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INSTALL.sh
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INSTALL.sh
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#!/usr/bin/env bash
set -e
rootdir=$( cd $(dirname $0) ; pwd -P )
exec > >(tee install.log)
exec 2>&1
cd $rootdir
cd thirdParty
mkdir -p $rootdir/bin
export PATH=$PATH:$rootdir/bin/:$rootdir/thirdParty/Anaconda2/bin
export CPLUS_INCLUDE_PATH=$rootdir/thirdParty/Anaconda2/include/:$CPLUS_INCLUDE_PATH
if [ ! -d $HOME ]; then export HOME=$rootdir; fi
gcc_version=$(gcc -dumpversion)
anaconda3bin=$rootdir/thirdParty/Anaconda3/bin
anaconda2bin=$rootdir/thirdParty/Anaconda2/bin
assembly_tools=( idba spades megahit lrasm racon unicycler )
annotation_tools=( prokka RATT tRNAscan barrnap BLAST+ blastall phageFinder glimmer aragorn prodigal tbl2asn ShortBRED antismash rgi )
utility_tools=( FaQCs bedtools R GNU_parallel tabix JBrowse bokeh primer3 samtools bcftools sratoolkit ea-utils omics-pathway-viewer NanoPlot Porechop seqtk Rpackages Chromium )
alignments_tools=( hmmer infernal bowtie2 bwa mummer diamond minimap2 rapsearch2 )
taxonomy_tools=( kraken2 metaphlan2 kronatools gottcha gottcha2 centrifuge miccr pangia )
phylogeny_tools=( FastTree RAxML )
perl_modules=( perl_parallel_forkmanager perl_excel_writer perl_archive_zip perl_string_approx perl_pdf_api2 perl_html_template perl_html_parser perl_JSON perl_bio_phylo perl_xml_twig perl_cgi_session perl_email_valid perl_mailtools )
python_packages=( Anaconda2 Anaconda3 )
metagenome_tools=( MaxBin checkM )
pipeline_tools=( DETEQT reference-based_assembly PyPiReT qiime2 )
all_tools=( "${pipeline_tools[@]}" "${python_packages[@]}" "${assembly_tools[@]}" "${annotation_tools[@]}" "${utility_tools[@]}" "${alignments_tools[@]}" "${taxonomy_tools[@]}" "${phylogeny_tools[@]}" "${metagenome_tools[@]}" "${perl_modules[@]}")
### Install functions ###
install_MaxBin(){
local VER=2.2.6
echo "------------------------------------------------------------------------------
Installing MaxBin
------------------------------------------------------------------------------
"
tar xzf FragGeneScan1.31.tar.gz
cd FragGeneScan1.31
make clean
make fgs
cd $rootdir/thirdParty
tar xzf MaxBin-$VER.tar.gz
cd MaxBin-$VER
cd src
make
cd ..
cat << _EOM > setting
[FragGeneScan] $rootdir/thirdParty/FragGeneScan1.31
[Bowtie2] $rootdir/bin
[HMMER3] $rootdir/bin
[IDBA_UD] $rootdir/bin
_EOM
ln -sf $rootdir/thirdParty/MaxBin-$VER $rootdir/bin/MaxBin
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
MaxBin installed
------------------------------------------------------------------------------
"
}
install_diamond(){
local VER=0.9.10
echo "------------------------------------------------------------------------------
Installing diamond aligner
------------------------------------------------------------------------------
"
tar xvzf diamond-linux64.tar.gz
rm -f diamond_manual.pdf
mv -f diamond $rootdir/bin/.
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
diamond aligner installed
------------------------------------------------------------------------------
"
}
install_reference-based_assembly(){
echo "------------------------------------------------------------------------------
Installing reference-based_assembly package
------------------------------------------------------------------------------
"
Org_PATH=$PATH;
export PATH=$rootdir/thirdParty/Anaconda3/bin:$rootdir/bin:$PATH;
tar xvzf reference-based_assembly.tgz
cd reference-based_assembly
./INSTALL.sh
ln -sf $rootdir/thirdParty/reference-based_assembly $rootdir/bin/
cd $rootdir/thirdParty
export PATH=$Org_PATH
echo "
------------------------------------------------------------------------------
reference-based_assembly package installed
------------------------------------------------------------------------------
"
}
install_FaQCs(){
local VER=2.09
echo "------------------------------------------------------------------------------
Installing FaQCs $VER
------------------------------------------------------------------------------
"
tar xvzf FaQCs-$VER.tar.gz
cd FaQCs
make
cp -f FaQCs $rootdir/bin/.
