sci-biology/tophat: Version BUmp; do parallel builds; handle debug build

Package-Manager: portage-2.2.0_alpha120/cvs/Linux x86_64

6 files changed, 190 insertions, 26 deletions

diff --git a/sci-biology/tophat/ChangeLog b/sci-biology/tophat/ChangeLog
index 93e0142cbc45..f8f1be7bbe04 100644
--- a/sci-biology/tophat/ChangeLog
+++ b/sci-biology/tophat/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/tophat
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/ChangeLog,v 1.8 2012/04/25 16:39:53 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/ChangeLog,v 1.9 2012/07/19 12:03:38 jlec Exp $
+
+*tophat-2.0.2 (19 Jul 2012)
+
+  19 Jul 2012; Justin Lecher <jlec@gentoo.org> tophat-2.0.0.ebuild,
+  +tophat-2.0.2.ebuild, +files/tophat-2.0.2-flags.patch, metadata.xml:
+  Version BUmp; do parallel builds; handle debug build
 
   25 Apr 2012; Justin Lecher <jlec@gentoo.org> tophat-1.0.12.ebuild,
   tophat-1.4.1.ebuild, tophat-2.0.0.ebuild:
diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest
index 21733330fe9b..30504ef117b3 100644
--- a/sci-biology/tophat/Manifest
+++ b/sci-biology/tophat/Manifest
@@ -1,18 +1,22 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA512
+Hash: SHA256
 
