commit: b42d6fd23f783fe21761e20fceb2291a21de61c0
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Nov 30 16:12:25 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Nov 30 16:12:25 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b42d6fd2
sci-biology/repeatmasker: version bump, escape >= to avoid shell redirect
This introduces new repeatmasker-4.0.8 which can use repeatmasker-libraries
releasded after 20160829.
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
Package-Manager: Portage-2.3.51, Repoman-2.3.11
.../files/repeatmasker-4.0.8__configure.patch | 118 +++++++++++++++++++++
.../repeatmasker/repeatmasker-4.0.6-r3.ebuild | 2 +-
....0.6-r3.ebuild => repeatmasker-4.0.8-r1.ebuild} | 8 +-
3 files changed, 123 insertions(+), 5 deletions(-)
diff --git a/sci-biology/repeatmasker/files/repeatmasker-4.0.8__configure.patch
b/sci-biology/repeatmasker/files/repeatmasker-4.0.8__configure.patch
new file mode 100644
index 000000000..728bb75b1
--- /dev/null
+++ b/sci-biology/repeatmasker/files/repeatmasker-4.0.8__configure.patch
@@ -0,0 +1,118 @@
+--- RepeatMasker/configure.ori 2018-11-30 16:50:39.918872258 +0100
++++ RepeatMasker/configure 2018-11-30 17:00:33.255400144 +0100
+@@ -78,11 +78,10 @@
+ ## unqualified from another installation directory.
+ ##
+ if ( cwd() ne $FindBin::RealBin ) {
+- print "\n The RepeatMasker configure script must be run from\n"
++ die "\n The RepeatMasker configure script must be run from\n"
+ . " inside the RepeatMasker installation directory:\n\n"
+ . " $FindBin::RealBin\n\n"
+ . " Perhaps this is not the \"configure\" you are looking for?\n\n";
+- exit;
+ }
+
+ ##
+@@ -228,12 +227,12 @@
+ print "\n -- Building FASTA database...";
+ system(
+ "$rmLocation/util/buildRMLibFromEMBL.pl
$rmLocation/Libraries/RepeatMaskerLib.embl >
$rmLocation/Libraries/RepeatMasker.lib 2>/dev/null"
+-);
++) and die "$rmLocation/util/buildRMLibFromEMBL.pl
$rmLocation/Libraries/RepeatMaskerLib.embl command filed with: $!";
+
+ ## Uncompress taxonomy.dat
+ if ( -s "$rmLocation/Libraries/taxonomy.dat.gz" ) {
+ print "\n -- Uncompressing taxonomy.dat...";
+- system( "gunzip $rmLocation/Libraries/taxonomy.dat.gz" );
++ system( "gunzip $rmLocation/Libraries/taxonomy.dat.gz" ) and die "gunzip
$rmLocation/Libraries/taxonomy.dat.gz failed with: $!";
+ }
+
+ ##
+@@ -278,7 +277,7 @@
+ } while ( $goodParam != 1 );
+
+ # Initialize config from template.
+-system( "cp RepeatMaskerConfig.tmpl RepeatMaskerConfig.pm" );
++system( "cp RepeatMaskerConfig.tmpl RepeatMaskerConfig.pm" ) and die "cp
RepeatMaskerConfig.tmpl RepeatMaskerConfig.pm failed with: $!";
+
+ # Make changes to file.
