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INSTALL.pl
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#!/usr/bin/env perl
=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.
=cut
=head1 NAME
INSTALL.pl - a script to install required code and data for the VEP
Version 86
by Will McLaren ([email protected])
=cut
use Getopt::Long;
use File::Path qw(mkpath rmtree);
use File::Copy;
use File::Copy::Recursive qw(dircopy);
use File::Basename;
use Archive::Extract;
use Net::FTP;
use Cwd;
use strict;
$| = 1;
our $VERSION = 86;
our $have_LWP;
our $use_curl = 0;
have_LWP();
# CONFIGURE
###########
our ($DEST_DIR, $ENS_CVS_ROOT, $API_VERSION, $ASSEMBLY, $ENS_GIT_ROOT, $BIOPERL_URL, $CACHE_URL, $CACHE_DIR, $PLUGINS, $PLUGIN_URL, $FASTA_URL, $FTP_USER, $help, $UPDATE, $SPECIES, $AUTO, $QUIET, $PREFER_BIN, $CONVERT, $TEST, $NO_HTSLIB, $LIB_DIR, $HTSLIB_DIR, $BIODBHTS_DIR, $REALPATH_DEST_DIR );
GetOptions(
'DESTDIR|d=s' => \$DEST_DIR,
'VERSION|v=i' => \$API_VERSION,
'ASSEMBLY|y=s' => \$ASSEMBLY,
'BIOPERL|b=s' => \$BIOPERL_URL,
'CACHEURL|u=s' => \$CACHE_URL,
'CACHEDIR|c=s' => \$CACHE_DIR,
'FASTAURL|f=s' => \$FASTA_URL,
'HELP|h' => \$help,
'UPDATE|n' => \$UPDATE,
'SPECIES|s=s' => \$SPECIES,
'PLUGINS|g=s' => \$PLUGINS,
'PLUGINURL=s' => \$PLUGIN_URL,
'AUTO|a=s' => \$AUTO,
'QUIET|q' => \$QUIET,
'PREFER_BIN|p' => \$PREFER_BIN,
'CONVERT|t' => \$CONVERT,
'TEST' => \$TEST,
'NO_HTSLIB|l' => \$NO_HTSLIB,
'CURL' => \$use_curl,
) or die("ERROR: Failed to parse arguments");
if(defined($help)) {
usage();
exit(0);
}
my $default_dir_used;
my $this_os = $^O;
# check if $DEST_DIR is default
if(defined($DEST_DIR)) {
print "Using non-default API installation directory $DEST_DIR.\n";
print "Please note this just specifies the location for downloaded API files. The variant_effect_predictor.pl script will remain in its current location where ensembl-tools was unzipped.\n";
print "Have you \n";
print "1. added $DEST_DIR to your PERL5LIB environment variable?\n";
print "2. added $DEST_DIR/htslib to your PATH environment variable?\n";
if( $this_os eq 'darwin' && !$NO_HTSLIB) {
print "3. added $DEST_DIR/htslib to your DYLD_LIBRARY_PATH environment variable?\n";
}
print "(y/n)";
my $ok = <>;
if($ok !~ /^y/i) {
print "Exiting. Please \n";
print "1. add $DEST_DIR to your PERL5LIB environment variable\n";
print "2. add $DEST_DIR/htslib to your PATH environment variable\n";
if( $this_os eq 'darwin' && !$NO_HTSLIB) {
print "3. add $DEST_DIR/htslib to your DYLD_LIBRARY_PATH environment variable\n";
}
exit(0);
}
if( ! -d $DEST_DIR ) {
mkdir $DEST_DIR || die "Could not make destination directory $DEST_DIR"
}
$default_dir_used = 0;
}
else {
$DEST_DIR ||= '.';
$default_dir_used = 1;
my $current_dir = cwd();
if( !$NO_HTSLIB && $this_os eq 'darwin' ) {
print "Have you \n";
print "1. added $current_dir/htslib to your DYLD_LIBRARY_PATH environment variable?\n";
print "(y/n)";
my $ok = <>;
if($ok !~ /^y/i) {
print "Exiting. Please \n";
print "1. add $current_dir/htslib to your DYLD_LIBRARY_PATH environment variable\n";
exit(0);
}
}
}
$LIB_DIR = $DEST_DIR;
$DEST_DIR .= '/Bio';
