[gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/files/, sci-biology/repeatmasker-libraries/, ...

2020-09-22 Thread Aisha Tammy 
commit: 97f8c547f73106de05bb51f7207263a9bbe4fdd8
Author: Aisha Tammy  aisha  cc>
AuthorDate: Tue Sep 22 11:09:22 2020 +
Commit: Aisha Tammy  aisha  cc>
CommitDate: Tue Sep 22 11:09:22 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=97f8c547

sci-biology/repeatmasker{,_libraries}: drop package

present in ::gentoo

Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Aisha Tammy  aisha.cc>

 sci-biology/repeatmasker-libraries/metadata.xml|   8 --
 .../repeatmasker-libraries-20150807.ebuild |  37 --
 .../repeatmasker-libraries-20160829.ebuild |  37 --
 .../repeatmasker-libraries-20181026.ebuild |  36 --
 .../files/repeatmasker-4.0.6__configure.patch  | 106 ---
 .../files/repeatmasker-4.0.8__configure.patch  | 118 -
 sci-biology/repeatmasker/metadata.xml  |  14 --
 .../repeatmasker/repeatmasker-4.0.6-r4.ebuild  | 142 -
 .../repeatmasker/repeatmasker-4.0.8-r2.ebuild  | 142 -
 9 files changed, 640 deletions(-)

diff --git a/sci-biology/repeatmasker-libraries/metadata.xml 
b/sci-biology/repeatmasker-libraries/metadata.xml
deleted file mode 100644
index 8417d1580..0
--- a/sci-biology/repeatmasker-libraries/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-   
-   sci-biol...@gentoo.org
-   Gentoo Biology Project
-   
-

diff --git 
a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20150807.ebuild 
b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20150807.ebuild
deleted file mode 100644
index 4b1222536..0
--- a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20150807.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="A special version of RepBase used by RepeatMasker"
-HOMEPAGE="http://repeatmasker.org/;
-SRC_URI="repeatmaskerlibraries-${PV}.tar.gz"
-
-LICENSE="all-rights-reserved"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND=""
-
-S="${WORKDIR}/Libraries"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-   einfo "Please register at http://www.girinst.org/ and go to"
-   einfo '"Repbase Update - RepeatMasker edition" link'
-   einfo 'which should take you to http://www.girinst.org/server/RepBase).'
-   einfo "Download repeatmaskerlibraries-${PV}.tar.gz and place it in 
'${DISTDIR}"
-   einfo "Older releases can be found in archive:"
-   einfo "https://www.girinst.org/repbase/update;
-   einfo "This one at https://www.girinst.org/server/archive/RepBase20.08;
-}
-
-src_install() {
-   insinto /usr/share/repeatmasker/Libraries
-   doins "${S}"/RepeatMaskerLib.embl
-   dodoc README
-   dodoc README.html
-}

diff --git 
a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20160829.ebuild 
b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20160829.ebuild
deleted file mode 100644
index 98521c4ba..0
--- a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20160829.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="A special version of RepBase used by RepeatMasker"
-HOMEPAGE="http://repeatmasker.org/;
-SRC_URI="repeatmaskerlibraries-${PV}.tar.gz"
-
-LICENSE="all-rights-reserved"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND=""
-
-S="${WORKDIR}/Libraries"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-   einfo "Please register at http://www.girinst.org/ and go to"
-   einfo '"Repbase Update - RepeatMasker edition" link'
-   einfo 'which should take you to http://www.girinst.org/server/RepBase).'
-   einfo "Download repeatmaskerlibraries-${PV}.tar.gz and place it in 
'${DISTDIR}"
-   einfo "Older releases can be found in archive:"
-   einfo "https://www.girinst.org/repbase/update;
-   einfo "This one at https://www.girinst.org/server/archive/RepBase21.12;
-}
-
-src_install() {
-   insinto /usr/share/repeatmasker/Libraries
-   doins "${S}"/RepeatMaskerLib.embl
-   dodoc README
-   dodoc README.html
-}

diff --git 
a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20181026.ebuild 
b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20181026.ebuild
deleted file mode 100644
index 5ea9ee4b5..0
--- a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20181026.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="A special version of RepBase used by RepeatMasker"
-HOMEPAGE="http://repeatmasker.org/;
-SRC_URI="RepBaseRepeatMaskerEdition-${PV}.tar.gz"
-
-LICENSE="all-rights-reserved"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-

[gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/files/, sci-biology/repeatmasker/

2018-11-30 Thread Martin Mokrejs 
commit: b42d6fd23f783fe21761e20fceb2291a21de61c0
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Fri Nov 30 16:12:25 2018 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Nov 30 16:12:25 2018 +
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  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 0..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 "\nThe RepeatMasker configure script must be run from\n"
++  die "\nThe 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 = (
+ "",
+@@ -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 $wuDefault = (
+ "",
+@@ -733,7 +732,7 @@
+   }
+ }
+ else {
+-  print "ERROR: Could not find nhmmer program in this directory!\n";
++  print "ERROR: Could not find nhmmer program in '$location' 
directory!\n";
+ }
+   }

[gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/files/, sci-biology/repeatmasker/

2015-11-30 Thread Martin Mokrejs 
commit: f7e2b8faced793d6f723a7da224fca410ae3c9ca
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Tue Dec  1 00:09:23 2015 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Dec  1 00:09:23 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f7e2b8fa

sci-biology/repeatmasker: added file checksum; add missing quotes

Package-Manager: portage-2.2.18

 ...ch => RepeatMasker-open-4-0-1__configure.patch} |  0
 ...ch => RepeatMasker-open-4-0-6__configure.patch} | 42 +++---
 ...r-4.0.1-r1.ebuild => repeatmasker-4.0.6.ebuild} |  6 ++--
 3 files changed, 16 insertions(+), 32 deletions(-)

diff --git a/sci-biology/repeatmasker/files/configure.patch 
b/sci-biology/repeatmasker/files/RepeatMasker-open-4-0-1__configure.patch
similarity index 100%
copy from sci-biology/repeatmasker/files/configure.patch
copy to sci-biology/repeatmasker/files/RepeatMasker-open-4-0-1__configure.patch

diff --git a/sci-biology/repeatmasker/files/configure.patch 
b/sci-biology/repeatmasker/files/RepeatMasker-open-4-0-6__configure.patch
similarity index 74%
rename from sci-biology/repeatmasker/files/configure.patch
rename to 
sci-biology/repeatmasker/files/RepeatMasker-open-4-0-6__configure.patch
index 0b8a75c..e404219 100644
--- a/sci-biology/repeatmasker/files/configure.patch
+++ b/sci-biology/repeatmasker/files/RepeatMasker-open-4-0-6__configure.patch
@@ -1,5 +1,5 @@
 configure.ori  2013-02-21 02:32:30.0 +0100
-+++ configure  2015-11-24 19:54:50.630202150 +0100
+--- configure.ori  2015-11-24 20:56:46.0 +0100
 configure  2015-11-24 20:59:58.0 +0100
 @@ -253,17 +253,16 @@
close INVERS;
  }
@@ -67,16 +67,16 @@
  
my $wuDefault = (
  "",
-@@ -748,7 +747,7 @@
- }
+@@ -756,7 +755,7 @@
}
-   else {
--print "ERROR: Could not find nhmmer program in this directory!\n";
-+print "ERROR: Could not find nhmmer program in '$location' 
directory!\n";
-   }
-   if ( $goodParam == 0 ) {
- print "\n";
-@@ -773,7 +772,7 @@
+ }
+ else {
+-  print "ERROR: Could not find nhmmer program in this directory!\n";
++  print "ERROR: Could not find nhmmer program in '$location' 
directory!\n";
+ }
+   }
+ 
+@@ -776,7 +775,7 @@
}
close IN;
close OUT;
@@ -85,7 +85,7 @@
  
my $default = (
  "",
-@@ -827,7 +826,7 @@
+@@ -830,7 +829,7 @@
}
close IN;
close OUT;
@@ -94,7 +94,7 @@
  
my $deDefault = (
  "",
-@@ -863,9 +862,6 @@
+@@ -866,9 +865,6 @@
  
my $answer = undef;
  
@@ -104,19 +104,3 @@
print "\n\n\n";
print $screenText;
my $numLines = ( $screenText =~ s/(\n)/$1/g );
 configure.ori  2015-11-24 20:10:58.640204679 +0100
-+++ configure  2015-11-24 20:11:00.970204685 +0100
-@@ -728,11 +728,12 @@
- # HMMER 3.0dev (March 2010); http://hmmer.org/
- # HMMER 3.1dev_0.33 (July 2012); http://hmmer.org
- # HMMER hmmer3.1-snap20120830 (August 2012); http://hmmer.org/
-+  # HMMER 3.1b2 (February 2015); http://hmmer.org/
- while ( $result =~ /([^\n\r]*)[\n\r]/ig ) {
-   my $line = $1;
- 
-   if ( $line =~ 
/^#\s+HMMER\s+(\d+\.\d+)((dev)?(_\d+\.\d+)?\s+\(.*\)).*/
--   || $line =~ /^#\s+HMMER\s+hmmer(\d+\.\d+)-snap.*/ )
-+   || $line =~ /^#\s+HMMER\s+hmmer(\d+\.\d+)-snap.*/ || $line =~ 
/^#\s+HMMER\s+(\d+\.\d+).*/)
-   {
- if ( $1 >= 3.1 ) {
-   $goodParam = 1;

diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.1-r1.ebuild 
b/sci-biology/repeatmasker/repeatmasker-4.0.6.ebuild
similarity index 94%
rename from sci-biology/repeatmasker/repeatmasker-4.0.1-r1.ebuild
rename to sci-biology/repeatmasker/repeatmasker-4.0.6.ebuild
index 0899978..89b7c7f 100644
--- a/sci-biology/repeatmasker/repeatmasker-4.0.1-r1.ebuild
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.6.ebuild
@@ -28,7 +28,7 @@ RDEPEND="
 S="${WORKDIR}/RepeatMasker"
 