-DIST tophat-1.0.12.tar.gz 468781 RMD160 b705ca7bde20bd143ba1cfd084b3a3e2815a7a4d SHA1 8a39af78dc9ec797f9f30853fb24b6b0e42d0ef6 SHA256 f67b3f89aa79c7e14b40bcdba87f5aba6d322f869ca4260503e64ffcd2b621b2
-DIST tophat-1.4.1.tar.gz 1420422 RMD160 45073bcf6c46f621595eae58d61a601dd6fe8d93 SHA1 0513bbcadb7194f12fbddeb3e4033e032f2fb29f SHA256 97fd6e09e3cafa90b969dac152585ce5bab4c86f32a980ce2c8ecaac846cd937
-DIST tophat-2.0.0.tar.gz 1750811 RMD160 d72eca16022a67000576034e51138b74fa77654b SHA1 279caa788cd6444d42dcd26091d0c605cd23010a SHA256 1c45812225906fd014ed9671a3696727c6ed0cc5be8f330b3c5ec39a9234be97
-EBUILD tophat-1.0.12.ebuild 948 RMD160 a505db7a21fda8477839ba4f63e81d367c000d84 SHA1 105952f6083033b5ab20aaa75ec5d7cc4f625296 SHA256 c850a45bf9b8463e7eddb461c9da4f84a3628579a56f335e0aeb138c358172b6
-EBUILD tophat-1.4.1.ebuild 703 RMD160 bf5edb3b88a4a87fcf5c5e1fa40f3288427bf3d7 SHA1 2efc29a2a63e86aba8cd62862bb94abe4fa1c1e6 SHA256 02f1b01a315ec444948ec1bca8a66e24c14fab274cf58ab9d0815f1104d1498d
-EBUILD tophat-2.0.0.ebuild 703 RMD160 146acf9a23c8b55a921b62abcdc91b095fc6e2fb SHA1 a49b3b94514a043637413e9816a5d1bade1e8f73 SHA256 a511178eb1d91d66b00e476169109552b3396c337847d5a1683a5f618543dad1
-MISC ChangeLog 1406 RMD160 7349d39859e6645ff0a835480bbefd2b26c7ad6a SHA1 5139895eef8c4ce8b658989440a04ed11ca78ca0 SHA256 02583f1a9438b84ddfff2332d871303d98561a62de874c774d101326f146e8bb
-MISC metadata.xml 335 RMD160 b22dd3122da8bf158936a405342e180ca6ae90e7 SHA1 5b45fd576038bb88399efb595c1866f274b372e4 SHA256 ba5318e09c3e0b3d36ac6e6d946da192f0b8dabb80298d5c0e7f8f879c3bcdc0
+AUX tophat-2.0.2-flags.patch 4717 SHA256 629bb862c0cf57001622205a0f67540867c0eba33dcd6118e07d4b7ed6ee1603 SHA512 f62047f6c57e30fa1ddd9e985b19b4c7d038f941136ec3ffb3998fe3e595d0d4db478b3530bf47d56bbd213fde3e773cf8dee842eab429543b91267bfba42710 WHIRLPOOL ae15cd1e6ef6eedcc99e84e120e1c92d8bed804aafc9d1ec6f04ba0a4def227e352d51cc6f1e5a8cf6e31b9406e0ce0ee55a6878edf8b7c4068806204989db23
+DIST tophat-1.0.12.tar.gz 468781 SHA256 f67b3f89aa79c7e14b40bcdba87f5aba6d322f869ca4260503e64ffcd2b621b2
+DIST tophat-1.4.1.tar.gz 1420422 SHA256 97fd6e09e3cafa90b969dac152585ce5bab4c86f32a980ce2c8ecaac846cd937
+DIST tophat-2.0.0.tar.gz 1750811 SHA256 1c45812225906fd014ed9671a3696727c6ed0cc5be8f330b3c5ec39a9234be97 SHA512 5bd1dcc79c301dc0b464dd95d6da2b2ed69c4e003bc1f9c5cb556a7974bcdb86cbe6f7d8912856691ca89e9a5a10cbe10fa7391c4bbdc163408e1e57afed7295 WHIRLPOOL ace795553630bcd1e9966cae2ed2c42195dea2f3845fe778d591ad0214afef28ca389f32f0bd53ad01d1e3a520be140e77305313992be16259c111a9aa5e8514