$REALPATH_DEST_DIR .= Cwd::realpath($DEST_DIR);
$ENS_GIT_ROOT ||= 'https://github.com/Ensembl/';
$BIOPERL_URL ||= 'https://github.com/bioperl/bioperl-live/archive/release-1-6-924.zip';
$API_VERSION ||= $VERSION;
$CACHE_URL ||= "ftp://ftp.ensembl.org/pub/release-$API_VERSION/variation/VEP";
$CACHE_DIR ||= $ENV{HOME} ? $ENV{HOME}.'/.vep' : 'cache';
$PLUGIN_URL ||= 'https://raw.githubusercontent.com/Ensembl/VEP_plugins';
$FTP_USER ||= 'anonymous';
$FASTA_URL ||= "ftp://ftp.ensembl.org/pub/release-$API_VERSION/fasta/";
$PREFER_BIN = 0 unless defined($PREFER_BIN);
$HTSLIB_DIR = $LIB_DIR.'/htslib';
$BIODBHTS_DIR = $LIB_DIR.'/biodbhts';
my $dirname = dirname(__FILE__) || '.';
#dev
# using PREFER_BIN can save memory when extracting archives
$Archive::Extract::PREFER_BIN = $PREFER_BIN == 0 ? 0 : 1;
$QUIET = 0 unless $UPDATE || $AUTO;
# set up the URLs
my $ensembl_url_tail = '/archive/release/';
my $archive_type = '.zip';
our (@store_species, @indexes, @files, $ftp, $ua);
# update?
if($UPDATE) {
update();
}
# auto?
elsif($AUTO) {
# check
die("ERROR: Failed to parse AUTO string - must contain any of a (API), l (FAIDX/htslib), c (cache), f (FASTA), p (plugins)\n") unless $AUTO =~ /^[alcfp]+$/i;
# require species
if($AUTO =~ /[cf]/i) {
die("ERROR: No species specified\n") unless $SPECIES;
$SPECIES = [split /\,/, $SPECIES];
}
# require plugin list
if($AUTO =~ /p/i) {
die("ERROR: No plugins specified\n") unless $PLUGINS;
$PLUGINS = [split /\,/, $PLUGINS];
}
# run subs
if($AUTO =~ /l/ && $AUTO !~ /a/) {
my $curdir = getcwd;
chdir $curdir;
install_biodbhts();
chdir $curdir;
# remove Bio dir if empty
opendir DIR, $DEST_DIR;
my @files = grep {!/^\./} readdir DIR;
closedir DIR;
if(scalar @files <= 1) {
rmtree($DEST_DIR.'/'.$files[0]);
rmtree($DEST_DIR);
}
}
api() if $AUTO =~ /a/;
cache() if $AUTO =~ /c/;
fasta() if $AUTO =~ /f/;
plugins() if $AUTO =~ /p/;
}
else {
print "\nHello! This installer is configured to install v$API_VERSION of the Ensembl API for use by the VEP.\nIt will not affect any existing installations of the Ensembl API that you may have.\n\nIt will also download and install cache files from Ensembl's FTP server.\n\n" unless $QUIET;
# run subs
api() if check_api();
cache();
fasta();
plugins();
}
# clean up
if(-d "$CACHE_DIR/tmp" && !$TEST) {
rmtree("$CACHE_DIR/tmp") or die "ERROR: Could not delete directory $CACHE_DIR/tmp\n";
}
print "\nAll done\n" unless $QUIET;
##########################################################################
##########################################################################
##########################################################################
# API
#####
sub api() {
setup_dirs();
my $curdir = getcwd;
bioperl();
unless($NO_HTSLIB) {
chdir $curdir;
install_biodbhts();
}
chdir $curdir;
install_api();
test();
}
# CHECK EXISTING
################
sub check_api() {
print "Checking for installed versions of the Ensembl API..." unless $QUIET;
# test if the user has the API installed
my $has_api = {
'ensembl' => 0,
'ensembl-variation' => 0,
'ensembl-functgenomics' => 0,
};
eval q{