+ my $configFile = "RepeatMaskerConfig.pm";
+@@ -290,7 +289,7 @@
+ }
+ close IN;
+ close OUT;
+-system( "mv $configFile.tmp $configFile" );
++system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp
$configFile failed with: $!";
+
+ ##
+ ## Search Engine Configuration
+@@ -452,7 +451,7 @@
+ }
+ close IN;
+ close OUT;
+- system( "mv $configFile.tmp $configFile" );
++ system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp
$configFile failed with: $!";
+ }
+
+ }
+@@ -590,9 +589,9 @@
+ my $rmLocation = "$FindBin::Bin";
+ print "Building RMBlast frozen libraries..\n";
+ system( "$pgLocation/makeblastdb -dbtype nucl -in "
+- . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" );
++ . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" ) and
die "$pgLocation/makeblastdb -dbtype nucl -in
$rmLocation/Libraries/RepeatMasker.lib failed: $!";
+ system( "$pgLocation/makeblastdb -dbtype prot -in "
+- . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" );
++ . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" ) and die
"$pgLocation/makeblastdb -dbtype prot -in $rmLocation/Libraries/RepeatPeps.lib
failed with: $!";
+
+ my $pgDefault = &promptScreen(
+ "",
+@@ -665,9 +664,9 @@
+ my $rmLocation = "$FindBin::Bin";
+ print "Building WUBlast/ABBlast frozen libraries..\n";
+ system( "$wuLocation/xdformat -n -I "
+- . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" );
++ . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" ) and
die "$wuLocation/xdformat -n -I $rmLocation/Libraries/RepeatMasker.lib failed
with: $!";
+ system( "$wuLocation/xdformat -p -I "
+- . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" );
++ . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" ) and die
"$wuLocation/xdformat -p -I $rmLocation/Libraries/RepeatPeps.lib failed with:
$!";
+
+ my $wuDefault = &promptScreen(
+ "",
+@@ -733,7 +732,7 @@
+ }
+ }
+ else {
+- print "ERROR: Could not find nhmmer program in this directory!\n";
++ print "ERROR: Could not find nhmmer program in '$location'
directory!\n";
+ }
+ }
+
+@@ -753,7 +752,7 @@
+ }
+ close IN;
+ close OUT;
+- system( "mv $configFile.tmp $configFile" );
++ system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp
$configFile failed with: $!";
+
+ my $default = &promptScreen(
+ "",
+@@ -807,7 +806,7 @@
+ }
+ close IN;
+ close OUT;
+- system( "mv $configFile.tmp $configFile" );
++ system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp
$configFile failed with: $!";
+
+ my $deDefault = &promptScreen(
+ "",
+@@ -843,9 +842,6 @@
+
+ my $answer = undef;
+
+- # Clear the screen
+- system( "clear" );
+-
+ print "\n\n\n";
+ print $screenText;
+ my $numLines = ( $screenText =~ s/(\n)/$1/g );
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
index 2ff6c8be6..d41784eb7 100644
--- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
@@ -104,7 +104,7 @@ pkg_postinst(){
einfo "Supported search engines are:"
optfeature "cross_match" sci-biology/phrap
optfeature "rmblast" sci-biology/rmblast
- optfeature "nhmmer" >=sci-biology/hmmer-3.1
+ optfeature "nhmmer" \>=sci-biology/hmmer-3.1
einfo "abblast/wublast from http://blast.advbiocomp.com/licensing";
einfo "repeatmasker-libraries-20160829 (RepBase 21.12) is the last"
einfo "version compatible with <repeatmasker-4.0.7"
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
b/sci-biology/repeatmasker/repeatmasker-4.0.8-r1.ebuild
similarity index 94%
copy from sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
copy to sci-biology/repeatmasker/repeatmasker-4.0.8-r1.ebuild
index 2ff6c8be6..9b4af2312 100644
--- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.8-r1.ebuild
@@ -20,7 +20,7 @@ DEPEND=">=dev-lang/perl-5.8"
RDEPEND="
dev-perl/Text-Soundex
sci-biology/phrap
- <=sci-biology/repeatmasker-libraries-20160829
+ >sci-biology/repeatmasker-libraries-20160829
sci-biology/rmblast
!sci-biology/trf
>=sci-biology/trf-bin-4.0.4
@@ -92,7 +92,7 @@ src_install() {
doins -r util Matrices Libraries *.help
keepdir /usr/share/${PN}/Libraries
- dodoc README INSTALL *.help
+ dodoc README.md INSTALL *.help
}
pkg_postinst(){
@@ -104,8 +104,8 @@ pkg_postinst(){
einfo "Supported search engines are:"
optfeature "cross_match" sci-biology/phrap
optfeature "rmblast" sci-biology/rmblast
- optfeature "nhmmer" >=sci-biology/hmmer-3.1
+ optfeature "nhmmer" \>=sci-biology/hmmer-3.1
einfo "abblast/wublast from http://blast.advbiocomp.com/licensing";
- einfo "repeatmasker-libraries-20160829 (RepBase 21.12) is the last"
+ einfo "repeatmasker-libraries-20160829 (RepBase 21.12) was the last"
einfo "version compatible with <repeatmasker-4.0.7"
}
