From f0dbf9bf16c34c4ab65abc0b41ff1ca261f3794f Mon Sep 17 00:00:00 2001 From: Nuno Agostinho Date: Mon, 13 Feb 2023 15:42:35 +0000 Subject: [PATCH 1/5] Remove deprecated VERSION argument from INSTALL.pl --- INSTALL.pl | 3 --- 1 file changed, 3 deletions(-) diff --git a/INSTALL.pl b/INSTALL.pl index f46ef3713..584546668 100755 --- a/INSTALL.pl +++ b/INSTALL.pl @@ -151,7 +151,6 @@ BEGIN GetOptions( $config, 'DESTDIR|d=s', - 'VERSION|v=i', # Deprecated 'CACHE_VERSION|e=i', 'ASSEMBLY|y=s', 'BIOPERL|b=s', @@ -198,7 +197,6 @@ sub read_config_from_environment { # Quick fix: this script should use $config instead of multiple global variables $DEST_DIR ||= $config->{DESTDIR}; -$API_VERSION ||= $config->{VERSION}; $DATA_VERSION ||= $config->{CACHE_VERSION}; $ASSEMBLY ||= $config->{ASSEMBLY}; $BIOPERL_URL ||= $config->{BIOPERL}; @@ -387,7 +385,6 @@ () my $current_branch = $CURRENT_VERSION_DATA->{'ensembl-vep'}->{release}; - # Check if the $API_VERSION has been set by the deprecated "--VERSION" flag my $api_branch = $API_VERSION; $api_branch =~ s/release\///; From 7702937bc7714ad2b1e9562a025ee98984a3f2d4 Mon Sep 17 00:00:00 2001 From: Nuno Agostinho Date: Mon, 13 Feb 2023 15:46:00 +0000 Subject: [PATCH 2/5] Update sub-version --- modules/Bio/EnsEMBL/VEP/Constants.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/Bio/EnsEMBL/VEP/Constants.pm b/modules/Bio/EnsEMBL/VEP/Constants.pm index 657c980c3..a3e73e86c 100755 --- a/modules/Bio/EnsEMBL/VEP/Constants.pm +++ b/modules/Bio/EnsEMBL/VEP/Constants.pm @@ -53,7 +53,7 @@ use warnings; use base qw(Exporter); our $VEP_VERSION = 109; -our $VEP_SUB_VERSION = 1; +our $VEP_SUB_VERSION = 2; our @EXPORT_OK = qw( @FLAG_FIELDS From 6ff18b296c8d9d4f3b4bfa4716255de0c8e2d96a Mon Sep 17 00:00:00 2001 From: Nuno Agostinho Date: Mon, 13 Feb 2023 15:49:44 +0000 Subject: [PATCH 3/5] Remove extra space in welcome message for consistency --- INSTALL.pl | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/INSTALL.pl b/INSTALL.pl index 584546668..2c80b143c 100755 --- a/INSTALL.pl +++ b/INSTALL.pl @@ -319,14 +319,14 @@ sub read_config_from_environment { else { my $api_msg = - " - Install v$API_VERSION of the Ensembl API for use by the VEP. " . + " - 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" + " - 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 From a5e720d110614a58fde72a7103d45eecb0a495e8 Mon Sep 17 00:00:00 2001 From: Nuno Agostinho Date: Mon, 13 Feb 2023 16:18:41 +0000 Subject: [PATCH 4/5] Remove unneeded code lines --- INSTALL.pl | 19 ------------------- 1 file changed, 19 deletions(-) diff --git a/INSTALL.pl b/INSTALL.pl index 2c80b143c..c86ddfccc 100755 --- a/INSTALL.pl +++ b/INSTALL.pl @@ -385,25 +385,6 @@ () my $current_branch = $CURRENT_VERSION_DATA->{'ensembl-vep'}->{release}; - my $api_branch = $API_VERSION; - $api_branch =~ s/release\///; - - # branch provided by the "--VERSION" flag - if ($api_branch != $current_branch) { - print "The 'VERSION' installation flag has been deprecated.\n\n"; - my $branch = looks_like_number($API_VERSION) ? 'release/'.$API_VERSION : $API_VERSION; - if(`which git` && -d $RealBin.'/.git') { - print "Please, use git to update '$module' using the commands:\n\n"; - print "\tgit pull\n"; - print "\tgit checkout $branch\n\n"; - } - else { - print "Please, re-download '$module' with the desired version.\n\n"; - } - print "Exit VEP install script\n"; - exit(0); - } - my $message; # don't have latest From 71d7e481beaafc4ed0da009d06c2b639a6ada4d5 Mon Sep 17 00:00:00 2001 From: Nuno Agostinho Date: Tue, 14 Feb 2023 16:43:54 +0000 Subject: [PATCH 5/5] Remove mention to VERSION argument --- INSTALL.pl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/INSTALL.pl b/INSTALL.pl index c86ddfccc..402173a26 100755 --- a/INSTALL.pl +++ b/INSTALL.pl @@ -1911,7 +1911,7 @@ sub usage { -h | --help Display this message and quit -d | --DESTDIR Set destination directory for API install (default = './') ---CACHE_VERSION Set data (cache, FASTA) version to install if different from --VERSION (default = $VERSION) +--CACHE_VERSION Set data (cache, FASTA) version to install (default = $VERSION) -c | --CACHEDIR Set destination directory for cache files (default = '$ENV{HOME}/.vep/') -a | --AUTO Run installer without user prompts. Use "a" (API + Faidx/htslib),