use Bio::EnsEMBL::Registry;
};
my $installed_version;
unless($@) {
$has_api->{ensembl} = 1;
$installed_version = Bio::EnsEMBL::Registry->software_version;
}
eval q{
use Bio::EnsEMBL::Variation::Utils::VEP;
};
$has_api->{'ensembl-variation'} = 1 unless $@;
eval q{
use Bio::EnsEMBL::Funcgen::RegulatoryFeature;
};
$has_api->{'ensembl-functgenomics'} = 1 unless $@;
print "done\n";
my $total = 0;
$total += $_ for values %$has_api;
my $message;
if($total == 3) {
if(defined($installed_version)) {
if($installed_version == $API_VERSION) {
$message = "It looks like you already have v$API_VERSION of the API installed.\nYou shouldn't need to install the API";
}
elsif($installed_version > $API_VERSION) {
$message = "It looks like this installer is for an older distribution of the API than you already have";
}
else {
$message = "It looks like you have an older version (v$installed_version) of the API installed.\nThis installer will install a limited set of the API v$API_VERSION for use by the VEP only";
}
}
else {
$message = "It looks like you have an unidentified version of the API installed.\nThis installer will install a limited set of the API v$API_VERSION for use by the VEP only"
}
}
elsif($total > 0) {
$message = "It looks like you already have the following API modules installed:\n\n".(join "\n", grep {$has_api->{$_}} keys %$has_api)."\n\nThe VEP requires the ensembl, ensembl-variation and optionally ensembl-functgenomics modules";
}
if(defined($message)) {
print $message unless $QUIET;
print "\n\nSkip to the next step (n) to install cache files\n\nDo you want to continue installing the API (y/n)? ";
my $ok = <>;
if($ok !~ /^y/i) {
print " - skipping API installation\n" unless $QUIET;
return 0;
}
else {
return 1;
}
}
else {
return 1;
}
}
# SETUP
#######
sub setup_dirs() {
print "\nSetting up directories\n" unless $QUIET;
# check if install dir exists
if(-e $DEST_DIR) {
my $ok;
if($AUTO) {
$ok = 'y';
}
else {
print "Destination directory $DEST_DIR already exists.\nDo you want to overwrite it (if updating VEP this is probably OK) (y/n)? ";
$ok = <>;
}
if($ok !~ /^y/i) {
print "Exiting\n";
exit(0);
}
else {
unless($default_dir_used || $AUTO) {
print "WARNING: You are using a non-default install directory.\nPressing \"y\" again will remove $DEST_DIR and its contents!!!\nAre you really, really sure (y/n)? ";
$ok = <>;
if($ok !~ /^y/i) {
print "Exiting\n";
exit(0);
}
}
# try to delete the existing dir
rmtree($DEST_DIR) or die "ERROR: Could not delete directory $DEST_DIR\n";
}
}
mkdir($DEST_DIR) or die "ERROR: Could not make directory $DEST_DIR\n";
mkdir($DEST_DIR.'/tmp') or die "ERROR: Could not make directory $DEST_DIR/tmp\n";
}
# INSTALL API
#############
sub install_api() {
print "\nDownloading required Ensembl API files\n" unless $QUIET;
foreach my $module(qw(ensembl ensembl-variation ensembl-funcgen)) {
my $url = $ENS_GIT_ROOT.$module.$ensembl_url_tail.$API_VERSION.$archive_type;
print " - fetching $module\n" unless $QUIET;
my $target_file = $DEST_DIR.'/tmp/'.$module.$archive_type;
if(!-e $DEST_DIR.'/tmp/')
{
mkdir( $DEST_DIR.'/tmp/' );