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
FaQCs $VER installed
------------------------------------------------------------------------------
"
}
install_omics-pathway-viewer(){
local VER=0.3
echo "------------------------------------------------------------------------------
Installing omics-pathway-viewer $VER
------------------------------------------------------------------------------
"
tar xvzf omics-pathway-viewer.tgz
cp $rootdir/thirdParty/omics-pathway-viewer/scripts/opaver_anno.pl $rootdir/bin/opaver_anno.pl
cp -fR $rootdir/thirdParty/omics-pathway-viewer/opaver_web $rootdir/edge_ui/
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
omics-pathway-viewer $VER installed
------------------------------------------------------------------------------
"
}
install_DETEQT(){
local VER=0.3.1
echo "------------------------------------------------------------------------------
Installing DETEQT $VER
------------------------------------------------------------------------------
"
tar xvzf DETEQT-$VER.tgz
cd DETEQT
./INSTALL.sh
ln -sf $rootdir/thirdParty/DETEQT $rootdir/bin/DETEQT
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
DETEQT $VER installed
------------------------------------------------------------------------------
"
}
install_PyPiReT(){
local VER=1.0.0
echo "------------------------------------------------------------------------------
Installing PyPiReT $VER
------------------------------------------------------------------------------
"
tar xvzf PyPiReT-$VER.tgz
cd PyPiReT
Org_PATH=$PATH;
export PATH=$rootdir/thirdParty/Anaconda3/bin:$rootdir/bin:$PATH;
if [ -e $rootdir/thirdParty/Anaconda3/envs/piret ]
then
rm -rf $rootdir/thirdParty/Anaconda3/envs/piret
fi
./installer.sh piret
ln -sf $rootdir/thirdParty/piret $rootdir/bin/piret
export PATH=$Org_PATH
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
PyPiReT $VER installed
------------------------------------------------------------------------------
"
}
install_idba()
{
echo "------------------------------------------------------------------------------
Compiling IDBA 1.1.1
------------------------------------------------------------------------------
"
tar xvzf idba-1.1.1.tar.gz
cd idba-1.1.1
sed -i.bak 's/kMaxShortSequence = 128/kMaxShortSequence = 351/' src/sequence/short_sequence.h
sed -i.bak 's/kNumUint64 = 4/kNumUint64 = 6/' src/basic/kmer.h
#src/sequence/short_sequence.h: static const uint32_t kMaxShortSequence = 128
./configure --prefix=$rootdir CXXFLAGS='-g -O2 -std=c++03'
make
make install
cp bin/idba_ud $rootdir/bin/.
cp bin/fq2fa $rootdir/bin/.
cd $rootdir/thirdParty
if [[ "$OSTYPE" == "darwin"* ]]
then
{
cp -f idba_ud_mac $rootdir/bin/idba_ud
}
fi
echo "
------------------------------------------------------------------------------
IDBA compiled
------------------------------------------------------------------------------
"
}
install_spades(){
local VER=3.13.0
echo "------------------------------------------------------------------------------
Installing SPAdes $VER
------------------------------------------------------------------------------
"
tar xvzf SPAdes-$VER-Linux.tar.gz
ln -sf $rootdir/thirdParty/SPAdes-$VER-Linux/bin/spades.py $rootdir/bin/spades.py
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
SPAdes $VER installed
------------------------------------------------------------------------------
"
}
install_megahit(){
local VER=1.1.3
## --version MEGAHIT v1.1.3
echo "------------------------------------------------------------------------------
Installing megahit $VER
------------------------------------------------------------------------------
"
tar xvzf megahit-$VER.tar.gz
cd megahit-$VER
make
cp -f megahit* $rootdir/bin/
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
megahit $VER installed
------------------------------------------------------------------------------
"
}
install_unicycler(){
local VER=0.4.8
echo "------------------------------------------------------------------------------
Installing Unicycler $VER
------------------------------------------------------------------------------"
if ( echo ${gcc_version%.*} | awk '{if($1>="4.9") exit 0; else exit 1}' )
then
tar xvzf Unicycler-$VER.tar.gz
sed -i.bak 's,min(8,min(4,g' Unicycler-$VER/setup.py
$anaconda3bin/pip install Unicycler-$VER/
else
$anaconda3bin/conda install -y -c bioconda unicycler
fi
echo "
------------------------------------------------------------------------------
Unicycler $VER installed
------------------------------------------------------------------------------
"
}
install_racon(){
local VER=1.4.13
echo "------------------------------------------------------------------------------
Installing racon $VER
------------------------------------------------------------------------------"
tar xvzf racon-v$VER.tar.gz
cd racon-v$VER
mkdir -p build
cd build
cmake -DCMAKE_BUILD_TYPE=Release -Dracon_build_wrapper=ON -Dspoa_optimize_for_portability=ON ..
