sci-biology/tophat: Version Bump, #502532; thanks José María Fernández González for the new ebuild

Package-Manager: portage-2.2.8-r1/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

4 files changed, 185 insertions, 8 deletions

diff --git a/sci-biology/tophat/ChangeLog b/sci-biology/tophat/ChangeLog
index 90c6c4831dd3..7fdca2b3f069 100644
--- a/sci-biology/tophat/ChangeLog
+++ b/sci-biology/tophat/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/tophat
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/ChangeLog,v 1.11 2013/03/13 16:33:37 jlec Exp $
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/ChangeLog,v 1.12 2014/03/06 09:46:50 jlec Exp $
+
+*tophat-2.0.9 (06 Mar 2014)
+
+  06 Mar 2014; Justin Lecher <jlec@gentoo.org> +tophat-2.0.9.ebuild,
+  +files/tophat-2.0.9-flags.patch:
+  Version Bump, #502532; thanks José María Fernández González for the new
+  ebuild
 
 *tophat-2.0.8 (13 Mar 2013)
 
diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest
index 41c85e890e37..600c26ceeb02 100644
--- a/sci-biology/tophat/Manifest
+++ b/sci-biology/tophat/Manifest
@@ -1,24 +1,39 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 AUX tophat-2.0.2-flags.patch 4717 SHA256 629bb862c0cf57001622205a0f67540867c0eba33dcd6118e07d4b7ed6ee1603 SHA512 f62047f6c57e30fa1ddd9e985b19b4c7d038f941136ec3ffb3998fe3e595d0d4db478b3530bf47d56bbd213fde3e773cf8dee842eab429543b91267bfba42710 WHIRLPOOL ae15cd1e6ef6eedcc99e84e120e1c92d8bed804aafc9d1ec6f04ba0a4def227e352d51cc6f1e5a8cf6e31b9406e0ce0ee55a6878edf8b7c4068806204989db23
 AUX tophat-2.0.8-flags.patch 4293 SHA256 da67d3186061d70cfb2b3b30073d189f2a3ab9a48fd06787ea895fbd85bf86a3 SHA512 297ba56bce4aaf991ad29bd198f73396e8a49e85ef69384c514e8fdb6afbb7715649f9628f2bcfd22b1618cbd64b5b61b67b596f7c971eea16443a5a90fafc92 WHIRLPOOL 1e162bfbf31588aa1bf25f07e45fae93955530e94f9f24a1a438e30df4303aaf22248946e0d49b29a77ccaf83098aaa81ba6f271179fb7a5fce8861acbf7c493
+AUX tophat-2.0.9-flags.patch 4446 SHA256 8405c1626d14db194480e74998e4e26171ccca0325030bfa4636fbda807fe8e3 SHA512 dae7931e7093f52caca99a8f953ef8af7a10db44e454aafed067735b040c5a8a580046d79bf08e7925f605877fba148ed42442f58ec844663f82586b83368de4 WHIRLPOOL 8b0913be28c62e8748ba1499463cecb58a5f508f834ef632d4bb98696eded0cf2280a61d67867fcc171ed81be24616271bca7809ca5ed7621ae776cf29ecdd99
 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
 DIST tophat-2.0.8.tar.gz 1757036 SHA256 07d323d295effc99d4e261439c5ba2e10d5530af078e5de97c1a7bf1cbdd0da1 SHA512 c69360cc2f558c37d14b6a0e006f2483771ce5cdb42dc8397dd15a944a61d762843158adbf7c2bc89c2d4db46d9a02633dbd2721bf3376ef5d3ae6fb153db100 WHIRLPOOL a97ad6d47be23089605578a6f8ff9434afcb27a9fa58118b5b923af1d79530614af9fcaf5ebda2043603bf2dd8b10c2b7636e7b14662b9ab4f6e2059da4cb2b2
