext/opt/HyPhy.zip;
unzip ext/opt/HyPhy.zip -d ext/opt/;
cd ext/opt/hyphy-master;
cmake -DINSTALL_PREFIX=$rootdir/ext
make MP2 && make install
make GTEST
./HYPHYGTEST
cd $rootdir
fi;
done_message " Done." "";

echo "Installing Perl dependencies..."

if hash cpanm 2>/dev/null; then
echo "cpanm found. Start installing Perl dependencies..."
else
echo "cpanm not found. Downloading from http://cpanmin.us..."
download_ext http://cpanmin.us ext/bin/cpanm;
chmod a+x ext/bin/cpanm;
fi
( set -xe;
perl -MGetopt::Long -e 1 > /dev/null 2>&1 || cpanm -v --notest -l ext Getopt::Long;
perl -MTime::HiRes -e 1 > /dev/null 2>&1 || cpanm -v --notest -l ext Time::HiRes;
perl -MFile::Path -e 1 > /dev/null 2>&1 || cpanm -v --notest -l ext File::Path;
perl -MFile::Basename -e 1 > /dev/null 2>&1 || cpanm -v --notest -l ext File::Basename;
perl -MFile::Copy -e 1 > /dev/null 2>&1 || cpanm -v --notest -l ext File::Copy;
perl -MIO::Handle -e 1 > /dev/null 2>&1 || cpanm -v --notest -l ext IO::Handle;
perl -MParallel::ForkManager -e 1 > /dev/null 2>&1 || cpanm -v --notest -l ext Parallel::ForkManager;
perl -MStatistics::Distributions -e 1 > /dev/null 2>&1 || cpanm -v --notest -l ext Statistics::Distributions;
)
done_message "Done installing Perl dependencies." "Failed installing Perl dependencies.";

echo -n "Moving scripts...";
( set -e;
cp src/*.pl bin/
chmod a+x bin/*
)
done_message " Done." "Failed installing PhaME scripts.";

rm -f ext/opt/*zip ext/opt/*gz
rm -f evolver.out messages.log

echo "
================================================================================
PhaME installed successfully.
================================================================================
Check phame.ctl for the control file
Quick start:
bin/runPhaME.pl phame.ctl
Check our github site for update:
https://github.com/LANL-Bioinformatics/PhaME
";
9 changes: 7 additions & 2 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ Provides evolutionary analyses (genes under positive selection) using CDS SNPs.

* SAMtools version 0.1.19 and vcftools - Convert BAM files created by Bowtie

* FastTree version >=2.1.7- Contruction of phylogenetic tree
* FastTree version >=2.1.8- Contruction of phylogenetic tree

* RAxML version >=8.0.26 - Maximum likelihood construction of phylogenetic tree

Expand All @@ -38,6 +38,11 @@ Provides evolutionary analyses (genes under positive selection) using CDS SNPs.
You can use "git" to obtain the package:

$ git clone https://github.com/LANL-Bioinformatics/PhaME.git

### Installing PhaME

$ cd PhaME
$ ./INSTALL.sh

--------------------------------------------------------------
### Running PhaME
Expand All @@ -64,7 +69,7 @@ INPUT files required

From the working directory that contains the control file run the following command to extract whole genome SNPs

$ runPhaME.pl
$ bin/runPhaME.pl test/phame.ctl

#### OUTPUT files

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