+DIST tophat-2.0.2.tar.gz 1759933 SHA256 f9e40ae123dab24d2f2d6896ebf191c8ae3c05c80da6d4d965defe7579d553e0 SHA512 8341d406bfc2b86323932a151ad60469c6d50031bace433c5e3b6678a92eaed3516744fb9077d0e8944018275642050e2e9aca0126b4dd69423754c3dc9ae83c WHIRLPOOL 45a52fc96b258f4ae0b5b7a4d1dc4c22885e0b9230891dde1db85671deeceb3213008de02878cc3b1f9dc6af68b40bc897f691a1835bd4abf29d1a2bde42e1c2
+EBUILD tophat-1.0.12.ebuild 948 SHA256 c850a45bf9b8463e7eddb461c9da4f84a3628579a56f335e0aeb138c358172b6 SHA512 15513bb5f6f3cd2a3bb3677b51fe689b358adb77bc511b4f0381794b8e1338c545d2d4d18427105112ebfd500fe0f90b8d22cbec31458f14f9ef8214f6ae211b WHIRLPOOL 300345f2477b5e7d9e1c17211ed4a5f4858714e5a4850a2e78681da8166a82bee09e9f762d6f8616e52ec98b07637e248ab0738484ca14da8d4b5256731fe3b0
+EBUILD tophat-1.4.1.ebuild 703 SHA256 02f1b01a315ec444948ec1bca8a66e24c14fab274cf58ab9d0815f1104d1498d SHA512 c317696046489b7555a56254b7dd6ea760cbd2034828bb75ab86672d203b23ca0bfc8e9a6ac868b13f7e8865d9006b5c5e0fed92064023be397482a65dc84561 WHIRLPOOL 00d02337391126e30d72419b8050fd0719f44155f977b8c7df1c966ddd6635d06b5b3d965cd967c8c36ad9ee5a767dd258f62df3a2dc994f747385686beaabd1
+EBUILD tophat-2.0.0.ebuild 752 SHA256 83e3db748159b21d7a8368949a2845ec98b44ba2c9b78211a3077bfa4580366e SHA512 7a8e526783b1522a0473610ca7b2746a7c8cfe9a7481f1714c11a92d26bb4060429274f1d20d1f532da7c5d37685c1f0ab487dc9b08ff9e39b063c10713325bf WHIRLPOOL fc5e129cdc70ebdf87c0bd2f4b049a9eee9a87852158f0a228eff616049f2e07b72b9c1a5fe12061c2b1330398af1046faaf0a52ab3f7a4830799b903e081c59
+EBUILD tophat-2.0.2.ebuild 745 SHA256 9310c42a36a69d1fc2cc879cf50864bcc35db2ae2f4a4593b25e1d402b09ab64 SHA512 e7c2ae8c28b04862cdbe692e1d728bb661e52d0bc4f774309729229dbacd467544f2148cdb45aebb51e394c25aae8a587c4dcb188575a0ff2bdef13bb7373eb0 WHIRLPOOL 2396eb1e9e9274d3471b57a4627dee824ffe5386ad8cba7d87be3197d73cc03d044c0dac06fc5ea68654f5d61722a2e960c14e379de3f4a7349147f456c1b6cf
+MISC ChangeLog 1630 SHA256 5d05c7a54fbb3acfd785a2220cc19f3b910f5e806b9c3cc903ad7d2c0a1a11d7 SHA512 f9d3402174999db418892158b4d7890423f5b641dd701d58aba8307bf595edc6eb9841d4914c421ff5017f0ca56c683a691d833e68f754096e76550976c36526 WHIRLPOOL 0b92a7a2824cfff1bb6fc35208a5bbab98d195552d8fa04b3eaeb7f9e9f9f966571db701d305b6a1e37f3ba35280a61ba85135a2d27f469629b7b7313824f92c
+MISC metadata.xml 335 SHA256 34e8792763f44cb9a18ae3489a4fdf8bbeb5b5f559093380cf25a607304ea8b5 SHA512 00ba3017973b634aa09ae2904875c8d70ff5eaddb0f7488bdea2ac6003ed99a6c507f532bd3d46d6f8efda5c08f599aa7fa52410717c922748a4eab884222eee WHIRLPOOL ddb479745c628bf4b1b5f9410a59c96cde73633c34bd260952a21271e3463c1fa483fd75cb1d2cbd65b46ff45e486e76e71e0e504b8e520edb5f52b8feff2add
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+Comment: GPGTools - http://gpgtools.org
 