 src_prepare(){
-   epatch "${FILESDIR}"/configure.patch
+   epatch "${FILESDIR}"/"${P}"__configure.patch
 }
 
 src_configure() {
@@ -37,11 +37,11 @@ src_configure() {
#  -- Building monolithic RM database...sh: 
/var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/image///usr/share/repeatmasker/Libraries/RepeatMasker.lib:
 No such file or directory
# -e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|'
sed -i -e 's/system( "clear" );//' "${S}/configure" || die
-   mkdir -p ${D}//usr/share/repeatmasker/Libraries/ || die
+   mkdir -p "${D}"/usr/share/repeatmasker/Libraries/ || die
#
# the below files is actually overwritten by buildRMLibFromEMBL.pl so 
the 'blah'
# item does not get installed
-   echo ">blah\natgc" > 
${D}//usr/share/repeatmasker/Libraries/RepeatMasker.lib || die
+   echo ">blah\natgc" > 
"${D}"/usr/share/repeatmasker/Libraries/RepeatMasker.lib || die
# below try to define paths to trf,

[gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/files/, sci-biology/repeatmasker/

2015-11-30 Thread Martin Mokrejs 
commit: 88c83795fd0b56239cc79b4b2c24e1d459dc348a
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Tue Dec  1 00:29:23 2015 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Dec  1 00:29:23 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=88c83795

sci-biology/repeatmasker: rename and move the patch file; drop old patch for a 
previous version

Package-Manager: portage-2.2.18

 sci-biology/repeatmasker/ChangeLog |   7 ++
 .../files/RepeatMasker-open-4-0-1__configure.patch | 122 -
 ...e.patch => repeatmasker-4.0.6__configure.patch} |   0
 3 files changed, 7 insertions(+), 122 deletions(-)

diff --git a/sci-biology/repeatmasker/ChangeLog 
b/sci-biology/repeatmasker/ChangeLog
index c7fadb6..872aa83 100644
--- a/sci-biology/repeatmasker/ChangeLog
+++ b/sci-biology/repeatmasker/ChangeLog
@@ -2,6 +2,13 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+  01 Dec 2015; Martin Mokrejs 
+  +files/repeatmasker-4.0.6__configure.patch,
+  -files/RepeatMasker-open-4-0-1__configure.patch,
+  -files/RepeatMasker-open-4-0-6__configure.patch:
+  sci-biology/repeatmasker: rename and move the patch file; drop old patch for 
a
+  previous version
+
   24 Nov 2015; Martin Mokrejs 
   repeatmasker-4.0.1-r1.ebuild:
   sci-biology/repeatmasker: improve einfo message

diff --git 
a/sci-biology/repeatmasker/files/RepeatMasker-open-4-0-1__configure.patch 
b/sci-biology/repeatmasker/files/RepeatMasker-open-4-0-1__configure.patch
deleted file mode 100644
index 0b8a75c..000
--- a/sci-biology/repeatmasker/files/RepeatMasker-open-4-0-1__configure.patch
+++ /dev/null
@@ -1,122 +0,0 @@
 configure.ori  2013-02-21 02:32:30.0 +0100
-+++ configure  2015-11-24 19:54:50.630202150 +0100
-@@ -253,17 +253,16 @@
-   close INVERS;
- }
- else {
--  print "\nYour RepeatMasker installation is missing a library file.\n"
-+  die "\nYour RepeatMasker installation is missing a library file.\n"
-   . "RepeatMasker requires a minimal set of library sequences to run\n"
-   . "properly.  Please check that all files were extracted from the\n"
-   . "distribution before re-running the configure program.\n\n";
--  exit;
- }
- 
- print "\n  -- Building monolithic RM 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: $!";
- 
- ##
- ## TRF location
-@@ -475,7 +474,7 @@
- }
- close IN;
- close OUT;
--system( "mv $configFile.tmp $configFile" );
-+system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp 
$configFile failed with: $!";
-   }
- 
- }
-@@ -607,15 +606,15 @@
-   }
-   close IN;
-   close OUT;
--  system( "mv $configFile.tmp $configFile" );
-+  system( "mv $configFile.tmp $configFile" ) and die "Faled to mv 
$configFile.tmp $configFile: $!";
- 
-   # Freeze RM and RMPep libraries for RepeatModeler use among others
-   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 = (
- "",
-@@ -682,15 +681,15 @@
-   }
-   close IN;
-   close OUT;
--  system( "mv $configFile.tmp $configFile" );
-+  system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp 
$configFile failed with: $!";
- 
-   # Freeze RM and RMPep libraries
-   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 = (
- "",
-@@ -748,7 +747,7 @@
- }
-   }
-   else {
--print "ERROR: Could not find