+DIST tophat-2.0.9.tar.gz 1766681 SHA256 9b506bbfdbb14b296d804557a50f41cc167480dfeed66a31c33e2ffb580afd38 SHA512 a81b801ee6c1f643d1fa507c2372d43ccdf4922d3f7ab76a34442c96aee78a3afc4a47ba164d46c6b6b6451aeae78b711c44c118e584da742940f74af7bc9610 WHIRLPOOL a67392251e592df62deb3fe58dcc4eadd0d0b1fe0a09389e48f1f30a7c591343794d1e1b2a27467c0a0f5a0e84dd5a5fbdef538a5bcf1b80ba8972e6ec02fbcf
 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
 EBUILD tophat-2.0.8.ebuild 845 SHA256 e80806405eb0e4a9dbb3ce84c08e7f77c3a3fe3ddd1e9a71bca647fa1315e4bf SHA512 530fdd83f6c43e94adc38f5ab78df4e291e06d90fa088715427e03f1bd2480ba68e057333904c84a58cabc0aa251aa45538593f5a9b2402177622abbbc05686e WHIRLPOOL 334a439bf9057459fe7ef342f93b764fe07d1ba3d3268500eaae90643c7cbde27b9ead47b289fa83263c77f6c6999af762f6dbf7c5fe62a2549ffb8f7d1658f5
-MISC ChangeLog 1948 SHA256 3a03a496ecff608e13872437bd4c2e9d60d26d010674fb3f80b8037be6a24448 SHA512 3f777cca434699cabf50996784ce2d188a0dbdaca6ba185c8c62e2742ffba4220e3c1c3327b74a44e79072a702aa5c9e97e40db60737bd9a61f311b2fdd68d28 WHIRLPOOL 6153e90b7110896be4c5369cee2d923bcdfb3b7b1a3651810a85aaf442bbca52a3bc030d7e8ba095453d31b12abce0ec468518c71eedb188687f0a634c46ae59
+EBUILD tophat-2.0.9.ebuild 981 SHA256 9185f5b81a05a1be619566ce0a504cbcb3cdb040d77f0f453efae289e2737d43 SHA512 37be753da3f1539d6726864a507183058a9c4e2fd9989b491f4be3098f65a9883671983440a194a46c1efb022af0b734618109175db4a3c0780329f7937c3b49 WHIRLPOOL 677e473310c7d288e8f3fabf22bec5039eea2f53eff9ff35e3c7f9f7e0b9f817a3697e4864cc95ed05f17f397758bf9353ffa54742dc2a01db2788d69b30dfcc
+MISC ChangeLog 2169 SHA256 76f0433b22c1c5c1407f67878e6d352e94a4d614ae96333a430b66bd1d934038 SHA512 b8ead8c84ed89b516ed8839fd862549f2baf75dabb7a922abfd6d5adc196b7173286946e8c3aa4539a0f7f4ca6e8589adfd74e306e5e985946b3afd00522eb0b WHIRLPOOL 158d593f0199d051138756714043a5eb8c6e965b34ff7d1b5f3af09ee48c947085b055c47124b73bfce0db42a5fe911fd59d8a1fccf8461982c1dfcc0fae2c94
 MISC metadata.xml 246 SHA256 0a6f02ccfb3c4276d398c803a9ba1acd5f1d665c27367b3374f37e3f20243038 SHA512 87e71ab4e7f1cadf71fb816efc3dc264f9beea32475d2a53f5084d6c578bf97df767a6ced30650a2436bdbbd535a4cdc298ff2d520e488d539bcd3130a787969 WHIRLPOOL 9f4b764db056117763124b2596be3b125419107243717474ab1cb31ee27f54ad6eb75789fdb9f59ff079c34715df87178566e3ac3ec55d940ae36ea6cfdef2e4
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.19 (GNU/Linux)
+Version: GnuPG v2.0.22 (GNU/Linux)
 