}
if(!-e $target_file) {
download_to_file($url, $target_file);
}
print " - unpacking $target_file\n" unless $QUIET;
unpack_arch("$DEST_DIR/tmp/$module$archive_type", "$DEST_DIR/tmp/");
print " - moving files\n" unless $QUIET;
if($module eq 'ensembl') {
move("$DEST_DIR/tmp/$module\-release\-$API_VERSION/modules/Bio/EnsEMBL", "$DEST_DIR/EnsEMBL") or die "ERROR: Could not move directory\n".$!;
}
elsif($module eq 'ensembl-variation') {
move("$DEST_DIR/tmp/$module\-release-$API_VERSION/modules/Bio/EnsEMBL/Variation", "$DEST_DIR/EnsEMBL/Variation") or die "ERROR: Could not move directory\n".$!;
# move test data
my $test_target = "$DEST_DIR/../t/testdata/";
mkpath($test_target) unless -d $test_target;
opendir TESTDATA, "$DEST_DIR/tmp/$module\-release-$API_VERSION/modules/t/testdata" or die "ERROR: Could not find ensembl-variation/modules/t/testdata directory";
foreach my $f(grep {!/^\./} readdir TESTDATA) {
if(-d $test_target.$f) {
rmtree($test_target.$f) or die "ERROR: Could not remove $test_target$f\n".$!;
}
elsif(-e $test_target.$f) {
unlink($test_target.$f) or die "ERROR: Could not remove $test_target$f\n".$!;
}
move("$DEST_DIR/tmp/$module\-release-$API_VERSION/modules/t/testdata/$f", $test_target.$f) or die "ERROR: Could not move $DEST_DIR/tmp/$module\-release-$API_VERSION/modules/t/testdata/$f to $test_target$f".$!;
}
closedir TESTDATA;
}
elsif($module eq 'ensembl-funcgen') {
move("$DEST_DIR/tmp/$module\-release-$API_VERSION/modules/Bio/EnsEMBL/Funcgen", "$DEST_DIR/EnsEMBL/Funcgen") or die "ERROR: Could not move directory\n".$!;
}
rmtree("$DEST_DIR/tmp/$module\-release-$API_VERSION") or die "ERROR: Failed to remove directory $DEST_DIR/tmp/$module\-release-$API_VERSION\n";
}
}
# HTSLIB download/make
######################
sub install_htslib() {
#actually decided to follow Bio::DB::Sam template
# STEP 0: various dependencies
my $git = 'which git';
$git or die <<END;
'git' command not in path. Please install git and try again.
(or to skip Bio::DB::HTS/htslib install re-run with --NO_HTSLIB)
On Debian/Ubuntu systems you can do this with the command:
apt-get install git
END
'which cc' or die <<END;
'cc' command not in path. Please install it and try again.
(or to skip Bio::DB::HTS/htslib install re-run with --NO_HTSLIB)
On Debian/Ubuntu systems you can do this with the command:
apt-get install build-essential
END
`which make` or die <<END;
'make' command not in path. Please install it and try again.
(or to skip Bio::DB::HTS/htslib install re-run with --NO_HTSLIB)
On Debian/Ubuntu systems you can do this with the command:
apt-get install build-essential
END
my $this_os = $^O;
if( $this_os ne 'darwin' ) {
-e '/usr/include/zlib.h' or die <<END;
zlib.h library header not found in /usr/include. Please install it and try again.
(or to skip Bio::DB::HTS/htslib install re-run with --NO_HTSLIB)
On Debian/Ubuntu systems you can do this with the command:
apt-get install zlib1g-dev
END
;
}
# STEP 1: Create a clean directory for building
my $htslib_install_dir = $LIB_DIR;
my $curdir = getcwd;
chdir $htslib_install_dir;
my $actualdir = getcwd;
