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From: "Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>
To: gentoo-commits@lists.gentoo.org
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Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>
Message-ID: <1448393264.62c5ffc75e7cea39f2488c7567ea47808c57b8f8.mmokrejs@gentoo>
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/, sci-biology/repeatmasker/files/
X-VCS-Repository: proj/sci
X-VCS-Files: sci-biology/repeatmasker/ChangeLog sci-biology/repeatmasker/files/configure.patch sci-biology/repeatmasker/metadata.xml sci-biology/repeatmasker/repeatmasker-4.0.1-r1.ebuild
X-VCS-Directories: sci-biology/repeatmasker/files/ sci-biology/repeatmasker/
X-VCS-Committer: mmokrejs
X-VCS-Committer-Name: Martin Mokrejs
X-VCS-Revision: 62c5ffc75e7cea39f2488c7567ea47808c57b8f8
X-VCS-Branch: master
Date: Tue, 24 Nov 2015 19:28:05 +0000 (UTC)
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commit: 62c5ffc75e7cea39f2488c7567ea47808c57b8f8
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Nov 24 19:27:44 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Nov 24 19:27:44 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=62c5ffc7
sci-biology/repeatmasker: heavily patch configure to return error codes and die upon error; add more DEPENDencies
Package-Manager: portage-2.2.18
sci-biology/repeatmasker/ChangeLog | 10 ++
sci-biology/repeatmasker/files/configure.patch | 122 +++++++++++++++++++++
sci-biology/repeatmasker/metadata.xml | 5 +
.../repeatmasker/repeatmasker-4.0.1-r1.ebuild | 100 +++++++++++++++++
4 files changed, 237 insertions(+)
diff --git a/sci-biology/repeatmasker/ChangeLog b/sci-biology/repeatmasker/ChangeLog
new file mode 100644
index 0000000..67ed4e6
--- /dev/null
+++ b/sci-biology/repeatmasker/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/repeatmasker
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Id$
+
+*repeatmasker-4.0.1-r1 (24 Nov 2015)
+
+ 24 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +files/configure.patch, +metadata.xml, +repeatmasker-4.0.1-r1.ebuild:
+ sci-biology/repeatmasker: heavily patch configure to return error codes and
+ die upon error; add more DEPENDencies
diff --git a/sci-biology/repeatmasker/files/configure.patch b/sci-biology/repeatmasker/files/configure.patch
new file mode 100644
index 0000000..0b8a75c
--- /dev/null
+++ b/sci-biology/repeatmasker/files/configure.patch
@@ -0,0 +1,122 @@
+--- configure.ori 2013-02-21 02:32:30.000000000 +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 = &promptScreen(
+ "",
+@@ -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 $wuDefault = &promptScreen(
+ "",
+@@ -748,7 +747,7 @@
+ }
+ }
+ else {
+- print "ERROR: Could not find nhmmer program in this directory!\n";
++ print "ERROR: Could not find nhmmer program in '$location' directory!\n";
+ }
+ if ( $goodParam == 0 ) {
+ print "<PRESS ENTER TO CONTINUE>\n";
+@@ -773,7 +772,7 @@
+ }
+ 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(
+ "",
+@@ -827,7 +826,7 @@
+ }
+ 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(
+ "",
+@@ -863,9 +862,6 @@
+
+ my $answer = undef;
+
+- # Clear the screen
+- system( "clear" );
+-
+ 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/metadata.xml b/sci-biology/repeatmasker/metadata.xml
new file mode 100644
index 0000000..f17a827
--- /dev/null
+++ b/sci-biology/repeatmasker/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.1-r1.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.1-r1.ebuild
new file mode 100644
index 0000000..9507e23
--- /dev/null
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.1-r1.ebuild
@@ -0,0 +1,100 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils
+
+MY_PV=${PV//\./-}
+
+DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA"
+HOMEPAGE="http://repeatmasker.org/"
+SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz"
+
+LICENSE="OSL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=">=dev-lang/perl-5.8"
+RDEPEND="
+ sci-biology/rmblast
+ >=sci-biology/trf-4.0.4
+ sci-biology/repeatmasker-libraries
+ sci-biology/phrap"
+# dev-perl/Text-Soundex see bug #566740
+
+S="${WORKDIR}/RepeatMasker"
+
+src_prepare(){
+ epatch "${FILESDIR}"/configure.patch
+}
+
+src_configure() {
+ # The below is wrong as it causes:
+ # Enter path [ /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/work/RepeatMasker ]:
+ # -- 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
+ #
+ # the below files is actually overwritten by buildRMLibFromEMBL.pl so the 'blah'
+ # item does not get installed
+ echo ">blah\natgc" > ${D}//usr/share/repeatmasker/Libraries/RepeatMasker.lib || die
+ # below try to define paths to trf, cross_match, rmblast and nhmmer as search tools
+ echo "
+env
+${S}
+/opt/bin
+1
+/usr/bin
+Y
+2
+/usr/bin
+Y
+4
+/usr/bin
+Y
+5" | "${S}/configure" || die "configure failed"
+ sed -i -e 's|use lib $FindBin::RealBin;|use lib "/usr/share/'${PN}'/lib";|' \
+ -e 's|".*\(taxonomy.dat\)"|"/usr/share/'${PN}'/\1"|' \
+ -e '/$REPEATMASKER_DIR/ s|$FindBin::RealBin|/usr/share/'${PN}'|' \
+ "${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die
+}
+# configure failed to 'cp RepeatMaskerConfig.tmpl RepeatMaskerConfig.pm'
+# replace also /u1/local/bin/perl with proper Gentoo PATH
+
+src_install() {
+ exeinto /usr/share/${PN}
+ for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do
+ doexe $i || die
+ dosym /usr/share/${PN}/$i /usr/bin/$i || die
+ done
+
+ dodir /usr/share/${PN}/lib
+ insinto /usr/share/${PN}/lib
+ doins "${S}"/*.pm || die
+
+ # if sci-biology/repeatmasker-libraries is installed prevent file collision
+ # and do NOT install Libraries/RepeatMaskerLib.embl file which contains
+ # a limited version of the file: 20110419-min
+ rm -rf Libraries/RepeatMaskerLib.embl
+ insinto /usr/share/${PN}
+ doins -r util Matrices Libraries taxonomy.dat *.help || die
+ keepdir /usr/share/${PN}/Libraries
+
+ dodoc README INSTALL *.help
+}
+
+pkg_postinst(){
+ einfo "RepeatMasker provides bundled human repeats database"
+ einfo "from Dfam-1.0 database www.dfam.org"
+ einfo "You can configure which search search engine is to be used and"
+ einfo "PATHs to the search binaries in RepeatMaskerConfig.pm"
+ einfo "Supported search engines are:"
+ einfo "cross_match from sci-biology/phrap"
+ einfo "rmblast from sci-biology/rmblast"
+ einfo "nhmmer from >=sci-biology/hmmer-3.1"
+ einfo "abblast/wublast from http://blast.advbiocomp.com/licensing"
+}