make
cp -f bin/racon* $rootdir/bin/
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
racon $VER installed
------------------------------------------------------------------------------
"
}
install_lrasm(){
local VER=0.3.0
echo "------------------------------------------------------------------------------
Installing long_read_assembly $VER
------------------------------------------------------------------------------
"
tar xvzf long_read_assembly-$VER.tgz
cd long_read_assembly
./INSTALL.sh
ln -sf $rootdir/thirdParty/long_read_assembly/lrasm $rootdir/bin/lrasm
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
long_read_assembly $VER installed
------------------------------------------------------------------------------
"
}
install_tRNAscan()
{
echo "------------------------------------------------------------------------------
Installing tRNAscan-SE 1.3.1
------------------------------------------------------------------------------
"
tar xvzf tRNAscan-SE-1.3.1.tar.gz
cd tRNAscan-SE-1.3.1
sed -i.bak 's,home,'"$rootdir"',' Makefile
make
make install
make clean
cd $rootdir/thirdParty
chmod -R +x $rootdir/bin/tRNAscanSE
chmod -R +r $rootdir/bin/tRNAscanSE
echo "
------------------------------------------------------------------------------
tRNAscan-SE 1.3.1 installed
------------------------------------------------------------------------------
"
}
install_prokka()
{
local VER=1.14.5
echo "------------------------------------------------------------------------------
Installing prokka-$VER
------------------------------------------------------------------------------
"
tar xvzf prokka-$VER.tar.gz
cd prokka-$VER
# remove old perl modules
# https://github.com/tseemann/prokka/issues/293
#rm -rf perl5
cd $rootdir/thirdParty
ln -sf $rootdir/thirdParty/prokka-$VER/bin/prokka $rootdir/bin/prokka
$rootdir/thirdParty/prokka-$VER/bin/prokka --setupdb
echo "
------------------------------------------------------------------------------
prokka-$VER installed
------------------------------------------------------------------------------
"
}
install_barrnap()
{
local VER=0.9
echo "------------------------------------------------------------------------------
Installing barrnap-$VER
------------------------------------------------------------------------------
"
tar xvzf barrnap-$VER.tar.gz
cd barrnap-$VER
cd $rootdir/thirdParty
ln -sf $rootdir/thirdParty/barrnap-$VER/bin/barrnap $rootdir/bin/barrnap
echo "
------------------------------------------------------------------------------
barrnap-$VER installed
------------------------------------------------------------------------------
"
}
install_seqtk(){
local VER=1.3
echo "------------------------------------------------------------------------------
Installing seqtk-$VER
------------------------------------------------------------------------------
"
tar xvzf seqtk-$VER.tgz
cd seqtk-$VER
make
cp -fR seqtk $rootdir/bin/.
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
seqtk-$VER installed
------------------------------------------------------------------------------
"
}
install_bedtools()
{
local VER=2.27.1
echo "------------------------------------------------------------------------------
Installing bedtools-$VER
------------------------------------------------------------------------------
"
tar xvzf bedtools-$VER.tar.gz
cd bedtools2
make
cp -fR bin/* $rootdir/bin/.
