[gentoo-commits] repo/gentoo:master commit in: sci-biology/tophat/files/, sci-biology/tophat/
commit: c22df03ee45b3384f0c929d4c1349de89d6f3153
Author: Mikle Kolyada gentoo org>
AuthorDate: Fri Feb 28 07:30:13 2020 +
Commit: Mikle Kolyada gentoo org>
CommitDate: Fri Feb 28 07:30:13 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c22df03e
sci-biology/tophat: remove last-rited package
Signed-off-by: Mikle Kolyada gentoo.org>
sci-biology/tophat/Manifest| 1 -
.../tophat/files/tophat-2.1.1-fix-c++14.patch | 14 --
.../files/tophat-2.1.1-python2-shebangs.patch | 42 --
.../tophat-2.1.1-unbundle-seqan-samtools.patch | 162 -
sci-biology/tophat/metadata.xml| 8 -
sci-biology/tophat/tophat-2.1.1-r5.ebuild | 83 ---
6 files changed, 310 deletions(-)
diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest
deleted file mode 100644
index 05897bbf09e..000
--- a/sci-biology/tophat/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST tophat-2.1.1.tar.gz 2259554 BLAKE2B
f01b08cc2046b7d143864d64aa3e34d3000c7c10d7e50a4e102d500556e8620996de03392463f9d08ae97858eaec85b2df3b5d5ee5b0b4f7a5c0ae06bb3d08e8
SHA512
e2e0943a6f3d34b83922e6e403b65a3bee480a2b2bb4bf2de0cae7e0ef5bb166b66fec923316c2b643e8550e43c842f0f1bcc2ca7249d20fbcf5a4733fbdeabc
diff --git a/sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch
b/sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch
deleted file mode 100644
index e8168bb9143..000
--- a/sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Fix building with C++14, which errors out due to broken perfect forwarding
signature.
-See also: https://bugs.gentoo.org/show_bug.cgi?id=594544
-
a/src/tophat_reports.cpp
-+++ b/src/tophat_reports.cpp
-@@ -2705,7 +2705,7 @@
- junction_stat.gtf_match = true;
- junction_stat.accepted = true;
-
-- gtf_junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense),
junction_stat));
-+ gtf_junctions.insert(make_pair(Junction(ref_id,
left_coord, right_coord, antisense), junction_stat));
- }
- }
- fprintf(stderr, "Loaded %d GFF junctions from %s.\n",
(int)(gtf_junctions.size()), gtf_juncs.c_str());
diff --git a/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch
b/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch
deleted file mode 100644
index 5c38bcc072e..000
--- a/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-Make Python 2 explicit in python scripts
-
a/src/bed_to_juncs
-+++ b/src/bed_to_juncs
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/env python2
- # encoding: utf-8
- """
- bed_to_juncs.py
a/src/contig_to_chr_coords
-+++ b/src/contig_to_chr_coords
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/env python2
- # encoding: utf-8
- """
- contig_to_chr_coords.py
a/src/sra_to_solid
-+++ b/src/sra_to_solid
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/env python2
-
- """
- sra_to_solid.py
a/src/tophat-fusion-post
-+++ b/src/tophat-fusion-post
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/env python2
-
-
- """
a/src/tophat.py
-+++ b/src/tophat.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/env python2
-
- # encoding: utf-8
- """
diff --git
a/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch
b/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch
deleted file mode 100644
index 9d0a2694051..000
--- a/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch
+++ /dev/null
@@ -1,162 +0,0 @@
-Unbundle the included samtools and SeqAn, and use system libraries.
-See also: https://bugs.gentoo.org/show_bug.cgi?id=566494
-
-Remove ancient ax_boost_base.m4 and ax_boost_thread.m4, and depend
-on >=sys-devel/autoconf-archive-2016.09.16 in the ebuild instead.
