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* [gentoo-commits] repo/gentoo:master commit in: sci-biology/tophat/files/, sci-biology/tophat/
@ 2016-04-09 18:57 David Seifert
  0 siblings, 0 replies; 5+ messages in thread
From: David Seifert @ 2016-04-09 18:57 UTC (permalink / raw
  To: gentoo-commits

commit:     5d6771c0711167003e2e7d729e04f8d5aa3603fd
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Apr  9 18:41:23 2016 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Apr  9 18:57:09 2016 +0000
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 ea62ce14aae28dc0cc2b18fde870a0d3c021d9fb0c2ffb728b02b008b5f5bd416f29176fe81ed2ad8b1a41014f8a7114e2b8032426e2767effe9cc6933417cee
-DIST tophat-1.4.1.tar.gz 1420422 SHA256 97fd6e09e3cafa90b969dac152585ce5bab4c86f32a980ce2c8ecaac846cd937 SHA512 f3f3823d7780cd7159c97d7dca38e4f8c599377a15d8ce4b9db804df2c619c050d3cc6a182e6aa21d2ff03af6a436ff0f2bd26c48c280360f205b1cd4e13539e WHIRLPOOL 0279af557ca2e473582068f8a2229b509ebaa5baedc3b60f89a63bee622f681b0dfcc8996c32fbf3df45e32b38a6d91446558bdc7d992da5874a4c2936e3ff7a
-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
 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..0000000
--- 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-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/files/tophat-2.0.8-flags.patch b/sci-biology/tophat/files/tophat-2.0.8-flags.patch
deleted file mode 100644
index 604f657..0000000
--- a/sci-biology/tophat/files/tophat-2.0.8-flags.patch
+++ /dev/null
@@ -1,105 +0,0 @@
- 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="$LDFLAGS"
-diff --git a/src/Makefile.am b/src/Makefile.am
-index dde692e..ebb9fcd 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -545,7 +545,7 @@ CLEANFILES = \
- 	tophat2
- 
- tophat2: tophat2.in
--	sed -e 's|__PREFIX__|$(prefix)|' tophat2.in > tophat2
-+	sed -e 's|__PREFIX__|$(prefix)|' $(top_srcdir)/src/tophat2.in > tophat2
- 
- #SUFFIXES = .py
- #.py:
-@@ -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/files/tophat-2.0.9-flags.patch b/sci-biology/tophat/files/tophat-2.0.9-flags.patch
deleted file mode 100644
index af89e72..0000000
--- a/sci-biology/tophat/files/tophat-2.0.9-flags.patch
+++ /dev/null
@@ -1,109 +0,0 @@
- 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/metadata.xml b/sci-biology/tophat/metadata.xml
index 63e216a..959160f 100644
--- a/sci-biology/tophat/metadata.xml
+++ b/sci-biology/tophat/metadata.xml
@@ -5,7 +5,4 @@
     <email>sci-biology@gentoo.org</email>
     <name>Gentoo Biology Project</name>
   </maintainer>
-  <use>
-    <flag name="bam">Compile support for the BAM format</flag>
-  </use>
 </pkgmetadata>

diff --git a/sci-biology/tophat/tophat-1.4.1.ebuild b/sci-biology/tophat/tophat-1.4.1.ebuild
deleted file mode 100644
index 3130c0d..0000000
--- a/sci-biology/tophat/tophat-1.4.1.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit flag-o-matic autotools
-
-DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
-HOMEPAGE="http://tophat.cbcb.umd.edu/"
-SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE="+bam"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="bam? ( sci-biology/samtools )"
-RDEPEND="${DEPEND}
-	sci-biology/bowtie"
-
-MAKEOPTS="${MAKEOPTS} -j1"
-
-src_prepare() {
-	filter-ldflags -Wl,--as-needed
-	eautoreconf
-}
-
-src_configure() {
-	econf \
-		$(use_with bam)
-}

diff --git a/sci-biology/tophat/tophat-2.0.0.ebuild b/sci-biology/tophat/tophat-2.0.0.ebuild
deleted file mode 100644
index 93159f6..0000000
--- a/sci-biology/tophat/tophat-2.0.0.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-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=( "${FILESDIR}"/${PN}-2.0.2-flags.patch )
-
-src_configure() {
-	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
deleted file mode 100644
index 7f68695..0000000
--- a/sci-biology/tophat/tophat-2.0.2.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-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
-}