# STEP 2: Check out HTSLIB / or make this a download?
print(" - checking out HTSLib\n");
system "git clone -b master https://github.com/samtools/htslib.git";
-d './htslib' or die "git clone seems to have failed. Could not find $htslib_install_dir/htslib directory";
chdir './htslib';
# Step 3: Build libhts.a
print(" - building HTSLIB in $htslib_install_dir/htslib\n");
print( "In ".getcwd."\n" );
# patch makefile
rename 'Makefile','Makefile.orig' or die "Couldn't rename Makefile to Makefile.orig: $!";
open my $in, '<','Makefile.orig' or die "Couldn't open Makefile for reading: $!";
open my $out,'>','Makefile.new' or die "Couldn't open Makefile.new for writing: $!";
while (<$in>) {
chomp;
if (/^CFLAGS/ && !/-fPIC/) {
s/#.+//; # get rid of comments
$_ .= " -fPIC -Wno-unused -Wno-unused-result";
}
}
continue {
print $out $_,"\n";
}
close $in;
close $out;
rename 'Makefile.new','Makefile' or die "Couldn't rename Makefile.new to Makefile: $!";
system "make";
-e 'libhts.a' or die "Compile didn't complete. No libhts.a library file found";
chdir $curdir;
my $retval = Cwd::realpath("$htslib_install_dir/htslib") ;
}
# INSTALL Bio::DB::HTS
######################
sub install_biodbhts() {
print "Attempting to install Bio::DB::HTS and htslib.\n\n>>> If this fails, try re-running with --NO_HTSLIB\n\n";
my $htslib_location = install_htslib();
rmtree( $DEST_DIR.'/tmp' );
#Now install Bio::DB::HTS proper
my $biodbhts_github_url = "https://github.com/Ensembl/Bio-HTS";
my $biodbhts_zip_github_url = "$biodbhts_github_url/archive/master.zip";
my $biodbhts_zip_download_file = $DEST_DIR.'/tmp/biodbhts.zip';
mkdir $DEST_DIR unless -d $DEST_DIR;
mkdir $DEST_DIR.'/tmp';
download_to_file($biodbhts_zip_github_url, $biodbhts_zip_download_file);
print " - unpacking $biodbhts_zip_download_file to $DEST_DIR/tmp/\n" unless $QUIET;
unpack_arch($biodbhts_zip_download_file, "$DEST_DIR/tmp/");
my $tmp_name = -d "$DEST_DIR/tmp/Bio-HTS-master" ? 'Bio-HTS-master' : 'Bio-DB-HTS-master';
print "$DEST_DIR/tmp/$tmp_name - moving files to $BIODBHTS_DIR\n" unless $QUIET;
rmtree($BIODBHTS_DIR);
move("$DEST_DIR/tmp/$tmp_name", $BIODBHTS_DIR) or die "ERROR: Could not move directory\n".$!;
print( " - making Bio::DB:HTS\n" );
# patch makefile
chdir $BIODBHTS_DIR;
rename 'Build.PL','Build.PL.orig' or die "Couldn't rename Build to Build.orig: $!";
open my $in, '<','Build.PL.orig' or die "Couldn't open Build.PL.orig for reading: $!";
open my $out,'>','Build.PL.new' or die "Couldn't open Build.PL.new for writing: $!";
while (<$in>) {
chomp;
if (/LIBS/) {
s/#.+//; # get rid of comments
$_ = "LIBS => ['-L../htslib/ -lhts -lz'],";
}
if (/INC/) {
s/#.+//; # get rid of comments
$_ = "INC => '-I. -I../htslib', ";
}
}
continue {
print $out $_,"\n";
}
close $in;
close $out;
rename 'Build.PL.new','Build.PL' or die "Couldn't rename Build.new to Build: $!";
system "perl Build.PL --htslib $htslib_location";
system "./Build";
chdir ".";
#move the library
my $pdir = getcwd;
#Perl modules to go alongside the API
dircopy("lib/Bio",$REALPATH_DEST_DIR);
#The shared object XS library
if( -e "blib/arch/auto/Bio/DB/HTS/HTS.so" ) {
copy( "blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so", "..")
or die "ERROR: Could not copy shared Faidx.so library:$!\n";
copy( "blib/arch/auto/Bio/DB/HTS/HTS.so", "..")
or die "ERROR: Could not copy shared HTS.so library:$!\n";
}
elsif( -e "blib/arch/auto/Bio/DB/HTS/HTS.bundle" ) {
copy( "blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.bundle", "..")
or die "ERROR: Could not copy shared Faidx.bundle library:$!\n";
copy( "blib/arch/auto/Bio/DB/HTS/HTS.bundle", "..")
