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commit: c22df03ee45b3384f0c929d4c1349de89d6f3153 |
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Author: Mikle Kolyada <zlogene <AT> gentoo <DOT> org> |
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AuthorDate: Fri Feb 28 07:30:13 2020 +0000 |
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Commit: Mikle Kolyada <zlogene <AT> gentoo <DOT> org> |
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CommitDate: Fri Feb 28 07:30:13 2020 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c22df03e |
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|
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sci-biology/tophat: remove last-rited package |
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|
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Signed-off-by: Mikle Kolyada <zlogene <AT> gentoo.org> |
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|
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sci-biology/tophat/Manifest | 1 - |
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.../tophat/files/tophat-2.1.1-fix-c++14.patch | 14 -- |
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.../files/tophat-2.1.1-python2-shebangs.patch | 42 ------ |
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.../tophat-2.1.1-unbundle-seqan-samtools.patch | 162 --------------------- |
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sci-biology/tophat/metadata.xml | 8 - |
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sci-biology/tophat/tophat-2.1.1-r5.ebuild | 83 ----------- |
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6 files changed, 310 deletions(-) |
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|
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diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest |
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deleted file mode 100644 |
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index 05897bbf09e..00000000000 |
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--- a/sci-biology/tophat/Manifest |
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+++ /dev/null |
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@@ -1 +0,0 @@ |
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-DIST tophat-2.1.1.tar.gz 2259554 BLAKE2B f01b08cc2046b7d143864d64aa3e34d3000c7c10d7e50a4e102d500556e8620996de03392463f9d08ae97858eaec85b2df3b5d5ee5b0b4f7a5c0ae06bb3d08e8 SHA512 e2e0943a6f3d34b83922e6e403b65a3bee480a2b2bb4bf2de0cae7e0ef5bb166b66fec923316c2b643e8550e43c842f0f1bcc2ca7249d20fbcf5a4733fbdeabc |
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|
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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 |
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deleted file mode 100644 |
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index e8168bb9143..00000000000 |
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--- a/sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch |
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+++ /dev/null |
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@@ -1,14 +0,0 @@ |
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-Fix building with C++14, which errors out due to broken perfect forwarding signature. |
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-See also: https://bugs.gentoo.org/show_bug.cgi?id=594544 |
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- |
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---- a/src/tophat_reports.cpp |
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-+++ b/src/tophat_reports.cpp |
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-@@ -2705,7 +2705,7 @@ |
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- junction_stat.gtf_match = true; |
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- junction_stat.accepted = true; |
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- |
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-- gtf_junctions.insert(make_pair<Junction, JunctionStats>(Junction(ref_id, left_coord, right_coord, antisense), junction_stat)); |
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-+ gtf_junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), junction_stat)); |
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- } |
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- } |
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- fprintf(stderr, "Loaded %d GFF junctions from %s.\n", (int)(gtf_junctions.size()), gtf_juncs.c_str()); |
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|
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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 |
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deleted file mode 100644 |
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index 5c38bcc072e..00000000000 |
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--- a/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch |
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+++ /dev/null |
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@@ -1,42 +0,0 @@ |
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-Make Python 2 explicit in python scripts |
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- |
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---- a/src/bed_to_juncs |
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-+++ b/src/bed_to_juncs |
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-@@ -1,4 +1,4 @@ |
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--#!/usr/bin/env python |
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-+#!/usr/bin/env python2 |
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- # encoding: utf-8 |
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- """ |
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- bed_to_juncs.py |
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---- a/src/contig_to_chr_coords |
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-+++ b/src/contig_to_chr_coords |
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-@@ -1,4 +1,4 @@ |
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--#!/usr/bin/env python |
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-+#!/usr/bin/env python2 |
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- # encoding: utf-8 |
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- """ |
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- contig_to_chr_coords.py |
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---- a/src/sra_to_solid |
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-+++ b/src/sra_to_solid |
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-@@ -1,4 +1,4 @@ |
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--#!/usr/bin/env python |
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-+#!/usr/bin/env python2 |
