* [gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/, sci-biology/repeatmasker/files/
@ 2015-11-24 19:28 Martin Mokrejs
0 siblings, 0 replies; 2+ messages in thread
From: Martin Mokrejs @ 2015-11-24 19:28 UTC (permalink / raw
To: gentoo-commits
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"
+}
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/, sci-biology/repeatmasker/files/
@ 2019-03-29 16:24 Martin Mokrejs
0 siblings, 0 replies; 2+ messages in thread
From: Martin Mokrejs @ 2019-03-29 16:24 UTC (permalink / raw
To: gentoo-commits
commit: 777780e24faa006c5883307c0dadd31cab8cecd8
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 29 16:24:12 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 29 16:24:12 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=777780e2
sci-biology/repeatmasker: rewamp configuration code
The changes are partly based on https://github.com/gentoo/sci/pull/580
from Michael Schubert but it seems we could figure out the paths
to binaries automatically using `which`.
Block between the USE options and allow only a single to be enabled,
that is what configure requires, otherwise it enters a loop.
The hmmer is the default in configure and preferred.
Tested with `USE="hmmer -wublast -phrap -rmblast"` and other
combinations while only one is allowed.
If users have wublast/abblast/rmblast/crossmatch in the PATHS we just
pick it.
`which` returns a '.' (dot) if a binary was not found, we need to zap it
otherwise configure enters a loop.
In the end, one can get:
Add a Search Engine:
1. CrossMatch: [ Configured ]
2. RMBlast - NCBI Blast with RepeatMasker extensions: [ Configured ]
3. WUBlast/ABBlast (required by DupMasker): [ Un-configured ]
4. HMMER3.1 & DFAM: [ Configured, Default ]
5. Done
properly written into
/usr/lib64/perl5/vendor_perl/5.28.0/RepeatMaskerConfig.pm
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
.../files/repeatmasker-4.0.6__configure.patch | 4 +-
sci-biology/repeatmasker/metadata.xml | 6 +
.../repeatmasker/repeatmasker-4.0.6-r3.ebuild | 111 ----------------
.../repeatmasker/repeatmasker-4.0.6-r4.ebuild | 142 +++++++++++++++++++++
.../repeatmasker/repeatmasker-4.0.8-r1.ebuild | 111 ----------------
.../repeatmasker/repeatmasker-4.0.8-r2.ebuild | 142 +++++++++++++++++++++
6 files changed, 292 insertions(+), 224 deletions(-)
diff --git a/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch b/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch
index e4042190f..c1e0cfb55 100644
--- a/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch
+++ b/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch
@@ -1,5 +1,5 @@
---- configure.ori 2015-11-24 20:56:46.000000000 +0100
-+++ configure 2015-11-24 20:59:58.000000000 +0100
+--- RepeatMasker/configure.ori 2015-11-24 20:56:46.000000000 +0100
++++ RepeatMasker/configure 2015-11-24 20:59:58.000000000 +0100
@@ -253,17 +253,16 @@
close INVERS;
}
diff --git a/sci-biology/repeatmasker/metadata.xml b/sci-biology/repeatmasker/metadata.xml
index 8417d1580..de382fa16 100644
--- a/sci-biology/repeatmasker/metadata.xml
+++ b/sci-biology/repeatmasker/metadata.xml
@@ -5,4 +5,10 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <use>
+ <flag name="phrap">Use cross_match search engine as default</flag>
+ <flag name="rmblast">Use RM-BLAST search engine as default</flag>
+ <flag name="hmmer">Use HMMER search engine as default</flag>
+ <flag name="wublast">Use wublast or abblast search engine as default</flag>
+ </use>
</pkgmetadata>
