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INSTALL.pl
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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 [2016-2024] 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 VEP
=cut
use strict;
use FindBin qw($RealBin);
use lib $RealBin.'/modules';
use Getopt::Long;
use File::Path qw(mkpath rmtree);
use File::Copy;
use File::Basename;
use Net::FTP;
use Cwd;
use Scalar::Util qw(looks_like_number);
use Bio::EnsEMBL::VEP::Utils qw(get_version_data get_version_string);
our (
$DEST_DIR,
$ENS_CVS_ROOT,
$API_VERSION,
$DATA_VERSION,
$ASSEMBLY,
$ENS_GIT_ROOT,
$BIOPERL_URL,
$CACHE_URL,
$CACHE_URL_INDEXED,
$CACHE_DIR,
$NO_PLUGINS,
$PLUGINS,
$PLUGIN_URL,
$PLUGINS_DIR,
$FASTA_URL,
$FTP_USER,
$HELP,
$NO_UPDATE,
$SPECIES,
$AUTO,
$QUIET,
$PREFER_BIN,
$CONVERT,
$TEST,
$NO_HTSLIB,
$LIB_DIR,
$HTSLIB_DIR,
$BIODBHTS_DIR,
$REALPATH_DEST_DIR,
$NO_TEST,
$NO_BIOPERL,
$ua,
$CAN_USE_CURL,
$CAN_USE_LWP,
$CAN_USE_HTTP_TINY,
$CAN_USE_ARCHIVE,
$CAN_USE_UNZIP,
$CAN_USE_GZIP,
$CAN_USE_TAR,
$CAN_USE_DBI,
$CAN_USE_DBD_MYSQL,
);
## VERSIONS OF INSTALLED SOFTWARE
## MAY BE UPDATED IF SUCCESSFULLY TESTED
########################################
our $HTSLIB_VERSION = '1.9'; # latest release as of release/98
our $BIOHTS_VERSION = '2.11'; # latest 2.X release as of release/98
our $BIOPERL_VERSION = 'release-1-6-924'; # frozen, no pressing need to update
## BEGIN BLOCK, CHECK WHAT MODULES ETC WE CAN USE
#################################################
BEGIN {
if(eval q{ use LWP::Simple qw(getstore get $ua); 1 }) {
$CAN_USE_LWP = 1;
# set up a user agent's proxy (excluding github)
$ua->env_proxy;
}
if(eval q{ use DBI; 1 }) {
$CAN_USE_DBI = 1;
}
if(eval q{ use DBD::mysql; 1 }) {
$CAN_USE_DBD_MYSQL = 1;
}
$CAN_USE_CURL = 1 if `which curl` =~ /\/curl/;
$CAN_USE_HTTP_TINY = 1 if eval q{ use HTTP::Tiny; 1 };
$CAN_USE_ARCHIVE = 1 if eval q{ use Archive::Extract; 1 };
$CAN_USE_UNZIP = 1 if `which unzip` =~ /\/unzip/;
$CAN_USE_GZIP = 1 if `which gzip` =~ /\/gzip/;
$CAN_USE_TAR = 1 if `which tar` =~ /\/tar/;
}
$| = 1;
# CONFIGURE
###########
# other global data
my @API_MODULES = (
{ name => 'ensembl', path => ' ', test_pm => 'Bio::EnsEMBL::Registry' },
{ name => 'ensembl-variation', path => 'Variation', test_pm => 'Bio::EnsEMBL::Variation::Variation' },
{ name => 'ensembl-funcgen', path => 'Funcgen', test_pm => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature' },
{ name => 'ensembl-io', path => 'IO,Utils', test_pm => 'Bio::EnsEMBL::IO::Parser' },
);
my $ensembl_url_tail = '/archive/';
my $archive_type = '.zip';
my $git_api_root = 'https://api.github.com/repos/Ensembl/';
my $VEP_MODULE_NAME = 'ensembl-vep';
our (@store_species, @indexes, @files, $ftp, $dirname);
my $config = {};
GetOptions(
$config,
'DESTDIR|DEST_DIR|d=s',
'CACHE_VERSION|e=i',
'ASSEMBLY|y=s',
'BIOPERL|BIOPERL_URL|b=s',
'CACHEURL|CACHE_URL|u=s',
'CACHEDIR|CACHE_DIR|c=s',
'FASTAURL|FASTA_URL|f=s',
'HELP|h',
'NO_UPDATE|n',
'SPECIES|s=s',
'NO_PLUGINS',
'PLUGINS|g=s',
'PLUGINSDIR|PLUGINS_DIR|r=s',
'PLUGINURL|PLUGIN_URL=s',
'AUTO|a=s',
'QUIET|q',
'PREFER_BIN|p',
'CONVERT|t',
'TEST',
'NO_HTSLIB|l',
'NO_TEST',
'NO_BIOPERL'
) or die("ERROR: Failed to parse arguments");