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diff --git a/sci-biology/tophat/files/tophat-2.0.2-flags.patch b/sci-biology/tophat/files/tophat-2.0.2-flags.patch
new file mode 100644
index 000000000000..ac1ca62da254
--- /dev/null
+++ b/sci-biology/tophat/files/tophat-2.0.2-flags.patch
@@ -0,0 +1,124 @@
+ configure.ac    |    6 +++---
+ src/Makefile.am |   30 +++++++++++++++---------------
+ 2 files changed, 18 insertions(+), 18 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 314a78e..f6933e6 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -68,7 +68,8 @@ AC_CANONICAL_HOST
+ # set CFLAGS and CXXFLAGS
+ #user_CFLAGS="${CXXFLAGS}"
+ user_CFLAGS=${CFLAGS}
+-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
++#generic_CFLAGS="-Wall -Wno-strict-aliasing -Wuninitialized"
++generic_CFLAGS=""
+ ext_CFLAGS=""
+ debug_CFLAGS=""
+ AC_ARG_ENABLE(intel64,      [  --enable-intel64        optimize for Intel64 CPU such as Xeon and Core2],
+@@ -84,7 +85,7 @@ AC_ARG_ENABLE([optim],
+               [if test "x$enable_optim" = xyes; then enable_optim=3; fi],
+               [enable_optim=3])
+ 
+-AS_IF([test "x$enable_optim" != xno], [ext_CFLAGS="$ext_CFLAGS -O$enable_optim"])	
++#AS_IF([test "x$enable_optim" != xno], [ext_CFLAGS="$ext_CFLAGS -O$enable_optim"])	
+ AS_IF([test "x$enable_debug" = xyes],
+       [debug_CFLAGS="-DDEBUG"],
+       [debug_CFLAGS="-DNDEBUG"])
+@@ -92,7 +93,6 @@ AS_IF([test "x$enable_debug" = xyes],
+ CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}"
+ CXXFLAGS="$CFLAGS"
+ CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS -I./SeqAn-1.3"
+-LDFLAGS="$ext_LDFLAGS"
+ 
+ AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign])
+ 
+diff --git a/src/Makefile.am b/src/Makefile.am
+index aa17841..42f9c0c 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -2,7 +2,7 @@
+ 
+ #SUBDIRS = samtools
+ 
+-#AM_CXXFLAGS = -I$(top_srcdir)/src/SeqAn-1.3
++AM_CXXFLAGS = -I$(top_srcdir)/src/SeqAn-1.3
+ 
+ # Generated with 
+ # find SeqAn-1.3 -type f -print | grep -v ".svn" | sed 's/$/ \\/g'
+@@ -550,7 +550,7 @@ CLEANFILES = \
+ 	tophat2
+ 
+ tophat2: tophat2.in
+-	sed -e 's|__PREFIX__|$(prefix)|' tophat2.in > tophat2
++	sed -e 's|__PREFIX__|$(prefix)|' $(top_srcdir)/src/tophat2.in > tophat2
+ 
+ #SUFFIXES = .py
+ #.py:
+@@ -621,53 +621,53 @@ libgc_a_SOURCES = \
+ #-- program sources
+ 
+ prep_reads_SOURCES = prep_reads.cpp
+-prep_reads_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
++prep_reads_LDADD = libtophat.a $(BAM_LIB)
+ prep_reads_LDFLAGS = $(BAM_LDFLAGS)
+ 
+ segment_juncs_SOURCES = segment_juncs.cpp
+-segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BAM_LIB)
++segment_juncs_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BAM_LIB)
+ segment_juncs_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
+ 
+ long_spanning_reads_SOURCES = long_spanning_reads.cpp
+-long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BAM_LIB)
++long_spanning_reads_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BAM_LIB)
+ long_spanning_reads_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
+ 
+ gtf_juncs_SOURCES = gtf_juncs.cpp
+-gtf_juncs_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
++gtf_juncs_LDADD = libtophat.a libgc.a $(BAM_LIB)
+ gtf_juncs_LDFLAGS = $(BAM_LDFLAGS)
+ 
+ juncs_db_SOURCES = juncs_db.cpp
+-juncs_db_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
++juncs_db_LDADD = libtophat.a $(BAM_LIB)
+ juncs_db_LDFLAGS = $(BAM_LDFLAGS)
+ 
+ tophat_reports_SOURCES = tophat_reports.cpp
+-tophat_reports_LDADD = $(top_builddir)/src/libtophat.a  $(BOOST_THREAD_LIB) $(BAM_LIB)
++tophat_reports_LDADD = libtophat.a  $(BOOST_THREAD_LIB) $(BAM_LIB)
+ tophat_reports_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
+ 
+ fix_map_ordering_SOURCES = fix_map_ordering.cpp
+-fix_map_ordering_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
++fix_map_ordering_LDADD = libtophat.a $(BAM_LIB)
+ fix_map_ordering_LDFLAGS = $(BAM_LDFLAGS)
+ 
+ bam2fastx_SOURCES = bam2fastx.cpp
+-bam2fastx_LDADD = $(top_builddir)/src/libgc.a $(BAM_LIB)
++bam2fastx_LDADD = libgc.a $(BAM_LIB)
+ bam2fastx_LDFLAGS = $(BAM_LDFLAGS)
+ 
+ bam_merge_SOURCES = bam_merge.cpp
+-bam_merge_LDADD = $(top_builddir)/src/libtophat.a $(top_builddir)/src/libgc.a $(BAM_LIB)
++bam_merge_LDADD = libtophat.a libgc.a $(BAM_LIB)
+ bam_merge_LDFLAGS = $(BAM_LDFLAGS)
+ 
+ closure_juncs_SOURCES = closures.cpp
+-closure_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
++closure_juncs_LDADD = libtophat.a $(BAM_LIB)
+ closure_juncs_LDFLAGS = $(BAM_LDFLAGS)
+ 
+ sam_juncs_SOURCES = sam_juncs.cpp
+-sam_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
++sam_juncs_LDADD = libtophat.a $(BAM_LIB)
+ sam_juncs_LDFLAGS = $(BAM_LDFLAGS)
+ 
+ map2gtf_SOURCES = map2gtf.cpp
+-map2gtf_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
++map2gtf_LDADD = libtophat.a libgc.a $(BAM_LIB)
+ map2gtf_LDFLAGS = $(BAM_LDFLAGS)
+ 
+ gtf_to_fasta_SOURCES = GTFToFasta.cpp FastaTools.cpp
+-gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
++gtf_to_fasta_LDADD = libtophat.a libgc.a $(BAM_LIB)
+ gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS)
diff --git a/sci-biology/tophat/metadata.xml b/sci-biology/tophat/metadata.xml
index 6631e9455420..8dc2f2067543 100644
--- a/sci-biology/tophat/metadata.xml
+++ b/sci-biology/tophat/metadata.xml
@@ -7,6 +7,6 @@
 	</maintainer>
 	<herd>sci-biology</herd>
 	<use>
-		<flag name='bam'>Compile support for the BAM format</flag>
+		<flag name="bam">Compile support for the BAM format</flag>
 	</use>
 </pkgmetadata>
diff --git a/sci-biology/tophat/tophat-2.0.0.ebuild b/sci-biology/tophat/tophat-2.0.0.ebuild
index b652da021077..de02f86fb3f4 100644
--- a/sci-biology/tophat/tophat-2.0.0.ebuild
+++ b/sci-biology/tophat/tophat-2.0.0.ebuild
@@ -1,10 +1,12 @@
 # Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/tophat-2.0.0.ebuild,v 1.2 2012/04/25 16:39:53 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/tophat-2.0.0.ebuild,v 1.3 2012/07/19 12:03:38 jlec Exp $
 
