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commit: 895b3abfbdacf52dbd7a0e817eb7ebf101ce55a7 |
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Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Sun Oct 9 14:52:52 2016 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Sun Oct 9 15:14:23 2016 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=895b3abf |
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|
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sci-biology/hmmer: Properly SLOT=2 hmmer-2.3.2 |
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|
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Gentoo-bug: 328911, 586960 |
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* EAPI=6 |
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* Introduce SLOT=2 and rename binaries and |
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static libraries |
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|
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Package-Manager: portage-2.3.1 |
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|
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.../hmmer-2.3.2-fix-build-system-destdir.patch | 22 +++++ |
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.../files/hmmer-2.3.2-fix-perl-shebangs.patch | 108 +++++++++++++++++++++ |
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sci-biology/hmmer/hmmer-2.3.2-r4.ebuild | 75 ++++++++++++++ |
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3 files changed, 205 insertions(+) |
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|
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diff --git a/sci-biology/hmmer/files/hmmer-2.3.2-fix-build-system-destdir.patch b/sci-biology/hmmer/files/hmmer-2.3.2-fix-build-system-destdir.patch |
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new file mode 100644 |
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index 00000000..110c61f |
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--- /dev/null |
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+++ b/sci-biology/hmmer/files/hmmer-2.3.2-fix-build-system-destdir.patch |
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@@ -0,0 +1,22 @@ |
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+Make the build system respect DESTDIR, in order to allow staged builds. |
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+ |
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+--- a/Makefile.in |
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++++ b/Makefile.in |
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+@@ -109,13 +109,13 @@ |
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+ # installs man pages in MANDIR/man1/ (e.g. if MANSUFFIX is 1) |
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+ # Creates these directories if they don't exist. |
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+ install: |
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+- mkdir -p ${BINDIR} |
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+- -mkdir -p ${MANDIR}/man${MANSUFFIX} |
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++ mkdir -p ${DESTDIR}${BINDIR} |
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++ -mkdir -p ${DESTDIR}${MANDIR}/man${MANSUFFIX} |
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+ for file in $(PROGS) $(PVMPROGS); do\ |
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+- cp src/$$file $(BINDIR)/;\ |
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++ cp src/$$file ${DESTDIR}$(BINDIR)/;\ |
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+ done |
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+ -for file in hmmer $(PROGS); do\ |
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+- $(INSTMAN) documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\ |
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++ $(INSTMAN) documentation/man/$$file.man ${DESTDIR}$(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\ |
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+ done |
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+ |
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+ # uninstall: Reverses the steps of "make install". |
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|
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diff --git a/sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch b/sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch |
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new file mode 100644 |
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index 00000000..783d053 |
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--- /dev/null |
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+++ b/sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch |
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@@ -0,0 +1,108 @@ |
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+* Fix ancient perl 4 modules that are long gone. |
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+* Fix perl shebangs to be portable and usable on Prefix. |
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+See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/ |
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+ |
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+--- a/squid/Testsuite/bug-1-sfetch-paths |
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++++ b/squid/Testsuite/bug-1-sfetch-paths |
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+@@ -1,4 +1,4 @@ |
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+-#! /usr/bin/perl |
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++#!/usr/bin/env perl |
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+ |
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+ # Test for bug #1: sfetch/SSI path bug. |
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+ # sfetch can't follow paths out of current directory if it's using |
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+--- a/squid/Testsuite/x-base-afetch |
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++++ b/squid/Testsuite/x-base-afetch |
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+@@ -1,4 +1,4 @@ |
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+-#! /usr/bin/perl |
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++#!/usr/bin/env perl |
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+ |
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+ use testsuite; |
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+ |
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+--- a/squid/Testsuite/x-base-alistat |
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++++ b/squid/Testsuite/x-base-alistat |
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+@@ -1,4 +1,4 @@ |
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+-#! /usr/bin/perl |
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++#!/usr/bin/env perl |
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+ |
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+ use testsuite; |
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+ |
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+--- a/squid/Testsuite/x-base-seqstat |
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++++ b/squid/Testsuite/x-base-seqstat |
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+@@ -1,4 +1,4 @@ |
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+-#! /usr/bin/perl |
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++#!/usr/bin/env perl |
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+ |
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+ use testsuite; |
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+ |
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+--- a/squid/Testsuite/x-base-sfetch |
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++++ b/squid/Testsuite/x-base-sfetch |
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+@@ -1,4 +1,4 @@ |
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+-#! /usr/bin/perl |
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++#!/usr/bin/env perl |
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+ |
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+ use testsuite; |
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+ |
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+--- a/squid/Testsuite/x-base-shuffle |
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++++ b/squid/Testsuite/x-base-shuffle |
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+@@ -1,4 +1,4 @@ |
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+-#! /usr/bin/perl |
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++#!/usr/bin/env perl |
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+ |
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+ use testsuite; |
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+ |
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+--- a/squid/Testsuite/x-base-sindex |
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++++ b/squid/Testsuite/x-base-sindex |
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+@@ -1,4 +1,4 @@ |
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+-#! /usr/bin/perl |
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++#!/usr/bin/env perl |
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+ |
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+ use testsuite; |
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+ |
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+--- a/squid/Testsuite/x-base-sreformat |
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++++ b/squid/Testsuite/x-base-sreformat |
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+@@ -1,4 +1,4 @@ |