# Read configuration from environment variables starting with VEP_
# Priority is given to command-line arguments
sub read_config_from_environment {
my $config = shift;
for my $key (keys %ENV) {
# Look for environment variables that start with VEP_
next unless $key =~ "^VEP_";
# Avoid setting empty strings
my $value = $ENV{$key};
next if $value eq "";
$key =~ s/^VEP_//ig;
# Prioritise previous values
$config->{$key} ||= $value;
}
return $config;
}
$config = read_config_from_environment($config);
# Quick fix: this script should use $config instead of multiple global variables
$DEST_DIR ||= $config->{DESTDIR};
$DATA_VERSION ||= $config->{CACHE_VERSION};
$ASSEMBLY ||= $config->{ASSEMBLY};
$BIOPERL_URL ||= $config->{BIOPERL};
$CACHE_URL ||= $config->{CACHEURL};
$CACHE_DIR ||= $config->{CACHEDIR};
$FASTA_URL ||= $config->{FASTAURL};
$HELP ||= $config->{HELP};
$NO_UPDATE ||= $config->{NO_UPDATE};
$SPECIES ||= $config->{SPECIES};
$NO_PLUGINS ||= $config->{NO_PLUGINS};
$PLUGINS ||= $config->{PLUGINS};
$PLUGINS_DIR ||= $config->{PLUGINSDIR};
$PLUGIN_URL ||= $config->{PLUGINURL};
$AUTO ||= $config->{AUTO};
$QUIET ||= $config->{QUIET};
$PREFER_BIN ||= $config->{PREFER_BIN};
$CONVERT ||= $config->{CONVERT};
$TEST ||= $config->{TEST};
$NO_HTSLIB ||= $config->{NO_HTSLIB};
$NO_TEST ||= $config->{NO_TEST};
$NO_BIOPERL ||= $config->{NO_BIOPERL};
# load version data
our $CURRENT_VERSION_DATA = get_version_data($RealBin.'/.version');
our $VERSION = $CURRENT_VERSION_DATA->{$VEP_MODULE_NAME}->{release};
$VERSION =~ s/release\///;
if($HELP) {
usage();
exit(0);
}
# check user has DBI and DBD::mysql
die(
"ERROR: DBI module not found. VEP requires the DBI perl module to function\n\n".
"http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#requirements\n"
) unless $CAN_USE_DBI;
warn(
"WARNING: DBD::mysql module not found. VEP can only run in offline (--offline) mode without DBD::mysql installed\n\n".
"http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#requirements\n"
) unless $CAN_USE_DBD_MYSQL;
my $default_dir_used = check_default_dir();
$LIB_DIR = $DEST_DIR;
$HTSLIB_DIR = $LIB_DIR.'/htslib';
$BIODBHTS_DIR = $LIB_DIR.'/biodbhts';
$REALPATH_DEST_DIR .= Cwd::realpath($DEST_DIR).'/Bio';
$DEST_DIR .= '/Bio';
$dirname = dirname(__FILE__) || '.';
$ENS_GIT_ROOT ||= 'https://github.com/Ensembl/';
$BIOPERL_URL ||= "https://github.com/bioperl/bioperl-live/archive/$BIOPERL_VERSION.zip";
$API_VERSION ||= $CURRENT_VERSION_DATA->{$VEP_MODULE_NAME}->{release};
$DATA_VERSION ||= $API_VERSION;
$CACHE_DIR ||= $ENV{HOME} ? $ENV{HOME}.'/.vep' : 'cache';
$PLUGINS_DIR ||= $CACHE_DIR.'/Plugins';
$FTP_USER ||= 'anonymous';
## Set the indexed cache url if it's been overwritten by the user
$CACHE_URL_INDEXED = $CACHE_URL;
$CACHE_URL ||= "https://ftp.ensembl.org/pub/release-$DATA_VERSION/variation/vep";
$CACHE_URL_INDEXED ||= "https://ftp.ensembl.org/pub/release-$DATA_VERSION/variation/indexed_vep_cache";
$FASTA_URL ||= "https://ftp.ensembl.org/pub/release-$DATA_VERSION/fasta/";
$PLUGIN_URL ||= 'https://raw.githubusercontent.com/Ensembl/VEP_plugins';
# using PREFER_BIN can save memory when extracting archives
$PREFER_BIN = 0 unless defined($PREFER_BIN);
$Archive::Extract::PREFER_BIN = $PREFER_BIN == 0 ? 0 : 1;
$QUIET = 0 unless $AUTO;