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
bedtools-$VER installed
------------------------------------------------------------------------------
"
}
install_sratoolkit()
{
local VER=2.9.6
echo "------------------------------------------------------------------------------
Installing sratoolkit.$VER-linux64
------------------------------------------------------------------------------
"
tar xvzf sratoolkit.$VER-linux64.tgz
cd sratoolkit.$VER-linux64
ln -sf $rootdir/thirdParty/sratoolkit.$VER-linux64/bin/fastq-dump $rootdir/bin/fastq-dump
ln -sf $rootdir/thirdParty/sratoolkit.$VER-linux64/bin/vdb-dump $rootdir/bin/vdb-dump
./bin/vdb-config --restore-defaults
./bin/vdb-config -s /repository/user/default-path=$rootdir/edge_ui/ncbi
./bin/vdb-config -s /repository/user/main/public/root=$rootdir/edge_ui/ncbi/public
if [[ -n ${HTTP_PROXY} ]]; then
proxy_without_protocol=${HTTP_PROXY#http://}
./bin/vdb-config --proxy $proxy_without_protocol
fi
if [[ -n ${http_proxy} ]]; then
proxy_without_protocol=${http_proxy#http://}
./bin/vdb-config --proxy $proxy_without_protocol
fi
ln -sf $HOME/.ncbi $rootdir/.ncbi
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
sratoolkit.$VER-linux64 installed
------------------------------------------------------------------------------
"
}
install_Chromium(){
echo "------------------------------------------------------------------------------
Installing Chromium
------------------------------------------------------------------------------
"
unzip chrome-linux.zip
echo "
------------------------------------------------------------------------------
Chromium 75.0.3767.0
------------------------------------------------------------------------------
"
}
install_ea-utils(){
echo "------------------------------------------------------------------------------
Installing ea-utils.1.1.2-537
------------------------------------------------------------------------------
"
tar xvzf ea-utils.1.1.2-537.tar.gz
cd ea-utils.1.1.2-537
PREFIX=$rootdir make install
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
ea-utils.1.1.2-537 installed
------------------------------------------------------------------------------
"
}
install_R()
{
local VER=3.6.3
echo "------------------------------------------------------------------------------
Compiling R $VER
------------------------------------------------------------------------------
"
tar xvzf R-$VER.tar.gz
cd R-$VER
./configure --prefix=$rootdir
make
make install
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
R compiled
------------------------------------------------------------------------------
"
}
install_Rpackages()
{
echo "------------------------------------------------------------------------------
installing R packages
------------------------------------------------------------------------------
"
local VER=3.6.3
tar xzf R-${VER}-Packages.tgz
echo "if(\"gridExtra\" %in% rownames(installed.packages()) == FALSE) {install.packages(c(\"gridExtra\"), repos = NULL, type=\"source\", contriburl=\"file:Rpackages/\")}" | $rootdir/bin/Rscript --no-init-file -
echo "if(\"devtools\" %in% rownames(installed.packages()) == FALSE) {install.packages(c(\"devtools\"), repos = NULL, type=\"source\", contriburl=\"file:Rpackages/\")}" | $rootdir/bin/Rscript --no-init-file -
echo "if(\"phyloseq\" %in% rownames(installed.packages()) == FALSE) {install.packages(c(\"phyloseq\"), repos = NULL, type=\"source\", contriburl=\"file:Rpackages/\")}" | $rootdir/bin/Rscript --no-init-file -
echo "if(\"dplyr\" %in% rownames(installed.packages()) == FALSE) {install.packages(c(\"dplyr\"), repos = NULL, type=\"source\", contriburl=\"file:Rpackages/\")}" | $rootdir/bin/Rscript --no-init-file -
echo "if(\"Cairo\" %in% rownames(installed.packages()) == FALSE) {install.packages(c(\"Cairo\"), repos = NULL, type=\"source\", contriburl=\"file:Rpackages/\")}" | $rootdir/bin/Rscript --no-init-file -
echo "if(\"plotly\" %in% rownames(installed.packages()) == FALSE) {install.packages(c(\"plotly\"), repos = NULL, type=\"source\", contriburl=\"file:Rpackages/\")}" | $rootdir/bin/Rscript --no-init-file -
echo "if(\"MetaComp\" %in% rownames(installed.packages()) == FALSE) {install.packages(c(\"MetaComp\"), repos = NULL, type=\"source\", contriburl=\"file:Rpackages/\")}" | $rootdir/bin/Rscript --no-init-file -