-See also: https://bugs.gentoo.org/show_bug.cgi?id=594810
-
a/configure.ac
-+++ b/configure.ac
-@@ -28,26 +28,15 @@
- AC_PROG_INSTALL
- AM_PATH_PYTHON([2.4])
-
--m4_include([ax_boost_base.m4])
--m4_include([ax_boost_thread.m4])
- # CXXFLAGS="$CXXFLAGS $threadLib"
- AX_BOOST_BASE([1.38.0])
-+AX_BOOST_SYSTEM
- AX_BOOST_THREAD
--if test -z "$BOOST_THREAD_LIBS"; then
-+if test -z "$BOOST_THREAD_LIB"; then
- AC_MSG_ERROR([boost.thread not found. Aborting.])
- fi
-
-
--# BAM related:
-- ac_bam_path=samtools-0.1.18
-- BAM_LIB="-lbam"
-- BAM_LDFLAGS="-L./$ac_bam_path"
-- BAM_CPPFLAGS="-I./$ac_bam_path"
-- AC_SUBST(BAM_CPPFLAGS)
-- AC_SUBST(BAM_LDFLAGS)
-- AC_SUBST(BAM_LIB)
--
--
- # Checks for header files.
- AC_CHECK_HEADERS([stdlib.h string.h unistd.h])
-
-@@ -80,32 +69,23 @@
- # set CFLAGS and CXXFLAGS
- #user_CFLAGS="${CXXFLAGS}"
- user_CFLAGS=${CFLAGS}
--generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2
[gentoo-commits] repo/gentoo:master commit in: sci-biology/tophat/files/, sci-biology/tophat/
commit: 95f436ca3a6e4e65e9db762b7d0da99172593042
Author: David Seifert gentoo org>
AuthorDate: Sun Sep 25 12:26:00 2016 +
Commit: David Seifert gentoo org>
CommitDate: Sun Sep 25 12:26:47 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=95f436ca
sci-biology/tophat: USE="threads" dep on dev-libs/boost
Gentoo-bug: 594810
* Remove autoconf macros from archive, depend on
sys-devel/autoconf instead for the latest versions.
Package-Manager: portage-2.3.1
.../tophat-2.1.1-unbundle-seqan-samtools.patch | 60 +++---
...phat-2.1.1-r1.ebuild => tophat-2.1.1-r2.ebuild} | 9 +++-
2 files changed, 61 insertions(+), 8 deletions(-)
diff --git
a/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch
b/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch
index c1e8bfd..9d0a269 100644
--- a/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch
+++ b/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch
@@ -1,9 +1,25 @@
Unbundle the included samtools and SeqAn, and use system libraries.
See also: https://bugs.gentoo.org/show_bug.cgi?id=566494
tophat-2.1.1/configure.ac
-+++ tophat-2.1.1/configure.ac
-@@ -38,16 +38,6 @@
+Remove ancient ax_boost_base.m4 and ax_boost_thread.m4, and depend
+on >=sys-devel/autoconf-archive-2016.09.16 in the ebuild instead.
+See also: https://bugs.gentoo.org/show_bug.cgi?id=594810
+
+--- a/configure.ac
b/configure.ac
+@@ -28,26 +28,15 @@
+ AC_PROG_INSTALL
+ AM_PATH_PYTHON([2.4])
+
+-m4_include([ax_boost_base.m4])
+-m4_include([ax_boost_thread.m4])
+ # CXXFLAGS="$CXXFLAGS $threadLib"
+ AX_BOOST_BASE([1.38.0])
++AX_BOOST_SYSTEM
+ AX_BOOST_THREAD
+-if test -z "$BOOST_THREAD_LIBS"; then
++if test -z "$BOOST_THREAD_LIB"; then
+ AC_MSG_ERROR([boost.thread not found. Aborting.])