or die "ERROR: Could not copy shared HTS.bundle library:$!\n";
}
else {
die "ERROR: Shared Bio::DB:HTS library not found\n";
}
chdir $pdir;
}
# INSTALL BIOPERL
#################
sub bioperl() {
# now get BioPerl
print " - fetching BioPerl\n" unless $QUIET;
my $bioperl_file = (split /\//, $BIOPERL_URL)[-1];
my $target_file = $DEST_DIR.'/tmp/'.$bioperl_file;
download_to_file($BIOPERL_URL, $target_file);
print " - unpacking $target_file\n" unless $QUIET;
unpack_arch("$DEST_DIR/tmp/$bioperl_file", "$DEST_DIR/tmp/");
print " - moving files\n" unless $QUIET;
my $bioperl_dir;
if($BIOPERL_URL =~ /github/) {
$bioperl_file =~ s/\.zip//;
$bioperl_dir = "bioperl-live-".$bioperl_file;
}
else {
$bioperl_file =~ /(bioperl.+?)\.tar\.gz/i;
$bioperl_dir = $1;
}
opendir BIO, "$DEST_DIR/tmp/$bioperl_dir/Bio/";
move("$DEST_DIR/tmp/$bioperl_dir/Bio/$_", "$DEST_DIR/$_") for readdir BIO;
closedir BIO;
rmtree("$DEST_DIR/tmp") or die "ERROR: Failed to remove directory $DEST_DIR/tmp\n";
}
# TEST
######
sub test() {
print "\nTesting VEP script\n" unless $QUIET;
eval q{use Test::Harness};
if(!$@) {
$ENV{PERL5LIB} = $ENV{PERL5LIB} ? $ENV{PERL5LIB}.':'.$DEST_DIR : $DEST_DIR;
opendir TEST, "$dirname\/t";
my @test_files = map {"$dirname\/t\/".$_} grep {!/_db/ && !/^\./ && /\.t$/} readdir TEST;
closedir TEST;
print "Warning: Tests failed, VEP may not run correctly\n" unless runtests(@test_files);
}
else {
my $test_vep = `perl -I $DEST_DIR $dirname/variant_effect_predictor.pl --help 2>&1`;
$test_vep =~ /ENSEMBL VARIANT EFFECT PREDICTOR/ or die "ERROR: Testing VEP script failed with the following error\n$test_vep\n";
}
print " - OK!\n" unless $QUIET;
}
# CACHE FILES
#############
sub cache() {
my $ok;
if($AUTO) {
$ok = $AUTO =~ /c/i ? 'y' : 'n';
}
else {
print "\nThe VEP can either connect to remote or local databases, or use local cache files.\nUsing local cache files is the fastest and most efficient way to run the VEP\n" unless $QUIET;
print "Cache files will be stored in $CACHE_DIR\n" unless $QUIET;
print "Do you want to install any cache files (y/n)? ";
$ok = <>;
}
if($ok !~ /^y/i) {
print "Skipping cache installation\n" unless $QUIET;
return;
}
# check cache dir exists
if(!(-e $CACHE_DIR)) {
if(!$AUTO) {
print "Cache directory $CACHE_DIR does not exists - do you want to create it (y/n)? ";
my $ok = <>;
if($ok !~ /^y/i) {
print "Exiting\n";
exit(0);
}
}
mkdir($CACHE_DIR) or die "ERROR: Could not create directory $CACHE_DIR\n";
}
mkdir($CACHE_DIR.'/tmp') unless -e $CACHE_DIR.'/tmp';
# get list of species
print "\Getting list of available cache files\n" unless $QUIET;
my $num = 1;
my $species_list;
if($CACHE_URL =~ /^ftp/i) {
$CACHE_URL =~ m/(ftp:\/\/)?(.+?)\/(.+)/;
$ftp = Net::FTP->new($2, Passive => 1) or die "ERROR: Could not connect to FTP host $2\n$@\n";
$ftp->login($FTP_USER) or die "ERROR: Could not login as $FTP_USER\n$@\n";
$ftp->binary();
foreach my $sub(split /\//, $3) {
$ftp->cwd($sub) or die "ERROR: Could not change directory to $sub\n$@\n";
}
push @files, sort grep {$_ =~ /tar.gz/} $ftp->ls;
}
else {
opendir DIR, $CACHE_URL;
@files = sort grep {$_ =~ /tar.gz/} readdir DIR;
closedir DIR;
}
# if we don't have a species list, we'll have to guess
if(!scalar(@files)) {
print "Could not get current species list - using predefined list instead\n";
print "For more species, see http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#pre\n";
@files = (
"bos_taurus_vep_".$API_VERSION."_UMD3.1.tar.gz",
"danio_rerio_vep_".$API_VERSION."_Zv9.tar.gz",
"homo_sapiens_vep_".$API_VERSION."_GRCh37.tar.gz",
"homo_sapiens_vep_".$API_VERSION."_GRCh38.tar.gz",
"mus_musculus_vep_".$API_VERSION."_GRCm38.tar.gz",
"rattus_norvegicus_vep_".$API_VERSION."_Rnor_5.0.tar.gz",
);
}
foreach my $file(@files) {
$species_list .= $num++." : ".$file."\n";
}
if($AUTO) {
if($SPECIES->[0] eq 'all') {