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+-#! /usr/bin/perl |
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++#!/usr/bin/env perl |
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+ |
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+ use testsuite; |
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+ |
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+--- a/testsuite/sqc |
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++++ b/testsuite/sqc |
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+@@ -1,4 +1,4 @@ |
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+-#! /usr/bin/perl |
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++#!/usr/bin/env perl |
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+ |
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+ # sqc |
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+ # quality control script for exercising code, regression testing, |
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+@@ -176,12 +176,11 @@ |
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+ # SRE, Tue Aug 6 11:16:39 2002 |
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+ # CVS $Id: sqc,v 1.3 2003/01/05 23:40:57 eddy Exp $ |
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+ |
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+-require "getopts.pl"; |
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+-require "importenv.pl"; |
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++use Getopt::Std; |
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+ |
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+ # Parse our command line |
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+ # |
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+-&Getopts('mp:r:v'); |
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++getopts('mp:r:v'); |
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+ if ($opt_m) { $do_memtest = 1; } |
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+ if ($opt_p) { push @prepdirs, $opt_p; } |
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+ if ($opt_r) { push @olddirs, $opt_r; } |
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+@@ -506,7 +505,7 @@ |
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+ # |
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+ sub tempname { |
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+ my ($dir, $name, $suffix); |
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+- if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";} |
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++ if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";} |
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+ |
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+ foreach $suffix ("aa".."zz") { |
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+ $name = "$dir"."sre".$suffix.$$; |
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+--- a/testsuite/test1-conversion.pl |
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++++ b/testsuite/test1-conversion.pl |
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+@@ -1,4 +1,4 @@ |
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+-#! /usr/bin/perl |
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++#!/usr/bin/env perl |
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+ |
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+ # Test hmmconvert. |
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+ # |
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|
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diff --git a/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild |
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new file mode 100644 |
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index 00000000..7cecfe6 |
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--- /dev/null |
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+++ b/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild |
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@@ -0,0 +1,75 @@ |
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+# Copyright 1999-2016 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+# $Id$ |
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+ |
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+EAPI=6 |
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+ |
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+DESCRIPTION="Sequence analysis using profile hidden Markov models" |
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+LICENSE="GPL-2" |
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+HOMEPAGE="http://hmmer.org/" |
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+SRC_URI="http://eddylab.org/software/${PN}/${PV}/${P}.tar.gz" |
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+ |
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+SLOT="2" |
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+IUSE="altivec test threads" |
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+KEYWORDS="~alpha ~amd64 ~ia64 ~ppc ~ppc64 ~sparc ~x86" |
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+ |
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+DEPEND="test? ( dev-lang/perl )" |
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+RDEPEND="" |
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+ |
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+PATCHES=( |
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+ "${FILESDIR}/${P}-fix-perl-shebangs.patch" |
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+ "${FILESDIR}/${P}-fix-build-system-destdir.patch" |
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+) |
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+ |
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+src_configure() { |
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+ # prevent stray environmental variable |
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+ # from causing issues in the test phase |
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+ unset TMPDIR |
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+ |
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+ econf \ |
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+ --enable-lfs \ |
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+ $(use_enable altivec) \ |
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+ $(use_enable threads) |
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+} |
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+ |
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+src_install() { |
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+ default |
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+ |
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+ newlib.a src/libhmmer.a libhmmer2.a |
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+ insinto /usr/include/hmmer2 |
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+ doins src/*.h |
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+ |
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+ dobin squid/{afetch,alistat,compalign,compstruct,revcomp,seqstat,seqsplit,sfetch,shuffle,sreformat,sindex,weight,translate} |
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+ dolib.a squid/libsquid.a |
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+ insinto /usr/include/hmmer2 |
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+ doins squid/*.h |
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+ |
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+ dodoc NOTES Userguide.pdf |
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+ newdoc 00README README |
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+ |
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+ # rename files due to collisions with hmmer-3 |
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+ # in order to make SLOTing possible |
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+ local i |
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+ |
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+ # first rename man pages... |
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+ pushd "${ED%/}"/usr/share/man/man1/ >/dev/null || die |
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+ for i in hmm*.1; do |
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+ mv ${i%.1}{,2}.1 || die |
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+ done |
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+ popd >/dev/null || die |
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+ |
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+ # ... then rename binaries |
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+ pushd "${ED%/}"/usr/bin/ >/dev/null || die |
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+ for i in hmm*; do |
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+ mv ${i}{,2} || die |
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+ done |
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+ popd >/dev/null || die |
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+} |
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+ |
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+pkg_postinst() { |
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+ elog "All ${P} binaries have been renamed, in order" |
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+ elog "to avoid collisions with hmmer-3. For instance" |
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+ elog |
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+ elog " hmmalign -> hmmalign2" |
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+ elog |
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+} |