diff --git a/sci-biology/tophat/tophat-2.0.8.ebuild b/sci-biology/tophat/tophat-2.0.8.ebuild
deleted file mode 100644
index 4a99dfd..0000000
--- a/sci-biology/tophat/tophat-2.0.8.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-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/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug"
-
-DEPEND="
-	dev-libs/boost
-	sci-biology/samtools
-	~sci-biology/seqan-1.3.1"
-RDEPEND="${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
-}

diff --git a/sci-biology/tophat/tophat-2.0.9.ebuild b/sci-biology/tophat/tophat-2.0.9.ebuild
deleted file mode 100644
index d362ebe..0000000
--- a/sci-biology/tophat/tophat-2.0.9.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-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/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug"
-
-DEPEND="
-	dev-libs/boost
-	sci-biology/samtools
-	~sci-biology/seqan-1.3.1"
-RDEPEND="${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
-}


^ permalink raw reply related	[flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/tophat/files/, sci-biology/tophat/
@ 2016-04-09 18:57 David Seifert
  0 siblings, 0 replies; 5+ messages in thread
From: David Seifert @ 2016-04-09 18:57 UTC (permalink / raw
  To: gentoo-commits

commit:     3bae7944956edffc244eb7d8e55bc0c786013ed0
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Apr  9 18:37:04 2016 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Apr  9 18:57:07 2016 +0000
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 0000000..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="$LDFLAGS"
+ 
+-AC_ARG_ENABLE(intel64,      [  --enable-intel64        optimize for Intel64 CPU such as Xeon and Core2],
+-			  [ext_CFLAGS="${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 $user_LDFLAGS"
+ 
+ AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign])
+--- tophat-2.1.1/src/Makefile.am
++++ tophat-2.1.1/src/Makefile.am
+@@ -683,17 +683,12 @@
+ SeqAn-1.4.2/seqan/system/system_thread.h \
+ SeqAn-1.4.2/seqan/version.h
+ 
+-SAMDIR = ./samtools-0.1.18
+-SAMLIB = libbam.a
+-SAMPROG = samtools_0.1.18
+-BAM_LIB = -lbam
+-BAM_CPPFLAGS = -I$(SAMDIR)
+-BAM_LDFLAGS = -L$(SAMDIR)
++BAM_LIB = -lbam-0.1-legacy
++AM_CPPFLAGS = -I/usr/include/bam-0.1-legacy/
+ 
+ #-- progs to be installed in $prefix/bin
+ 
+ bin_PROGRAMS = \
+-	$(SAMPROG) \
+ 	prep_reads \
+ 	gtf_to_fasta \
+ 	fix_map_ordering \
+@@ -722,9 +717,6 @@
+ 	tophat2 \
+ 	tophat
+ 
+-clean-local:
+-	cd $(SAMDIR) && make clean
+-
+ tophat2: tophat2.sh
+ 	cp tophat2.sh tophat2 && chmod 755 tophat2
+ 
+@@ -732,7 +724,7 @@
+ 	sed -e 's|__VERSION__|$(VERSION)|' tophat.py > tophat && chmod 755 tophat
+ 
+ #-- tophat library for linking convienence
+-noinst_LIBRARIES = $(SAMLIB) libgc.a libtophat.a
++noinst_LIBRARIES = libgc.a libtophat.a
+ 
+ noinst_HEADERS = \
+ 	reads.h \
+@@ -844,15 +836,5 @@
+ gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
+ gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS)
+ 
+-
+-libbam_a_SOURCES = 
+-samtools_0_1_18_SOURCES = 
+-
+-$(SAMPROG): $(SAMLIB)
+-	
+-
+-$(SAMLIB):
+-	cd $(SAMDIR) && make $(SAMPROG) && cp $(SAMLIB) $(SAMPROG) ..
+-
+ install-data-hook:
+ 	cp -r intervaltree sortedcontainers $(DESTDIR)$(bindir)