@indexes = (1..(scalar @files));
}
else {
foreach my $sp(@$SPECIES) {
my @matches;
for my $i(0..$#files) {
if($sp =~ /refseq|merged/i) {
push @matches, $i + 1 if $files[$i] =~ /$sp/i;
}
else {
push @matches, $i + 1 if $files[$i] =~ /$sp/i && $files[$i] !~ /refseq|merged/i;
}
}
# grep assembly if supplied
@matches = grep {$files[$_ - 1] =~ /\_$ASSEMBLY\./} @matches if $ASSEMBLY;
if(scalar @matches == 1) {
push @indexes, @matches;
}
elsif(scalar @matches > 1) {
# xenopus_tropicalis_vep_76_JGI_4.2.tar.gz
my @assemblies = ();
foreach my $m(@matches) {
$files[$m-1] =~ m/\_vep\_$API_VERSION\_(.+?)\.tar\.gz/;
push @assemblies, $1 if $1;
}
die("ERROR: Multiple assemblies found (".join(", ", @assemblies).") for $sp; select one using --ASSEMBLY [name]\n")
}
}
}
die("ERROR: No matching species found") unless scalar @indexes;
# uniquify and sort
@indexes = sort {$a <=> $b} keys %{{map {$_ => 1} @indexes}};
}
else {
print "The following species/files are available; which do you want (can specify multiple separated by spaces or 0 for all): \n$species_list\n? ";
@indexes = split /\s+/, <>;
# user wants all species found
if(scalar @indexes == 1 && $indexes[0] == 0) {
@indexes = 1..(scalar @files);
}
}
foreach my $file(@indexes) {
die("ERROR: File number $file not valid\n") unless defined($file) && $file =~ /^[0-9]+$/ && defined($files[$file - 1]);
my $file_path = $files[$file - 1];
my $refseq = 0;
my ($species, $assembly, $file_name);
if($file_path =~ /\//) {
($species, $file_name) = (split /\//, $file_path);
$file_name =~ m/^(\w+?)\_vep\_\d+\_(.+?)\.tar\.gz/;
$assembly = $2;
}
else {
$file_name = $file_path;
$file_name =~ m/^(\w+?)\_vep\_\d+\_(.+?)\.tar\.gz/;
$species = $1;
$assembly = $2;
}
push @store_species, $species;
# check if user already has this species and version
if(-e "$CACHE_DIR/$species/$API_VERSION\_$assembly") {
my $ok;
print "\nWARNING: It looks like you already have the cache for $species $assembly (v$API_VERSION) installed.\n" unless $QUIET;
if($AUTO) {
print "\nDelete the folder $CACHE_DIR/$species/$API_VERSION\_$assembly and re-run INSTALL.pl if you want to re-install\n";
}
else {
print "If you continue the existing cache will be overwritten.\nAre you sure you want to continue (y/n)? ";
$ok = <>;
}
if($ok !~ /^y/i) {
print " - skipping $species\n" unless $QUIET;
next;
}
rmtree("$CACHE_DIR/$species/$API_VERSION\_$assembly") or die "ERROR: Could not delete directory $CACHE_DIR/$species/$API_VERSION\_$assembly\n";
}
if($species =~ /refseq/i) {
print "NB: Remember to use --refseq when running the VEP with this cache!\n" unless $QUIET;
}
if($species =~ /merged/i) {
print "NB: Remember to use --merged when running the VEP with this cache!\n" unless $QUIET;
}
my $target_file = "$CACHE_DIR/tmp/$file_name";
if($CACHE_URL =~ /^ftp/) {
print " - downloading $CACHE_URL/$file_path\n" unless $QUIET;
if(!$TEST) {
$ftp->get($file_name, $target_file) or download_to_file("$CACHE_URL/$file_path", $target_file);
my $checksums = "CHECKSUMS";
my $checksums_target_file = "$CACHE_DIR/tmp/$checksums";
$ftp->get($checksums, $checksums_target_file) or download_to_file("$CACHE_URL/$checksums", $checksums_target_file);
if (-e $checksums_target_file) {
my $sum_download = `sum $target_file`;
$sum_download =~ m/([0-9]+)(\s+)([0-9]+)/;
my $checksum_download = $1;
$checksum_download =~ s/^0*//;
my $sum_ftp = `grep $file_name $checksums_target_file`;
$sum_ftp =~ s/^0*//;
if ($sum_download && $sum_ftp) {
die("ERROR: checksum for $target_file doesn't match checksum in CHECKSUMS file on FTP site\n") if ($sum_ftp !~ m/^$checksum_download\s+/);
}
}
}
}
else {
print " - copying $CACHE_URL/$file_path\n" unless $QUIET;
copy("$CACHE_URL/$file_path", $target_file) unless $TEST;
}
print " - unpacking $file_name\n" unless $QUIET;
unpack_arch($target_file, $CACHE_DIR.'/tmp/') unless $TEST;