echo "if(\"gplots\" %in% rownames(installed.packages()) == FALSE) {install.packages(c(\"gplots\"), repos = NULL, type=\"source\", contriburl=\"file:Rpackages/\")}" | $rootdir/bin/Rscript --no-init-file -
rm -r Rpackages/
echo "options(bitmapType='cairo')" > $HOME/.Rprofile
echo "
------------------------------------------------------------------------------
R packages installed
------------------------------------------------------------------------------
"
}
install_GNU_parallel()
{
local VER=20190422
echo "------------------------------------------------------------------------------
Compiling GNU parallel
------------------------------------------------------------------------------
"
tar xvzf parallel-$VER.tar.gz
cd parallel-$VER
./configure --prefix=$rootdir
make
make install
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
GNU parallel compiled
------------------------------------------------------------------------------
"
}
install_BLAST+()
{
local VER=2.10.0
echo "------------------------------------------------------------------------------
Install ncbi-blast-$VER+-x64
------------------------------------------------------------------------------
"
BLAST_ZIP=ncbi-blast-$VER+-x64-linux.tar.gz
if [[ "$OSTYPE" == "darwin"* ]]
then
{
VER=2.2.29
BLAST_ZIP=ncbi-blast-$VER+-universal-macosx.tar.gz
}
fi
tar xvzf $BLAST_ZIP
cd ncbi-blast-$VER+
cp -fR bin/* $rootdir/bin/
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
ncbi-blast-$VER+-x64 installed
------------------------------------------------------------------------------
"
}
install_blastall()
{
echo "------------------------------------------------------------------------------
Install blast-2.2.26-x64-linux
------------------------------------------------------------------------------
"
BLAST_ZIP=blast-2.2.26-x64-linux.tar.gz
if [[ "$OSTYPE" == "darwin"* ]]
then
{
BLAST_ZIP=blast-2.2.26-universal-macosx.tar.gz
}
fi
tar xvzf $BLAST_ZIP
cd blast-2.2.26
cp -fR bin/* $rootdir/bin/.
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
blast-2.2.26-x64 installed
------------------------------------------------------------------------------
"
}
install_kraken2()
{
local VER=2.0.7
echo "------------------------------------------------------------------------------
Install kraken-$VER-beta
------------------------------------------------------------------------------
"
tar xvzf kraken-$VER.tgz
cd kraken2-$VER-beta
./install_kraken2.sh $rootdir/bin/
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
kraken-$VER installed
------------------------------------------------------------------------------
"
}
install_centrifuge()
{
local VER=1.0.4
echo "------------------------------------------------------------------------------
Install centrifuge-$VER
------------------------------------------------------------------------------
"
tar xvzf centrifuge-$VER-beta.tgz
cd centrifuge-$VER-beta
make
cp centrifuge $rootdir/bin/
cp centrifuge-* $rootdir/bin/
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
centrifuge-$VER installed
------------------------------------------------------------------------------
"
}
install_JBrowse()
{
local VER=1.16.8
echo "------------------------------------------------------------------------------
Installing JBrowse-$VER
------------------------------------------------------------------------------
"
tar xvzf JBrowse-$VER.tar.gz
if [ -e $rootdir/edge_ui/JBrowse/data ]
then
mv $rootdir/edge_ui/JBrowse/data $rootdir/edge_ui/JBrowse_olddata
fi
if [ -e $rootdir/edge_ui/JBrowse ]
then
rm -rf $rootdir/edge_ui/JBrowse
fi
mv JBrowse-$VER $rootdir/edge_ui/JBrowse
cd $rootdir/edge_ui/JBrowse
./setup.sh
if [ -e $rootdir/edge_ui/JBrowse_olddata ]
then
mv $rootdir/edge_ui/JBrowse_olddata $rootdir/edge_ui/JBrowse/data
else
mkdir -p -m 775 data
fi
cd $rootdir/thirdParty
#ln -sf $rootdir/thirdParty/JBrowse-1.11.6 $rootdir/edge_ui/JBrowse
echo "
------------------------------------------------------------------------------
JBrowse-$VER installed
------------------------------------------------------------------------------
"
}
install_tabix()
{
echo "------------------------------------------------------------------------------
Compiling tabix bgzip
------------------------------------------------------------------------------
"
tar xvzf tabix.tgz
cd tabix
make
cp tabix $rootdir/bin/.
cp bgzip $rootdir/bin/.