# updates to ensembl-vep available?
update() unless $NO_UPDATE;
# auto?
if($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 {
my $api_msg =
" - Install v$API_VERSION of the Ensembl API for use by the VEP. " .
"It will not affect any existing installations of the Ensembl API that you may have.\n";
print "Hello! This installer will help you set up VEP v$API_VERSION, including:\n" .
($NO_UPDATE ? "" : $api_msg) .
" - Download and install cache files from Ensembl's FTP server.\n" .
" - Download FASTA files from Ensembl's FTP server.\n" .
($NO_PLUGINS ? "" : " - Download VEP plugins.\n") . "\n"
unless $QUIET;
# run subs
api() if check_api();
cache();
fasta();
plugins() unless $NO_PLUGINS;
}
# clean up
if(-d "$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;
##########################################################################
##########################################################################
##########################################################################
# UPDATE
########
sub update() {
my $module = $VEP_MODULE_NAME;
# check for major version update
my $repo_file = "$RealBin/$$.repo_file";
download_to_file(
"$git_api_root$module",
$repo_file
);
my $default_branch;
open IN, $repo_file;
while(<IN>) {
if(/default_branch.+\:.+\"(.+?)\"/) {
$default_branch = $1;
last;
}
}
close IN;
unlink($repo_file);
unless($default_branch) {
print "WARNING: Unable to carry out version check for '$module'\n" unless $QUIET;
return;
}
my $default_branch_number = $default_branch;
$default_branch_number =~ s/release\/// if $default_branch_number;
my $current_branch = $CURRENT_VERSION_DATA->{'ensembl-vep'}->{release};
my $message;
# don't have latest
if($current_branch < $default_branch_number) {
$message =
"Version check reports a newer release of '$module' is available ".
"(installed: $current_branch, available: $default_branch_number)\n";
}
# do have latest, but there might be updates
elsif($current_branch == $default_branch_number) {
my $git_sub = get_vep_sub_version($current_branch);
my $have_sub = $CURRENT_VERSION_DATA->{$module}->{sub};
$message = sprintf(
"Version check reports there are post-release updates available of %s (installed: %s.%.7s, available: %s.%.7s)\n",
$module,
$current_branch, $have_sub,
$current_branch, $git_sub
) unless $git_sub eq $have_sub;
}
if($message) {
print "\n$message\n";
# user has git, suggest they use that instead
if(`which git` && -d $RealBin.'/.git') {
print "We recommend using git to update '$module', by exiting this installer and running:\n\n";
print "\tgit pull\n";
print "\tgit checkout $default_branch\n" if $current_branch ne $default_branch_number;
}
else {
print "You should exit this installer and re-download '$module' if you wish to update\n";
}
print "\nDo you wish to exit so you can get updates (y) or continue (n): ";
my $ok = <>;
if($ok !~ /^n/i) {
print "OK, bye!\n";
print "\nNB: Remember to re-run INSTALL.pl after updating to check for API updates\n";
exit(0);
}
}
else {
return;
}
}
# CHECKS DIR SETUP AND PATHS ETC
################################
sub is_url {
my $url = shift;
return $url =~ /^(http|ftp)/i;
}
sub check_default_dir {
my $this_os = $^O;
my $default_dir_used;
# 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 vep script will remain in its current location where ensembl-vep was unzipped.\n";
if(!defined($AUTO)){
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);
}
}
else {
print "\n%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n\n";
print "PLEASE REMEMBER TO \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";
print "\n%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n";
}
}
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 "Installation on OSX requires that you set up some paths before running this installer.\n";
if(!defined($AUTO)){
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);
}
}
else{
print "\n%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n";
#print "\nPLEASE REMEMBER TO ADD $current_dir/htslib TO YOUR DYLD_LIBRARY_PATH ENVIRONMENT VARIABLE\n";
print "\nPLEASE REMEMBER TO \n";