# does species dir exist?
if(!-e "$CACHE_DIR/$species" && !$TEST) {
mkdir("$CACHE_DIR/$species") or die "ERROR: Could not create directory $CACHE_DIR/$species\n";
}
# move files
unless($TEST) {
opendir CACHEDIR, "$CACHE_DIR/tmp/$species/";
move("$CACHE_DIR/tmp/$species/$_", "$CACHE_DIR/$species/$_") for readdir CACHEDIR;
closedir CACHEDIR;
}
# convert?
if($CONVERT && !$TEST) {
print " - converting cache\n" unless $QUIET;
system("perl $dirname/convert_cache.pl --dir $CACHE_DIR --species $species --version $API_VERSION\_$assembly") == 0 or print STDERR "WARNING: Failed to run convert script\n";
}
}
}
# FASTA FILES
#############
sub fasta() {
### SPECIAL CASE GRCh37
if((grep {$files[$_ - 1] =~ /GRCh37/} @indexes) || (defined($ASSEMBLY) && $ASSEMBLY eq 'GRCh37')) {
# can't install other species at same time as the FASTA URL has to be changed
if(grep {$files[$_ - 1] !~ /GRCh37/} @indexes) {
die("ERROR: For technical reasons this installer is unable to install GRCh37 caches alongside others; please install them separately\n");
}
# change URL to point to last e! version that had GRCh37 downloads
elsif($FASTA_URL =~ /ftp/) {
print "\nWARNING: Changing FTP URL for GRCh37\n";
$FASTA_URL =~ s/$API_VERSION/75/;
}
}
my $ok;
if($AUTO) {
$ok = $AUTO =~ /f/i ? 'y' : 'n';
}
else {
print "\nThe VEP can use FASTA files to retrieve sequence data for HGVS notations and reference sequence checks.\n" unless $QUIET;
print "FASTA files will be stored in $CACHE_DIR\n" unless $QUIET;
print "Do you want to install any FASTA files (y/n)? ";
$ok = <>;
}
if($ok !~ /^y/i) {
print "Skipping FASTA installation - Exiting\n";
return;
}
my @dirs = ();
if($FASTA_URL =~ /^ftp/i) {
$FASTA_URL =~ m/(ftp:\/\/)?(.+?)\/(.+)/;
$ftp = Net::FTP->new($2, Passive => 1) or die "ERROR: Could not connect to FTP host $2\n$@\n";
$ftp->login($FTP_USER) or die "ERROR: Could not login as $FTP_USER\n$@\n";
$ftp->binary();
foreach my $sub(split /\//, $3) {
$ftp->cwd($sub) or die "ERROR: Could not change directory to $sub\n$@\n";
}
push @dirs, sort $ftp->ls;
}
else {
opendir DIR, $FASTA_URL;
@dirs = grep {-d $FASTA_URL.'/'.$_ && $_ !~ /^\./} readdir DIR;
closedir DIR;
}
my $species_list = '';
my $num = 1;
foreach my $dir(@dirs) {
$species_list .= $num++." : ".$dir."\n";
}
my @species;
if($AUTO) {
if($SPECIES->[0] eq 'all') {
@species = scalar @store_species ? @store_species : @dirs;
}
else {
@species = scalar @store_species ? @store_species : @$SPECIES;
}