fi
@@ -20,7 +36,7 @@ See also: https://bugs.gentoo.org/show_bug.cgi?id=566494
# Checks for header files.
AC_CHECK_HEADERS([stdlib.h string.h unistd.h])
-@@ -80,32 +70,23 @@
+@@ -80,32 +69,23 @@
# set CFLAGS and CXXFLAGS
#user_CFLAGS="${CXXFLAGS}"
user_CFLAGS=${CFLAGS}
@@ -55,8 +71,17 @@ See also: https://bugs.gentoo.org/show_bug.cgi?id=566494
LDFLAGS="$BAM_LDFLAGS $BOOST_LDFLAGS $user_LDFLAGS"
AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign])
tophat-2.1.1/src/Makefile.am
-+++ tophat-2.1.1/src/Makefile.am
+@@ -122,7 +102,7 @@
+ -- ${PACKAGE_STRING} Configuration Results --
+ C++ compiler:${CXX} ${CXXFLAGS}
+ Linker flags:${LDFLAGS}
+- BOOST libraries: ${BOOST_THREAD_LIBS}"
++ BOOST libraries: ${BOOST_THREAD_LIB}"
+
+ if test x"${GCC}" = x"yes" ; then
+gcc_version=`${CC} --version | head -n 1`
+--- a/src/Makefile.am
b/src/Makefile.am
@@ -683,17 +683,12 @@
SeqAn-1.4.2/seqan/system/system_thread.h \
SeqAn-1.4.2/seqan/version.h
@@ -96,6 +121,29 @@ See also: https://bugs.gentoo.org/show_bug.cgi?id=566494
noinst_HEADERS = \
reads.h \
+@@ -801,11 +793,11 @@
+ prep_reads_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS)
+
+ segment_juncs_SOURCES = segment_juncs.cpp
+-segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS)
$(BOOST_SYSTEM_LIB) $(BAM_LIB)
++segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB)
$(BOOST_SYSTEM_LIB) $(BAM_LIB)
+ segment_juncs_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS)
+
+ long_spanning_reads_SOURCES = long_spanning_reads.cpp
+-long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a
$(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
++long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a
$(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+ long_spanning_reads_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS)
+
+ gtf_juncs_SOURCES = gtf_juncs.cpp
+@@ -817,7 +809,7 @@
+ juncs_db_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS)
+
+ tophat_reports_SOURCES = tophat_reports.cpp
+-tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS)
$(BOOST_SYSTEM_LIB) $(BAM_LIB)
++tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB)
$(BOOST_SYSTEM_LIB) $(BAM_LIB)
+ tophat_reports_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS)
+
+ fix_map_ordering_SOURCES = fix_map_ordering.cpp
@@ -844,15 +836,5 @@
gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS)
diff --git a/sci-biology/tophat/tophat-2.1.1-r1.ebuild
b/sci-biology/tophat/tophat-2.1.1-r2.ebuild
similarity index 88%
rename from sci-biology/tophat/tophat-2.1.1-r1.ebuild
rename to sci-biology/tophat/tophat-2.1.1-r2.ebuild
index 6c6690a..52a75a6 100644
--- a/sci-biology/tophat/tophat-2.1.1-r1.ebuild
+++ b/sci-biology/tophat/tophat-2.1.1-r2.ebuild
@@ -19,12 +19,13 @@ IUSE="debug"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
RDEPEND="${PYTHON_DEPS}
- dev-libs/boost:=
+ dev-libs/boost:=[threads]
sci-biology/samtools:0.1-legacy
sci-biology/bowtie:2"
[gentoo-commits] repo/gentoo:master commit in: sci-biology/tophat/files/, sci-biology/tophat/
commit: 3bae7944956edffc244eb7d8e55bc0c786013ed0
Author: David Seifert gentoo org>
AuthorDate: Sat Apr 9 18:37:04 2016 +
Commit: David Seifert gentoo org>