print "1. add $current_dir/htslib to your DYLD_LIBRARY_PATH environment variable\n";
print "\n%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n";
}
}
}
return $default_dir_used;
}
# API
#####
sub api() {
setup_dirs();
my $curdir = getcwd;
unless($NO_BIOPERL) {
bioperl();
}
# htslib needs to find bioperl to pass tests
$ENV{PERL5LIB} = $ENV{PERL5LIB} ? $ENV{PERL5LIB}.':'.$DEST_DIR : $DEST_DIR;
unless($NO_HTSLIB) {
chdir $curdir;
install_biodbhts();
}
chdir $curdir;
install_api();
test() unless $NO_TEST;
}
# CHECK EXISTING
################
sub check_api() {
return 0 if $NO_UPDATE;
print "Checking for installed versions of the Ensembl API..." unless $QUIET;
my $has_api = {};
my $updates = {};
my $core_version;
my @unknown_versions = ();
foreach my $module_hash(@API_MODULES) {
my $module = $module_hash->{name};
my $test_pm = $module_hash->{test_pm};
eval "require $test_pm";
$has_api->{$module} = $@ ? 0 : 1;
if($has_api->{$module}) {
my $have_sub = $CURRENT_VERSION_DATA->{$module} ? ($CURRENT_VERSION_DATA->{$module}->{sub} || '') : '';
my $git_sub = get_module_sub_version($module);
if($have_sub) {
$updates->{$module} = [$have_sub, $git_sub] if $have_sub ne $git_sub;
}
else {
push @unknown_versions, $module;
}
if($module eq 'ensembl') {
$core_version = Bio::EnsEMBL::Registry->software_version;
}
}
}
print "done\n";
my $total = 0;
$total += $_ for values %$has_api;
my $message;
if($total == scalar @API_MODULES) {
if(defined($core_version)) {
if(!looks_like_number($API_VERSION)) {
$message = "Your reported version ($API_VERSION) is a non-standard release number";
}
elsif($core_version == $API_VERSION) {
if(scalar keys %$updates) {
$message =
"There are updates available for these modules:\n ".
join(
"\n ",
map {
sprintf(
"%-20s : installed = %.7s, available = %.7s",
$_, $updates->{$_}->[0], $updates->{$_}->[1]
)
} keys %$updates
);
}
else {
$message = "It looks like you already have v$API_VERSION of the API installed.\n";
if(@unknown_versions) {
$message .=
"No version information was available for the following modules:\n".
join("\n", map {" - ".$_} @unknown_versions).
"\nUpdates may be available but you will need to perform these manually.";
}
else {
$message .= "You shouldn't need to install the API";
}
}
}
elsif($core_version > $API_VERSION) {
$message = "It looks like this installer is for an older distribution ($API_VERSION) of the API than you already have ($core_version)";
}
else {
$message = "It looks like you have an older version ($core_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-io, ensembl-variation and ensembl-funcgen modules";
}
if($AUTO =~ /a/ || !defined($message)) {
return 1;
}
else {
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;
}
}
}
# 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;
my $release_url_string = looks_like_number($API_VERSION) ? 'release/'.$API_VERSION : $API_VERSION;
my $release_path_string = looks_like_number($API_VERSION) ? 'release-'.$API_VERSION : $API_VERSION;
foreach my $module_hash(@API_MODULES) {
my $module = $module_hash->{name};
# do we need to update this?
my $have_sub = $CURRENT_VERSION_DATA->{$module} ? ($CURRENT_VERSION_DATA->{$module}->{sub} || '') : '';
my $url = $ENS_GIT_ROOT.$module.$ensembl_url_tail.$release_url_string.$archive_type;
print " - fetching $module\n" unless $QUIET;
my $target_file = $DEST_DIR.'/tmp/'.$module.$archive_type;
mkdir($DEST_DIR.'/tmp/') unless -d $DEST_DIR.'/tmp/';
download_to_file($url, $target_file) unless -e $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;
foreach my $module_path (split(',',$module_hash->{path})) {
my $module_dir_suffix = $module_path eq ' ' ? '' : '/'.$module_path;
my $module_dir_from = "$DEST_DIR/tmp/$module\-$release_path_string/modules/Bio/EnsEMBL$module_dir_suffix";
my $module_dir_to = "$DEST_DIR/EnsEMBL$module_dir_suffix";
# If the target directory already exist, we can't overwrite it.
if (-d $module_dir_to) {
# One solution is to move the content of the directory instead.
# However we need to loop over the files/directories within the module directory because the 'move()' method doesn't allow wildcards.