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
tabix bgzip compiled
------------------------------------------------------------------------------
"
}
install_hmmer()
{
echo "------------------------------------------------------------------------------
Compiling hmmer-3.1b1
------------------------------------------------------------------------------
"
tar xvzf hmmer-3.1b1.tar.gz
cd hmmer-3.1b1/
./configure --prefix=$rootdir && make && make install
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
hmmer-3.1b1 compiled
------------------------------------------------------------------------------
"
}
install_infernal()
{
echo "------------------------------------------------------------------------------
Installing infernal-1.1rc4
------------------------------------------------------------------------------
"
tar xzvf infernal-1.1rc4.tar.gz
cd infernal-1.1rc4/
./configure --prefix=$rootdir && make && make install
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
infernal-1.1rc4 installed
------------------------------------------------------------------------------
"
}
install_phageFinder()
{
echo "------------------------------------------------------------------------------
Installing phage_finder_v2.1
------------------------------------------------------------------------------
"
tar xvzf phage_finder_v2.1.tar.gz
cd phage_finder_v2.1
cd $rootdir/thirdParty
chmod -R +x phage_finder_v2.1
chmod -R +r phage_finder_v2.1
echo "
------------------------------------------------------------------------------
phage_finder_v2.1 installed
------------------------------------------------------------------------------
"
}
install_bowtie2()
{
local VER=2.4.1
echo "------------------------------------------------------------------------------
Install bowtie2 $VER
------------------------------------------------------------------------------
"
tar xvzf bowtie2-$VER-linux-x86_64.tgz
cd bowtie2-$VER-linux-x86_64
cp bowtie2* $rootdir/bin/.
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
bowtie2 $VER installed
------------------------------------------------------------------------------
"
}
install_gottcha()
{
echo "------------------------------------------------------------------------------
Compiling gottcha-1.0b
------------------------------------------------------------------------------
"
tar xzf gottcha.tar.gz
rm -rf gottcha/ext/opt/dmd2/
tar xzf dmd.2.082.0.linux.tgz -C gottcha/ext/opt
cd gottcha
./INSTALL.sh
ln -sf $PWD/bin/gottcha.pl $rootdir/bin/
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
gottcha-1.0b compiled
------------------------------------------------------------------------------
"
}
install_gottcha2()
{
echo "------------------------------------------------------------------------------
Compiling gottcha-2.1 BETA
------------------------------------------------------------------------------
"
tar xvzf gottcha2.tar.gz
cd gottcha2
#ln -sf $PWD/gottcha.py $rootdir/bin/
ln -sf $rootdir/database/GOTTCHA2 ./database
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
gottcha-2.1 BETA installed
------------------------------------------------------------------------------
"
}
install_miccr()
{
local VER=0.0.2
echo "------------------------------------------------------------------------------
Installing miccr-$VER
------------------------------------------------------------------------------
"
tar xvzf miccr-$VER.tgz
cd miccr
ln -sf $rootdir/database/miccrDB ./database
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
miccr-$VER installed
------------------------------------------------------------------------------
"
}
install_pangia()
{
local VER=1.0.0
echo "------------------------------------------------------------------------------
Installing PANGIA $VER BETA
------------------------------------------------------------------------------
"
if [ -e $rootdir/thirdParty/pangia/pangia-vis/data ]
then
mv $rootdir/thirdParty/pangia/pangia-vis/data $rootdir/thirdParty/pangia-vis-data
fi
if [ -e $rootdir/thirdParty/pangia ]
then
rm -rf $rootdir/thirdParty/pangia
fi
tar xvzf pangia-$VER.tar.gz
cd pangia
if [ -e $rootdir/thirdParty/pangia-vis-data ]
then
cp -rf $rootdir/thirdParty/pangia-vis-data/* $rootdir/thirdParty/pangia/pangia-vis/data/
rm -rf $rootdir/thirdParty/pangia-vis-data
fi
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
pangia-$VER BETA
------------------------------------------------------------------------------
"
}
install_metaphlan2()
{
local VER=2.7.7
echo "------------------------------------------------------------------------------
Installing metaphlan-$VER
------------------------------------------------------------------------------
"
tar xvzf metaphlan-$VER.tgz
cd metaphlan-$VER
cp -fR metaphlan2.py $rootdir/bin/.