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
deleted file mode 100644
index d41784eb7..000000000
--- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
+++ /dev/null
@@ -1,111 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils perl-module
-
-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-${MY_PV}.tar.gz"
-
-LICENSE="OSL-2.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=dev-lang/perl-5.8"
-RDEPEND="
- dev-perl/Text-Soundex
- sci-biology/phrap
- <=sci-biology/repeatmasker-libraries-20160829
- sci-biology/rmblast
- !sci-biology/trf
- >=sci-biology/trf-bin-4.0.4
-"
-
-S="${WORKDIR}/RepeatMasker"
-
-PATCHES=( "${FILESDIR}"/"${P}"__configure.patch )
-
-src_configure() {
- sed \
- -e "s#/usr/bin/which#which#g" \
- -e "s#/usr/bin/perl#perl#g" \
- -i "${S}"/configure || die
- perl_set_version
- insinto ${VENDOR_LIB}
- sed -e "s#/usr/perl5/lib/#${VENDOR_LIB}/#g" -i "${S}"/configure || die
- # 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 "${ED}"/usr/share/repeatmasker/Libraries/ || die
- #
- # the below files is actually overwritten by buildRMLibFromEMBL.pl so the 'blah'
- # item does not get installed
- echo ">blah\natgc" > "${ED}"/usr/share/repeatmasker/Libraries/RepeatMasker.lib || die
- # below try to define paths to trf, cross_match, rmblast and nhmmer as search tools
- echo "
-env
-${S}
-${EPREFIX}/opt/trf/bin
-1
-${EPREFIX}/usr/bin
-Y
-2
-${EPREFIX}/usr/bin
-Y
-4
-${EPREFIX}/usr/bin
-Y
-5" | "${S}"/configure || die "configure failed"
- sed -i -e "s|use lib $FindBin::RealBin;|use lib ${EPREFIX}/usr/share/${PN}/lib;|" \
- -e "s|.*\(taxonomy.dat\)|${EPREFIX}/usr/share/${PN}/Libraries/\1|" \
- -e "/$REPEATMASKER_DIR/ s|$FindBin::RealBin|${EPREFIX}/usr/share/${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 $i
- dosym ../share/${PN}/$i /usr/bin/$i
- done
-
- perl_set_version
- insinto "${VENDOR_LIB}"
- doins "${S}"/*.pm "${S}"/Libraries/*.pm
- # zap the supposedly misplaced RepeatAnnotationData.pm file
- rm -r "${S}"/Libraries/*.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 -r Libraries/RepeatMaskerLib.embl || die
- insinto /usr/share/${PN}
- doins -r util Matrices Libraries *.help
- keepdir /usr/share/${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 are defined in"
- einfo "${EPREFIX}/usr/share/${PN}/lib/RepeatMaskerConfig.pm"
- einfo "Supported search engines are:"
- optfeature "cross_match" sci-biology/phrap
- optfeature "rmblast" sci-biology/rmblast
- 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-r4.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r4.ebuild
new file mode 100644
index 000000000..8216bfe7f
--- /dev/null
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.6-r4.ebuild
@@ -0,0 +1,142 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit eutils perl-module
+
+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="phrap rmblast hmmer wublast"
+# RepeatMaskerConfig.pm says:
+# Default search tool can be one of "hmmer", "crossmatch", "wublast", "decypher" or "ncbi".
+# Upstream uses "hmmer" as the default.
+
+DEPEND=">=dev-lang/perl-5.8"
+RDEPEND="
+ <=sci-biology/repeatmasker-libraries-20160829
+ dev-perl/Text-Soundex
+ phrap? ( !hmmer? ( !rmblast? ( !wublast? ( sci-biology/phrap ) ) ) )
+ rmblast? ( !hmmer? ( !phrap? ( !wublast? ( sci-biology/rmblast ) ) ) )
+ hmmer? ( !phrap? ( !wublast? ( !rmblast? ( sci-biology/hmmer ) ) ) )
+ !sci-biology/trf
+ >=sci-biology/trf-bin-4.0.4
+"
+# wublast? ( sci-biology/wublast || sci-biology/abblast )
+# ncbi? ( would that be ncbi-tools++ or ncbi-blast+ ) ???