opendir DH, $module_dir_from;
while(my $file_or_dir = readdir DH) {
next if ($file_or_dir =~ /^\.+$/);
move("$module_dir_from/$file_or_dir", "$module_dir_to/$file_or_dir") or die "ERROR: Could not move '$module_dir_from/$file_or_dir'\n".$!;
}
closedir DH;
}
else {
move($module_dir_from, $module_dir_to) or die "ERROR: Could not move the directory '$module_dir_from'\n".$!;
}
}
# now get latest commit from github API
print " - getting version information\n" unless $QUIET;
my $git_sub = get_module_sub_version($module);
mkdir("$RealBin/.version/") unless -d "$RealBin/.version/";
open OUT, ">$RealBin/.version/$module" or die $!;
print OUT "release $API_VERSION\nsub $git_sub\n";
close OUT;
rmtree("$DEST_DIR/tmp/$module\-$release_path_string") or die "ERROR: Failed to remove directory: $!\n";
}
}
sub get_module_sub_version {
my $module = shift;
my $sub_file = "$RealBin/$$\.$module.sub";
my $release_url_string = looks_like_number($API_VERSION) ? 'release/'.$API_VERSION : $API_VERSION;
download_to_file(
"$git_api_root$module/commits?sha=$release_url_string",
$sub_file
);
open IN, $sub_file or die $!;
my $sub;
while(<IN>) {
if(/\"sha\": \"(.+?)\"/) {
$sub = $1;
last;
}
}
close IN;
unlink($sub_file);
return $sub;
}
sub get_vep_sub_version {
my $release = shift || $API_VERSION;
my $sub_file = "$RealBin/$$\.$VEP_MODULE_NAME.sub";
my $release_url_string = looks_like_number($release) ? 'release/'.$release : $release;
download_to_file(
sprintf(
'https://raw.githubusercontent.com/Ensembl/%s/%s/modules/Bio/EnsEMBL/VEP/Constants.pm',
$VEP_MODULE_NAME,
$release_url_string
),
$sub_file
);
open IN, $sub_file or die $!;
my $sub;
while(<IN>) {
if(/VEP_SUB_VERSION \= (.+)\;/) {
$sub = $1;
last;
}
}
close IN;
unlink($sub_file);
return $sub;
}
# 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
# List the required libraries with their packages
my %libs = (
'zlib.h' => 'zlib1g-dev',
'lzma.h' => 'liblzma-dev',
'bzlib.h' => 'libbz2-dev'
);
my $msg = '';
my $this_os = $^O;
if ($this_os ne 'darwin' ) {
my $default_msg = qq{%s library header(s) 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 %s};
my @missing_header = ();
my @missing_library = ();
# Loop over the required libraries
foreach my $lib (sort(keys(%libs))) {
unless(-e '/usr/include/'.$lib){
push(@missing_header, $lib);
push(@missing_library, $libs{$lib});
}
}
my $header_string = join( ', ', @missing_header);
my $install_string = join( ' ', @missing_library);
die(sprintf($default_msg, $header_string, $install_string). "\n\n") if($header_string ne '');
}
# 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 $HTSLIB_VERSION 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-DB-HTS";
my $biodbhts_zip_github_url = "$biodbhts_github_url/archive/$BIOHTS_VERSION.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-$BIOHTS_VERSION" ? "Bio-HTS-$BIOHTS_VERSION" : "Bio-DB-HTS-$BIOHTS_VERSION";
print "$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;
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 $pdir;
}
sub dircopy {
my ($from, $to) = @_;
opendir FROM, $from;
foreach my $file(grep {!/^\.\.?/} readdir FROM) {
# dir?
if(-d "$from/$file") {
mkdir("$to/$file") unless -d "$to/$file";