diff --git a/sci-biology/tophat/tophat-2.1.1.ebuild b/sci-biology/tophat/tophat-2.1.1.ebuild
new file mode 100644
index 0000000..fc80ea8
--- /dev/null
+++ b/sci-biology/tophat/tophat-2.1.1.ebuild
@@ -0,0 +1,69 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools eutils flag-o-matic python-single-r1
+
+DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie2"
+HOMEPAGE="https://ccb.jhu.edu/software/tophat/"
+SRC_URI="https://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="debug"
+
+RDEPEND="dev-libs/boost
+	sci-biology/samtools:0.1-legacy
+	sci-biology/bowtie:2"
+DEPEND="${RDEPEND}
+	sci-biology/seqan:1.4"
+
+PATCHES=(
+	"${FILESDIR}/${P}-unbundle-seqan-samtools.patch"
+)
+
+src_prepare() {
+	default
+
+	# remove bundled libs
+	rm -rf src/samtools-0.1.18/ src/SeqAn-1.4.2/ || die
+
+	sed -e "s:samtools_0.1.18:${EPREFIX}/usr/bin/samtools-0.1-legacy/samtools:" \
+		-i src/tophat.py src/common.cpp || die
+
+	sed -e "s:/usr/include/bam-0.1-legacy/:${EPREFIX}/usr/include/bam-0.1-legacy/:" \
+		-e '/^samtools-0\.1\.18\//d' \
+		-e '/^SeqAn-1\.4\.2\//d' \
+		-e 's:sortedcontainers/sortedset.py \\:sortedcontainers/sortedset.py:' \
+		-e 's:\$(top_builddir)\/src\/::' \
+		-i src/Makefile.am || die
+	sed -e 's:\$(top_builddir)\/src\/::' -i src/Makefile.am || die
+
+	# innocuous non-security flags, prevent log pollution
+	append-cflags -Wno-unused-but-set-variable -Wno-unused-variable
+	append-cppflags "$(pkg-config --cflags seqan-1.4)"
+
+	eautoreconf
+}
+
+src_configure() {
+	econf $(use_enable debug)
+}
+
+src_install() {
+	default
+
+	local i
+	for i in bed_to_juncs contig_to_chr_coords sra_to_solid tophat tophat-fusion-post; do
+		python_fix_shebang "${ED}"/usr/bin/${i}
+	done
+}
+
+pkg_postinst() {
+	optfeature "ABI SOLiD colorspace reads" sci-biology/bowtie:1
+}


^ permalink raw reply related	[flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/tophat/files/, sci-biology/tophat/
@ 2016-09-25 12:27 David Seifert
  0 siblings, 0 replies; 5+ messages in thread
From: David Seifert @ 2016-09-25 12:27 UTC (permalink / raw
  To: gentoo-commits

commit:     95f436ca3a6e4e65e9db762b7d0da99172593042
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Sep 25 12:26:00 2016 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Sep 25 12:26:47 2016 +0000
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="${PYTHON_DEPS}
-	dev-libs/boost:=
+	dev-libs/boost:=[threads]
 	sci-biology/samtools:0.1-legacy
 	sci-biology/bowtie:2"
 DEPEND="${RDEPEND}
 	virtual/pkgconfig
-	sci-biology/seqan:1.4"
+	sci-biology/seqan:1.4
+	>=sys-devel/autoconf-archive-2016.09.16"
 
 PATCHES=(
 	"${FILESDIR}/${P}-unbundle-seqan-samtools.patch"
@@ -52,6 +53,10 @@ src_prepare() {
 	append-cflags -Wno-unused-but-set-variable -Wno-unused-variable
 	append-cppflags "$($(tc-getPKG_CONFIG) --cflags seqan-1.4)"
 
+	# remove ancient autoconf archive macros, wreaking havoc,
+	# depend on sys-devel/autoconf-archive instead, bug #594810
+	rm {ax_boost_thread,ax_boost_base}.m4 || die
+
 	eautoreconf
 }
 


^ permalink raw reply related	[flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/tophat/files/, sci-biology/tophat/
@ 2017-04-01 12:10 David Seifert
  0 siblings, 0 replies; 5+ messages in thread
From: David Seifert @ 2017-04-01 12:10 UTC (permalink / raw
  To: gentoo-commits

commit:     d16351c8ea24af193b4fa3f7cd9321924ceffc40
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Apr  1 12:09:16 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Apr  1 12:09:58 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d16351c8

sci-biology/tophat: Unbundle python modules

Bug: https://bugs.gentoo.org/show_bug.cgi?id=614370
Package-Manager: Portage-2.3.5, Repoman-2.3.2

 .../files/tophat-2.1.1-python2-shebangs.patch      | 42 ++++++++++++++++++++++
 ...phat-2.1.1-r3.ebuild => tophat-2.1.1-r4.ebuild} | 19 +++++-----
 2 files changed, 50 insertions(+), 11 deletions(-)