+
+S="${WORKDIR}/RepeatMasker"
+
+PATCHES=( "${FILESDIR}"/"${P}"__configure.patch )
+
+src_configure() {
+ sed \
+ -e "s#/usr/bin/which#which#g" \
+ -e "s#/usr/bin/perl#perl#g" \
+ -i "${S}"/configure || die
+ perl_set_version
+ insinto ${VENDOR_LIB}
+ sed -e "s#/usr/perl5/lib/#${VENDOR_LIB}/#g" -i "${S}"/configure || die
+ # 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 "${ED}"/usr/share/repeatmasker/Libraries/ || die
+ #
+ # the below files is actually overwritten by buildRMLibFromEMBL.pl so the 'blah'
+ # item does not get installed
+ echo ">blah\natgc" > "${ED}"/usr/share/repeatmasker/Libraries/RepeatMasker.lib || die
+ # below try to define paths to trf, cross_match, rmblast and nhmmer as search tools
+ #
+ local my_crossmatch=`which cross_match 2>/dev/null`
+ local my_rmblastn=`which rmblastn 2>/dev/null`
+ local my_hmmer=`which nhmmscan 2>/dev/null`
+ local my_wublast=`which xdformat 2>/dev/null` # actually configure looks for 'setdb' executable
+ # configure is inconsistent at first, we must pass even a wrong path for cross_match, rmblastn, hmmer otherwise it enters a loop
+ # but, for wublast we must pass in an empty string otherwise it looks for 'setdb' executable in the non-existing directory and enters a loop
+ if [ "$my_crossmatch" != '.' ]; then local crossmatchdir=`dirname "$my_crossmatch"` else local crossmatchdir="${EPREFIX}/usr/bin"; fi
+ if [ "$my_rmblastn" != '.' ]; then local rmblastdir=`dirname "$my_rmblastn"` else local rmblastdir="${EPREFIX}/usr/bin"; fi
+ if [ "$my_hmmer" != '.' ]; then local hmmerdir=`dirname "$my_hmmer"` else local hmmerdir="${EPREFIX}/usr/bin"; fi
+ if [ "$my_wublast" != '.' ]; then local wublastdir=`dirname "$my_wublast"` else local wublastdir=""; fi
+ echo "crossmatchdir=${crossmatchdir} rmblastdir=${rmblastdir} wublastdir=${wublastdir} hmmerdir=${hmmerdir}"
+ # pick the preferred-one
+ local CONF=( x env ${S} "${EPREFIX}"/opt/bin )
+ if use phrap; then
+ CONF+=( 1 "${crossmatchdir}" Y )
+ else
+ CONF+=( 1 "${crossmatchdir}" N )
+ fi
+ if use rmblast; then
+ CONF+=( 2 "${rmblastdir}" Y )
+ else
+ CONF+=( 2 "${rmblastdir}" N )
+ fi
+ if use wublast; then
+ # no ebuild available but pick anything from PATH
+ CONF+=( 3 "${wublastdir}" Y )
+ else
+ CONF+=( 3 "${wublastdir}" N )
+ fi
+ if use hmmer; then
+ CONF+=( 4 "${hmmerdir}" Y )
+ else
+ CONF+=( 4 "${hmmerdir}" N )
+ fi
+ CONF+=( 5 )
+ echo "Will feed configure with: ${CONF[@]}"
+ printf '%s\n' "${CONF[@]}" | "${S}/configure" || die "configure failed"
+
+ sed -i -e "/use lib/s|\"\$FindBin::RealBin|\"${EPREFIX}/usr/share/${PN}/lib|" \
+ -e "/use lib/s|\$FindBin::RealBin|\"${EPREFIX}/usr/share/${PN}/lib\"|" \
+ -e "/\$REPEATMASKER_DIR/ s|\$FindBin::RealBin|${EPREFIX}/usr/share/${PN}|" \
+ "${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die
+}
+
+src_install() {
+ exeinto /usr/share/${PN}
+ for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do
+ doexe $i
+ dosym ../share/${PN}/$i /usr/bin/$i
+ done
+
+ perl_set_version
+ insinto "${VENDOR_LIB}"
+ doins "${S}"/*.pm "${S}"/Libraries/*.pm
+ # zap the supposedly misplaced RepeatAnnotationData.pm file