cp -fR utils/read_fastx.py $rootdir/bin/.
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
metaphlan-$VER installed
------------------------------------------------------------------------------
"
}
install_RATT()
{
echo "------------------------------------------------------------------------------
Installing RATT
------------------------------------------------------------------------------
"
tar xvzf RATT.tar.gz
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
RATT installed
------------------------------------------------------------------------------
"
}
install_glimmer()
{
echo "------------------------------------------------------------------------------
Compiling glimmer 3.02
------------------------------------------------------------------------------
"
tar xvzf glimmer302b.tar.gz
cd glimmer3.02/SimpleMake
make
cp ../bin/* $rootdir/bin/.
cp ../scripts/* $rootdir/bin/.
for i in $rootdir/bin/*.csh
do
sed -i.bak 's!/fs/szgenefinding/Glimmer3!'$rootdir'!' $i
sed -i.bak 's!/fs/szgenefinding/Glimmer3!'$rootdir'!' $i
done
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
glimmer3.02 compiled
------------------------------------------------------------------------------
"
}
install_aragorn()
{
echo "------------------------------------------------------------------------------
Compiling aragorn1.2.36
------------------------------------------------------------------------------
"
tar xvzf aragorn1.2.36.tgz
cd aragorn1.2.36
gcc -O3 -ffast-math -finline-functions -o aragorn aragorn1.2.36.c
cp -fR aragorn $rootdir/bin/.
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
aragorn1.2.36 compiled
------------------------------------------------------------------------------
"
}
install_prodigal()
{
echo "------------------------------------------------------------------------------
Compiling prodigal.v2_60
------------------------------------------------------------------------------
"
tar xvzf prodigal.v2_60.tar.gz
cd prodigal.v2_60/
make
cp -fR prodigal $rootdir/bin
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
prodigal.v2_60 compiled
------------------------------------------------------------------------------
"
}
install_ShortBRED()
{
echo "------------------------------------------------------------------------------
Installing ShortBRED
------------------------------------------------------------------------------
"
tar xvzf ShortBRED-0.9.4M.tgz
ln -sf $rootdir/thirdParty/ShortBRED-0.9.4M $rootdir/bin/ShortBRED
echo "
------------------------------------------------------------------------------
ShortBRED installed
------------------------------------------------------------------------------
"
}
install_tbl2asn()
{
echo "------------------------------------------------------------------------------
Installing NCBI tbl2asn
------------------------------------------------------------------------------
"
if [[ "$OSTYPE" == "darwin"* ]]
then
{
tar xvzf mac.tbl2asn.tgz
chmod +x mac.tbl2asn
ln -sf $rootdir/thirdParty/mac.tbl2asn $rootdir/bin/tbl2asn
}
else
{
tar xvzf linux64.tbl2asn.tgz
chmod +x linux64.tbl2asn
ln -sf $rootdir/thirdParty/linux64.tbl2asn $rootdir/bin/tbl2asn.orig
}
fi
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
NCBI tbl2asn installed
------------------------------------------------------------------------------
"
}
install_bwa()
{
echo "------------------------------------------------------------------------------
Compiling bwa 0.7.12
------------------------------------------------------------------------------
"
tar xvzf bwa-0.7.12.tar.gz
cd bwa-0.7.12
make clean && make
cp bwa $rootdir/bin/.
cd $rootdir/thirdParty
echo "
------------------------------------------------------------------------------
bwa compiled
------------------------------------------------------------------------------
"
}
install_minimap2()