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
new file mode 100644
index 00000000000..5c38bcc072e
--- /dev/null
+++ b/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch
@@ -0,0 +1,42 @@
+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/tophat-2.1.1-r3.ebuild b/sci-biology/tophat/tophat-2.1.1-r4.ebuild
similarity index 81%
rename from sci-biology/tophat/tophat-2.1.1-r3.ebuild
rename to sci-biology/tophat/tophat-2.1.1-r4.ebuild
index cf684593109..590f6eb2d20 100644
--- a/sci-biology/tophat/tophat-2.1.1-r3.ebuild
+++ b/sci-biology/tophat/tophat-2.1.1-r4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -19,6 +19,8 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 RDEPEND="${PYTHON_DEPS}
 	dev-libs/boost:=[threads]
+	dev-python/intervaltree[${PYTHON_USEDEP}]
+	dev-python/sortedcontainers[${PYTHON_USEDEP}]
 	sci-biology/samtools:0.1-legacy
 	sci-biology/bowtie:2"
 DEPEND="${RDEPEND}
@@ -27,8 +29,9 @@ DEPEND="${RDEPEND}
 	>=sys-devel/autoconf-archive-2016.09.16"
 
 PATCHES=(
-	"${FILESDIR}/${P}-unbundle-seqan-samtools.patch"
-	"${FILESDIR}/${P}-fix-c++14.patch"
+	"${FILESDIR}"/${P}-unbundle-seqan-samtools.patch
+	"${FILESDIR}"/${P}-fix-c++14.patch
+	"${FILESDIR}"/${P}-python2-shebangs.patch
 )
 
 src_prepare() {
@@ -66,16 +69,10 @@ src_configure() {
 src_install() {
 	default
 
+	# delete bundled python modules
 	local i
-	# install scripts properly
-	for i in bed_to_juncs contig_to_chr_coords sra_to_solid tophat tophat-fusion-post; do
-		python_fix_shebang "${ED%/}/usr/bin/${i}"
-	done
-
-	# install python modules properly
 	for i in intervaltree sortedcontainers; do
-		python_domodule "${ED%/}/usr/bin/${i}"
-		rm -rf "${ED%/}/usr/bin/${i}" || die
+		rm -r "${ED%/}"/usr/bin/${i} || die
 	done
 }
 


^ permalink raw reply related	[flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/tophat/files/, sci-biology/tophat/
@ 2020-02-28  7:30 Mikle Kolyada
  0 siblings, 0 replies; 5+ messages in thread
From: Mikle Kolyada @ 2020-02-28  7:30 UTC (permalink / raw
  To: gentoo-commits

commit:     c22df03ee45b3384f0c929d4c1349de89d6f3153
Author:     Mikle Kolyada <zlogene <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 28 07:30:13 2020 +0000
Commit:     Mikle Kolyada <zlogene <AT> gentoo <DOT> org>
CommitDate: Fri Feb 28 07:30:13 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c22df03e

sci-biology/tophat: remove last-rited package

Signed-off-by: Mikle Kolyada <zlogene <AT> 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..00000000000
--- 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..00000000000
--- 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, JunctionStats>(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..00000000000
--- 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..00000000000
--- 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=${CFLAGS}
--generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
-+generic_CFLAGS=""
- ext_CFLAGS=""
- debug_CFLAGS=""
- user_LDFLAGS="$LDFLAGS"
- 
--AC_ARG_ENABLE(intel64,      [  --enable-intel64        optimize 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])
-@@ -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=`${CC} --version | head -n 1`
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -683,17 +683,12 @@
- SeqAn-1.4.2/seqan/system/system_thread.h \
- SeqAn-1.4.2/seqan/version.h
- 
--SAMDIR = ./samtools-0.1.18
--SAMLIB = libbam.a
--SAMPROG = samtools_0.1.18
--BAM_LIB = -lbam
--BAM_CPPFLAGS = -I$(SAMDIR)
--BAM_LDFLAGS = -L$(SAMDIR)
-+BAM_LIB = -lbam-0.1-legacy
-+AM_CPPFLAGS = -I/usr/include/bam-0.1-legacy/
- 
- #-- progs to be installed in $prefix/bin
- 
- bin_PROGRAMS = \
--	$(SAMPROG) \
- 	prep_reads \
- 	gtf_to_fasta \
- 	fix_map_ordering \
-@@ -722,9 +717,6 @@
- 	tophat2 \
- 	tophat
- 
--clean-local:
--	cd $(SAMDIR) && make clean
--
- tophat2: tophat2.sh
- 	cp tophat2.sh tophat2 && chmod 755 tophat2
- 
-@@ -732,7 +724,7 @@
- 	sed -e 's|__VERSION__|$(VERSION)|' tophat.py > tophat && chmod 755 tophat
- 
- #-- tophat library for linking convienence
--noinst_LIBRARIES = $(SAMLIB) libgc.a libtophat.a
-+noinst_LIBRARIES = libgc.a libtophat.a
- 
- 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) $(LDFLAGS)
- 
--
--libbam_a_SOURCES = 
--samtools_0_1_18_SOURCES = 
--
--$(SAMPROG): $(SAMLIB)
--	
--
--$(SAMLIB):
--	cd $(SAMDIR) && make $(SAMPROG) && cp $(SAMLIB) $(SAMPROG) ..
--
- install-data-hook:
- 	cp -r intervaltree sortedcontainers $(DESTDIR)$(bindir)