+ rm -r "${S}"/Libraries/*.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 -r Libraries/RepeatMaskerLib.embl || die
+ insinto /usr/share/${PN}
+ doins -r util Matrices Libraries *.help
+ keepdir /usr/share/${PN}/Libraries
+
+ dodoc README INSTALL *.help
+}
+
+pkg_postinst(){
+ cd "${S}" || die
+ einfo "RepeatMasker provides bundled human repeats database from"
+ einfo " Dfam-1.0 database www.dfam.org"
+ einfo "You can configure which search search engine is to be used and"
+ einfo "Current default search engine defined in"
+ einfo " ${EPREFIX}${VENDOR_LIB}/RepeatMaskerConfig.pm is:"
+ einfo `grep 'DEFAULT_SEARCH_ENGINE =' RepeatMaskerConfig.pm`
+ einfo "\nSupported search engines are:"
+ optfeature "cross_match" sci-biology/phrap
+ optfeature "rmblast" sci-biology/rmblast
+ optfeature "nhmmer" \>=sci-biology/hmmer-3.1
+ einfo "abblast/wublast from http://blast.advbiocomp.com/licensing"
+ einfo "\nThe repeatmasker-libraries-20160829 (RepBase 21.12) was the last"
+ einfo "version compatible with <repeatmasker-4.0.7"
+}
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.8-r1.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.8-r1.ebuild
deleted file mode 100644
index 9b4af2312..000000000
--- a/sci-biology/repeatmasker/repeatmasker-4.0.8-r1.ebuild
+++ /dev/null
@@ -1,111 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils perl-module
-
-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="
- dev-perl/Text-Soundex
- sci-biology/phrap
- >sci-biology/repeatmasker-libraries-20160829
- sci-biology/rmblast
- !sci-biology/trf
- >=sci-biology/trf-bin-4.0.4
-"
-
-S="${WORKDIR}/RepeatMasker"
-
-PATCHES=( "${FILESDIR}"/"${P}"__configure.patch )
-
-src_configure() {
- sed \
- -e "s#/usr/bin/which#which#g" \
- -e "s#/usr/bin/perl#perl#g" \
- -i "${S}"/configure || die
- perl_set_version
- insinto ${VENDOR_LIB}
- sed -e "s#/usr/perl5/lib/#${VENDOR_LIB}/#g" -i "${S}"/configure || die
- # 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 "${ED}"/usr/share/repeatmasker/Libraries/ || die
- #
- # the below files is actually overwritten by buildRMLibFromEMBL.pl so the 'blah'
- # item does not get installed
- echo ">blah\natgc" > "${ED}"/usr/share/repeatmasker/Libraries/RepeatMasker.lib || die
- # below try to define paths to trf, cross_match, rmblast and nhmmer as search tools
- echo "
-env
-${S}
-${EPREFIX}/opt/trf/bin
-1
-${EPREFIX}/usr/bin
-Y
-2
-${EPREFIX}/usr/bin
-Y
-4
-${EPREFIX}/usr/bin
-Y
-5" | "${S}"/configure || die "configure failed"
- sed -i -e "s|use lib $FindBin::RealBin;|use lib ${EPREFIX}/usr/share/${PN}/lib;|" \
- -e "s|.*\(taxonomy.dat\)|${EPREFIX}/usr/share/${PN}/Libraries/\1|" \
- -e "/$REPEATMASKER_DIR/ s|$FindBin::RealBin|${EPREFIX}/usr/share/${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 $i
- dosym ../share/${PN}/$i /usr/bin/$i
- done
-
- perl_set_version
- insinto "${VENDOR_LIB}"
- doins "${S}"/*.pm "${S}"/Libraries/*.pm
- # zap the supposedly misplaced RepeatAnnotationData.pm file
- rm -r "${S}"/Libraries/*.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 -r Libraries/RepeatMaskerLib.embl || die