-iEYEAREIAAYFAlFAqmIACgkQgAnW8HDreRZNxgCeO7aLp39ZR50aw7yZsqyzV6va
-O6YAoK2hHr+GCvdWfO3Qd5g2WK65k1IR
-=53wD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+=qGGs
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/tophat/files/tophat-2.0.9-flags.patch b/sci-biology/tophat/files/tophat-2.0.9-flags.patch
new file mode 100644
index 000000000000..af89e72084bf
--- /dev/null
+++ b/sci-biology/tophat/files/tophat-2.0.9-flags.patch
@@ -0,0 +1,109 @@
+ configure.ac    |  3 ++-
+ src/Makefile.am | 50 +++++++++++++++++++++++++-------------------------
+ 2 files changed, 27 insertions(+), 26 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 75e9218..98b05d2 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 -g -gdwarf-2 -Wuninitialized"
++generic_CFLAGS=""
+ ext_CFLAGS=""
+ debug_CFLAGS=""
+ user_LDFLAGS="$LDFLAGS"
+diff --git a/src/Makefile.am b/src/Makefile.am
+index dde692e..ebb9fcd 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -545,10 +545,10 @@ CLEANFILES = \
+ 	tophat2
+ 
+ tophat2: tophat2.in
+-	sed -e 's|__PREFIX__|$(prefix)|' tophat2.in > tophat2
++	sed -e 's|__PREFIX__|$(prefix)|' $(top_srcdir)/src/tophat2.in > tophat2
+ 
+ tophat: tophat.py
+-	sed -e 's|__VERSION__|$(VERSION)|' tophat.py > tophat
++	sed -e 's|__VERSION__|$(VERSION)|' $(top_srcdir)/src/tophat.py > tophat
+ 
+ #SUFFIXES = .py
+ #.py:
+@@ -617,49 +617,49 @@ libgc_a_SOURCES = \
+ #-- program sources
+ 
+ prep_reads_SOURCES = prep_reads.cpp
+-prep_reads_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
+-prep_reads_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) 
++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) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+-segment_juncs_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
++segment_juncs_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_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) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+-long_spanning_reads_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
++long_spanning_reads_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_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_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++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_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++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) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+-tophat_reports_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
++tophat_reports_LDADD = libtophat.a  $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_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_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++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_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++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_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++bam_merge_LDADD = libtophat.a libgc.a $(BAM_LIB)
++bam_merge_LDFLAGS = $(BAM_LDFLAGS)
+ 
+ sam_juncs_SOURCES = sam_juncs.cpp
+-sam_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
+-sam_juncs_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++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_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++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_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++gtf_to_fasta_LDADD = libtophat.a libgc.a $(BAM_LIB)
++gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS)
diff --git a/sci-biology/tophat/tophat-2.0.9.ebuild b/sci-biology/tophat/tophat-2.0.9.ebuild
new file mode 100644
index 000000000000..3f63f7f88d7b
--- /dev/null
+++ b/sci-biology/tophat/tophat-2.0.9.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/tophat-2.0.9.ebuild,v 1.1 2014/03/06 09:46:50 jlec Exp $
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=yes
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools-utils python-single-r1
+
+DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
+HOMEPAGE="http://tophat.cbcb.umd.edu/"
+SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="debug"
+
+DEPEND="
+	dev-libs/boost
+	sci-biology/samtools
+	sci-biology/seqan"
+RDEPEND="${DEPEND}
+	sci-biology/bowtie"
+
+PATCHES=( "${FILESDIR}"/${P}-flags.patch )
+
+src_prepare() {
+	rm -rf src/SeqAn* || die
+	autotools-utils_src_prepare
+}
+
+src_configure() {
+	local myeconfargs=(
+		--disable-optim
+		$(use_enable debug)
+	)
+	autotools-utils_src_configure
+}
+
+src_install() {
+	autotools-utils_src_install
+	python_fix_shebang "${ED}"/usr/bin/tophat
+}