CommitDate: Sat Apr 9 18:57:07 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3bae7944
sci-biology/tophat: Version bump, use samtools:0.1-legacy
Gentoo-Bug: 545154, 546816, 566494, 572054
* EAPI=6
* Unbundle samtools and SeqAn
* Fix broken shebangs in python scripts
Package-Manager: portage-2.2.28
sci-biology/tophat/Manifest| 1 +
.../tophat-2.1.1-unbundle-seqan-samtools.patch | 114 +
sci-biology/tophat/tophat-2.1.1.ebuild | 69 +
3 files changed, 184 insertions(+)
diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest
index 72e6371..b269f5d 100644
--- a/sci-biology/tophat/Manifest
+++ b/sci-biology/tophat/Manifest
@@ -4,3 +4,4 @@ DIST tophat-2.0.0.tar.gz 1750811 SHA256
1c45812225906fd014ed9671a3696727c6ed0cc5
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
+DIST tophat-2.1.1.tar.gz 2259554 SHA256
37840b96f3219630082b15642c47f5ef95d14f6ee99c06a369b08b3d05684da5 SHA512
e2e0943a6f3d34b83922e6e403b65a3bee480a2b2bb4bf2de0cae7e0ef5bb166b66fec923316c2b643e8550e43c842f0f1bcc2ca7249d20fbcf5a4733fbdeabc
WHIRLPOOL
1e0d2bc4031eaa56a3b77ca5966c2ed439a85c9b05f028f69f4477d517e51371156bbe73d499536148eb42d60641af7f294641ee79bc855fcc4df74d70dae26c
diff --git
a/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch
b/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch
new file mode 100644
index 000..c1e8bfd
--- /dev/null
+++ b/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch
@@ -0,0 +1,114 @@
+Unbundle the included samtools and SeqAn, and use system libraries.
+See also: https://bugs.gentoo.org/show_bug.cgi?id=566494
+
+--- tophat-2.1.1/configure.ac
tophat-2.1.1/configure.ac
+@@ -38,16 +38,6 @@
+ fi
+
+
+-# BAM related:
+- ac_bam_path=samtools-0.1.18
+- BAM_LIB="-lbam"
+- BAM_LDFLAGS="-L./$ac_bam_path"
+- BAM_CPPFLAGS="-I./$ac_bam_path"
+- AC_SUBST(BAM_CPPFLAGS)
+- AC_SUBST(BAM_LDFLAGS)
+- AC_SUBST(BAM_LIB)
+-
+-
+ # Checks for header files.
+ AC_CHECK_HEADERS([stdlib.h string.h unistd.h])
+
+@@ -80,32 +70,23 @@
+ # set CFLAGS and CXXFLAGS
+ #user_CFLAGS="${CXXFLAGS}"
+ user_CFLAGS=${CFLAGS}
+-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
++generic_CFLAGS=""
+ ext_CFLAGS=""
+ debug_CFLAGS=""
+ user_LDFLAGS="$LDFLAGS"
+
+-AC_ARG_ENABLE(intel64, [ --enable-intel64optimize for Intel64
CPU such as Xeon and Core2],
+-[ext_CFLAGS="${ext_CFLAGS} -mtune=nocona"], [])
+-
+ AC_ARG_ENABLE([debug],
+ [AS_HELP_STRING([--enable-debug],
+ [enable debugging info (default is no)])],
+ [], [enable_debug=no])
+-AC_ARG_ENABLE([optim],
+- [AS_HELP_STRING([--enable-optim@<:@=0|1|2|3@:>@],
+-[set optimization level (default is 3)])],
+- [if test "x$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_debug" = xyes],
+ [debug_CFLAGS="-DDEBUG"],
+ [debug_CFLAGS="-DNDEBUG"])
+
+ CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}"
+ CXXFLAGS="$CFLAGS"
+-CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS -I./SeqAn-1.4.2"
++CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS"
+ LDFLAGS="$BAM_LDFLAGS $BOOST_LDFLAGS $user_LDFLAGS"
+
+ AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign])
+--- tophat-2.1.1/src/Makefile.am
tophat-2.1.1/src/Makefile.am
+@@ -683,17 +683,12 @@
+ SeqAn-1.4.2/seqan/system/system_thread.h \