- insinto /usr/share/${PN}
- doins -r util Matrices Libraries *.help
- keepdir /usr/share/${PN}/Libraries
-
- dodoc README.md 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 are defined in"
- einfo "${EPREFIX}/usr/share/${PN}/lib/RepeatMaskerConfig.pm"
- einfo "Supported search engines are:"
- optfeature "cross_match" sci-biology/phrap
- optfeature "rmblast" sci-biology/rmblast
- optfeature "nhmmer" \>=sci-biology/hmmer-3.1
- einfo "abblast/wublast from http://blast.advbiocomp.com/licensing"
- einfo "repeatmasker-libraries-20160829 (RepBase 21.12) was the last"
- einfo "version compatible with <repeatmasker-4.0.7"
-}
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.8-r2.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.8-r2.ebuild
new file mode 100644
index 000000000..02700ba2b
--- /dev/null
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.8-r2.ebuild
@@ -0,0 +1,142 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit eutils perl-module
+
+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="phrap rmblast hmmer wublast"
+# RepeatMaskerConfig.pm says:
+# Default search tool can be one of "hmmer", "crossmatch", "wublast", "decypher" or "ncbi".
+# Upstream uses "hmmer" as the default.
+
+DEPEND=">=dev-lang/perl-5.8"
+RDEPEND="
+ >sci-biology/repeatmasker-libraries-20160829
+ dev-perl/Text-Soundex
+ phrap? ( !hmmer? ( !rmblast? ( !wublast? ( sci-biology/phrap ) ) ) )
+ rmblast? ( !hmmer? ( !phrap? ( !wublast? ( sci-biology/rmblast ) ) ) )
+ hmmer? ( !phrap? ( !wublast? ( !rmblast? ( sci-biology/hmmer ) ) ) )
+ !sci-biology/trf
+ >=sci-biology/trf-bin-4.0.4
+"
+# wublast? ( sci-biology/wublast || sci-biology/abblast )
+# ncbi? ( would that be ncbi-tools++ or ncbi-blast+ ) ???
+
+S="${WORKDIR}/RepeatMasker"
+
+PATCHES=( "${FILESDIR}"/"${P}"__configure.patch )
+
+src_configure() {
+ sed \
+ -e "s#/usr/bin/which#which#g" \
+ -e "s#/usr/bin/perl#perl#g" \
+ -i "${S}"/configure || die
+ perl_set_version
+ insinto ${VENDOR_LIB}
+ sed -e "s#/usr/perl5/lib/#${VENDOR_LIB}/#g" -i "${S}"/configure || die
+ # 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 "${ED}"/usr/share/repeatmasker/Libraries/ || die
+ #
+ # the below files is actually overwritten by buildRMLibFromEMBL.pl so the 'blah'
+ # item does not get installed
+ echo ">blah\natgc" > "${ED}"/usr/share/repeatmasker/Libraries/RepeatMasker.lib || die
+ # below try to define paths to trf, cross_match, rmblast and nhmmer as search tools
+ #
+ local my_crossmatch=`which cross_match 2>/dev/null`
+ local my_rmblastn=`which rmblastn 2>/dev/null`
+ local my_hmmer=`which nhmmscan 2>/dev/null`
+ local my_wublast=`which xdformat 2>/dev/null` # actually configure looks for 'setdb' executable
+ # configure is inconsistent at first, we must pass even a wrong path for cross_match, rmblastn, hmmer otherwise it enters a loop
+ # but, for wublast we must pass in an empty string otherwise it looks for 'setdb' executable in the non-existing directory and enters a loop
+ if [ "$my_crossmatch" != '.' ]; then local crossmatchdir=`dirname "$my_crossmatch"` else local crossmatchdir="${EPREFIX}/usr/bin"; fi