 EAPI=4
 
-inherit flag-o-matic autotools
+AUTOTOOLS_AUTORECONF=yes
+
+inherit autotools-utils
 
 DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
 HOMEPAGE="http://tophat.cbcb.umd.edu/"
@@ -12,21 +14,18 @@ SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz"
 
 LICENSE="Artistic"
 SLOT="0"
-IUSE="+bam"
 KEYWORDS="~amd64 ~x86"
+IUSE="+bam debug"
 
-DEPEND="bam? ( sci-biology/samtools )"
+DEPEND="
+	dev-libs/boost
+	bam? ( sci-biology/samtools )"
 RDEPEND="${DEPEND}
 	sci-biology/bowtie"
 
-MAKEOPTS="${MAKEOPTS} -j1"
-
-src_prepare() {
-	filter-ldflags -Wl,--as-needed
-	eautoreconf
-}
+PATCHES=( "${FILESDIR}"/${PN}-2.0.2-flags.patch )
 
 src_configure() {
-	econf \
-		$(use_with bam)
+	local myeconfargs=( $(use_enable debug) )
+	autotools-utils_src_configure
 }
diff --git a/sci-biology/tophat/tophat-2.0.2.ebuild b/sci-biology/tophat/tophat-2.0.2.ebuild
new file mode 100644
index 000000000000..b84186581aca
--- /dev/null
+++ b/sci-biology/tophat/tophat-2.0.2.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/tophat-2.0.2.ebuild,v 1.1 2012/07/19 12:03:38 jlec Exp $
+
+EAPI=4
+
+AUTOTOOLS_AUTORECONF=yes
+
+inherit autotools-utils
+
+DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
+HOMEPAGE="http://tophat.cbcb.umd.edu/"
+SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="+bam debug"
+
+DEPEND="
+	dev-libs/boost
+	bam? ( sci-biology/samtools )"
+RDEPEND="${DEPEND}
+	sci-biology/bowtie"
+
+PATCHES=( "${FILESDIR}"/${P}-flags.patch )
+
+src_configure() {
+	local myeconfargs=( $(use_enable debug) )
+	autotools-utils_src_configure
+}