+ SeqAn-1.4.2/seqan/version.h
+
[gentoo-commits] repo/gentoo:master commit in: sci-biology/tophat/files/, sci-biology/tophat/
commit: 5d6771c0711167003e2e7d729e04f8d5aa3603fd
Author: David Seifert gentoo org>
AuthorDate: Sat Apr 9 18:41:23 2016 +
Commit: David Seifert gentoo org>
CommitDate: Sat Apr 9 18:57:09 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5d6771c0
sci-biology/tophat: Remove old and broken
Package-Manager: portage-2.2.28
sci-biology/tophat/Manifest | 5 -
sci-biology/tophat/files/tophat-2.0.2-flags.patch | 124 --
sci-biology/tophat/files/tophat-2.0.8-flags.patch | 105 --
sci-biology/tophat/files/tophat-2.0.9-flags.patch | 109 ---
sci-biology/tophat/metadata.xml | 3 -
sci-biology/tophat/tophat-1.4.1.ebuild| 32 --
sci-biology/tophat/tophat-2.0.0.ebuild| 31 --
sci-biology/tophat/tophat-2.0.2.ebuild| 31 --
sci-biology/tophat/tophat-2.0.8.ebuild| 40 ---
sci-biology/tophat/tophat-2.0.9.ebuild| 46
10 files changed, 526 deletions(-)
diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest
index b269f5d..2bf8121 100644
--- a/sci-biology/tophat/Manifest
+++ b/sci-biology/tophat/Manifest
@@ -1,7 +1,2 @@
DIST tophat-1.0.12.tar.gz 468781 SHA256
f67b3f89aa79c7e14b40bcdba87f5aba6d322f869ca4260503e64ffcd2b621b2 SHA512
275e14cb6fb5f7a0874adcf843aabfda6c6868f835faa2d03e6561646ca1fc80804fe1887c51a375125f2f5ed6242e304f97ff12774a7d676b4964614d4a5bf1
WHIRLPOOL
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-DIST tophat-1.4.1.tar.gz 1420422 SHA256
97fd6e09e3cafa90b969dac152585ce5bab4c86f32a980ce2c8ecaac846cd937 SHA512
f3f3823d7780cd7159c97d7dca38e4f8c599377a15d8ce4b9db804df2c619c050d3cc6a182e6aa21d2ff03af6a436ff0f2bd26c48c280360f205b1cd4e13539e
WHIRLPOOL
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-DIST tophat-2.0.0.tar.gz 1750811 SHA256
1c45812225906fd014ed9671a3696727c6ed0cc5be8f330b3c5ec39a9234be97 SHA512
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WHIRLPOOL
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-DIST tophat-2.0.2.tar.gz 1759933 SHA256
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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
DIST tophat-2.1.1.tar.gz 2259554 SHA256
37840b96f3219630082b15642c47f5ef95d14f6ee99c06a369b08b3d05684da5 SHA512
e2e0943a6f3d34b83922e6e403b65a3bee480a2b2bb4bf2de0cae7e0ef5bb166b66fec923316c2b643e8550e43c842f0f1bcc2ca7249d20fbcf5a4733fbdeabc
WHIRLPOOL
1e0d2bc4031eaa56a3b77ca5966c2ed439a85c9b05f028f69f4477d517e51371156bbe73d499536148eb42d60641af7f294641ee79bc855fcc4df74d70dae26c
diff --git a/sci-biology/tophat/files/tophat-2.0.2-flags.patch
b/sci-biology/tophat/files/tophat-2.0.2-flags.patch
deleted file mode 100644
index ac1ca62..000
--- a/sci-biology/tophat/files/tophat-2.0.2-flags.patch
+++ /dev/null
@@ -1,124 +0,0 @@
- 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=${CFLAGS}
--generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
-+#generic_CFLAGS="-Wall -Wno-strict-aliasing -Wuninitialized"
-+generic_CFLAGS=""
- ext_CFLAGS=""
- debug_CFLAGS=""
- AC_ARG_ENABLE(intel64, [ --enable-intel64optimize for Intel64
CPU such as Xeon and Core2],
-@@ -84,7 +85,7 @@ AC_ARG_ENABLE([optim],
- [if test "x$enable_optim" = xyes; then