+ if [ "$my_rmblastn" != '.' ]; then local rmblastdir=`dirname "$my_rmblastn"` else local rmblastdir="${EPREFIX}/usr/bin"; fi
+ if [ "$my_hmmer" != '.' ]; then local hmmerdir=`dirname "$my_hmmer"` else local hmmerdir="${EPREFIX}/usr/bin"; fi
+ if [ "$my_wublast" != '.' ]; then local wublastdir=`dirname "$my_wublast"` else local wublastdir=""; fi
+ echo "crossmatchdir=${crossmatchdir} rmblastdir=${rmblastdir} wublastdir=${wublastdir} hmmerdir=${hmmerdir}"
+ # pick the preferred-one
+ local CONF=( x env ${S} "${EPREFIX}"/opt/bin )
+ if use phrap; then
+ CONF+=( 1 "${crossmatchdir}" Y )
+ else
+ CONF+=( 1 "${crossmatchdir}" N )
+ fi
+ if use rmblast; then
+ CONF+=( 2 "${rmblastdir}" Y )
+ else
+ CONF+=( 2 "${rmblastdir}" N )
+ fi
+ if use wublast; then
+ # no ebuild available but pick anything from PATH
+ CONF+=( 3 "${wublastdir}" Y )
+ else
+ CONF+=( 3 "${wublastdir}" N )
+ fi
+ if use hmmer; then
+ CONF+=( 4 "${hmmerdir}" Y )
+ else
+ CONF+=( 4 "${hmmerdir}" N )
+ fi
+ CONF+=( 5 )
+ echo "Will feed configure with: ${CONF[@]}"
+ printf '%s\n' "${CONF[@]}" | "${S}/configure" || die "configure failed"
+
+ sed -i -e "/use lib/s|\"\$FindBin::RealBin|\"${EPREFIX}/usr/share/${PN}/lib|" \
+ -e "/use lib/s|\$FindBin::RealBin|\"${EPREFIX}/usr/share/${PN}/lib\"|" \
+ -e "/\$REPEATMASKER_DIR/ s|\$FindBin::RealBin|${EPREFIX}/usr/share/${PN}|" \
+ "${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die
+}
+
+src_install() {
+ exeinto /usr/share/${PN}
+ for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do
+ doexe $i
+ dosym ../share/${PN}/$i /usr/bin/$i
+ done
+
+ perl_set_version
+ insinto "${VENDOR_LIB}"
+ doins "${S}"/*.pm "${S}"/Libraries/*.pm
+ # zap the supposedly misplaced RepeatAnnotationData.pm file
+ rm -r "${S}"/Libraries/*.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 -r Libraries/RepeatMaskerLib.embl || die
+ insinto /usr/share/${PN}
+ doins -r util Matrices Libraries *.help
+ keepdir /usr/share/${PN}/Libraries
+
+ dodoc README.md INSTALL *.help
+}
+
+pkg_postinst(){
+ cd "${S}" || die
+ einfo "RepeatMasker provides bundled human repeats database from"
+ einfo " Dfam-1.0 database www.dfam.org"
+ einfo "You can configure which search search engine is to be used and"
+ einfo "Current default search engine defined in"
+ einfo " ${EPREFIX}${VENDOR_LIB}/RepeatMaskerConfig.pm is:"
+ einfo `grep 'DEFAULT_SEARCH_ENGINE =' RepeatMaskerConfig.pm`
+ einfo "\nSupported search engines are:"
+ optfeature "cross_match" sci-biology/phrap
+ optfeature "rmblast" sci-biology/rmblast
+ optfeature "nhmmer" \>=sci-biology/hmmer-3.1
+ einfo "abblast/wublast from http://blast.advbiocomp.com/licensing"
+ einfo "\nThe repeatmasker-libraries-20160829 (RepBase 21.12) was the last"
+ einfo "version compatible with <repeatmasker-4.0.7"
+}
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2015-11-24 19:28 [gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/, sci-biology/repeatmasker/files/ Martin Mokrejs
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2019-03-29 16:24 Martin Mokrejs
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