diff --git a/sci-biology/tophat/metadata.xml b/sci-biology/tophat/metadata.xml
deleted file mode 100644
index 959160fe46b..00000000000
--- a/sci-biology/tophat/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>

diff --git a/sci-biology/tophat/tophat-2.1.1-r5.ebuild b/sci-biology/tophat/tophat-2.1.1-r5.ebuild
deleted file mode 100644
index 75318877138..00000000000
--- a/sci-biology/tophat/tophat-2.1.1-r5.ebuild
+++ /dev/null
@@ -1,83 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools eutils flag-o-matic python-single-r1 toolchain-funcs
-
-DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie2"
-HOMEPAGE="https://ccb.jhu.edu/software/tophat/"
-SRC_URI="https://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	dev-libs/boost:=[threads]
-	$(python_gen_cond_dep '
-		dev-python/intervaltree[${PYTHON_MULTI_USEDEP}]
-		dev-python/sortedcontainers[${PYTHON_MULTI_USEDEP}]
-	')
-	sci-biology/samtools:0.1-legacy
-	sci-biology/bowtie:2"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	sci-biology/seqan:1.4
-	>=sys-devel/autoconf-archive-2016.09.16"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-unbundle-seqan-samtools.patch
-	"${FILESDIR}"/${P}-fix-c++14.patch
-	"${FILESDIR}"/${P}-python2-shebangs.patch
-)
-
-src_prepare() {
-	default
-
-	# remove bundled libs
-	rm -rf src/samtools-0.1.18/ src/SeqAn-1.4.2/ || die
-
-	sed -e "s:samtools_0.1.18:${EPREFIX}/usr/bin/samtools-0.1-legacy/samtools:" \
-		-i src/tophat.py src/common.cpp || die
-
-	sed -e "s:/usr/include/bam-0.1-legacy/:${EPREFIX}/usr/include/bam-0.1-legacy/:" \
-		-e '/^samtools-0\.1\.18\//d' \
-		-e '/^SeqAn-1\.4\.2\//d' \
-		-e 's:sortedcontainers/sortedset.py \\:sortedcontainers/sortedset.py:' \
-		-e 's:\$(top_builddir)\/src\/::' \
-		-i src/Makefile.am || die
-	sed -e 's:\$(top_builddir)\/src\/::' -i src/Makefile.am || die
-
-	# innocuous non-security flags, prevent log pollution
-	append-cflags -Wno-unused-but-set-variable -Wno-unused-variable
-	append-cppflags "$($(tc-getPKG_CONFIG) --cflags seqan-1.4)"
-
-	# remove ancient autoconf archive macros, wreaking havoc,
-	# depend on sys-devel/autoconf-archive instead, bug #594810
-	rm {ax_boost_thread,ax_boost_base}.m4 || die
-
-	eautoreconf
-}
-
-src_configure() {
-	econf $(use_enable debug)
-}
-
-src_install() {
-	default
-
-	# delete bundled python modules
-	local i
-	for i in intervaltree sortedcontainers; do
-		rm -r "${ED%/}"/usr/bin/${i} || die
-	done
-}
-
-pkg_postinst() {
-	optfeature "ABI SOLiD colorspace reads" sci-biology/bowtie:1
-}


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2016-09-25 12:27 [gentoo-commits] repo/gentoo:master commit in: sci-biology/tophat/files/, sci-biology/tophat/ David Seifert
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2020-02-28  7:30 Mikle Kolyada
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