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- |
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- """ |
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- sra_to_solid.py |
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---- a/src/tophat-fusion-post |
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-+++ b/src/tophat-fusion-post |
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-@@ -1,4 +1,4 @@ |
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--#!/usr/bin/env python |
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-+#!/usr/bin/env python2 |
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- |
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- |
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- """ |
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---- a/src/tophat.py |
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-+++ b/src/tophat.py |
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-@@ -1,4 +1,4 @@ |
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--#!/usr/bin/env python |
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-+#!/usr/bin/env python2 |
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- |
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- # encoding: utf-8 |
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- """ |
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|
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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 |
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deleted file mode 100644 |
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index 9d0a2694051..00000000000 |
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--- a/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch |
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+++ /dev/null |
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@@ -1,162 +0,0 @@ |
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-Unbundle the included samtools and SeqAn, and use system libraries. |
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-See also: https://bugs.gentoo.org/show_bug.cgi?id=566494 |
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- |
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-Remove ancient ax_boost_base.m4 and ax_boost_thread.m4, and depend |
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-on >=sys-devel/autoconf-archive-2016.09.16 in the ebuild instead. |
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-See also: https://bugs.gentoo.org/show_bug.cgi?id=594810 |
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- |
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---- a/configure.ac |
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-+++ b/configure.ac |
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-@@ -28,26 +28,15 @@ |
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- AC_PROG_INSTALL |
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- AM_PATH_PYTHON([2.4]) |
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- |
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--m4_include([ax_boost_base.m4]) |
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--m4_include([ax_boost_thread.m4]) |
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- # CXXFLAGS="$CXXFLAGS $threadLib" |
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- AX_BOOST_BASE([1.38.0]) |
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-+AX_BOOST_SYSTEM |
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- AX_BOOST_THREAD |
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--if test -z "$BOOST_THREAD_LIBS"; then |
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-+if test -z "$BOOST_THREAD_LIB"; then |
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- AC_MSG_ERROR([boost.thread not found. Aborting.]) |
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- fi |
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- |
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- |
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--# BAM related: |
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-- ac_bam_path=samtools-0.1.18 |
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-- BAM_LIB="-lbam" |
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-- BAM_LDFLAGS="-L./$ac_bam_path" |
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-- BAM_CPPFLAGS="-I./$ac_bam_path" |
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-- AC_SUBST(BAM_CPPFLAGS) |
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-- AC_SUBST(BAM_LDFLAGS) |
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-- AC_SUBST(BAM_LIB) |
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-- |
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-- |
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- # Checks for header files. |
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- AC_CHECK_HEADERS([stdlib.h string.h unistd.h]) |
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- |
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-@@ -80,32 +69,23 @@ |
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- # set CFLAGS and CXXFLAGS |
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- #user_CFLAGS="${CXXFLAGS}" |
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- user_CFLAGS=${CFLAGS} |
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--generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized" |
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-+generic_CFLAGS="" |
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- ext_CFLAGS="" |
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- debug_CFLAGS="" |
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- user_LDFLAGS="$LDFLAGS" |
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- |
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--AC_ARG_ENABLE(intel64, [ --enable-intel64 optimize for Intel64 CPU such as Xeon and Core2], |
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-- [ext_CFLAGS="${ext_CFLAGS} -mtune=nocona"], []) |
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-- |
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- AC_ARG_ENABLE([debug], |
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- [AS_HELP_STRING([--enable-debug], |
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- [enable debugging info (default is no)])], |
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- [], [enable_debug=no]) |
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--AC_ARG_ENABLE([optim], |
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-- [AS_HELP_STRING([--enable-optim@<:@=0|1|2|3@:>@], |
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-- [set optimization level (default is 3)])], |
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-- [if test "x$enable_optim" = xyes; then enable_optim=3; fi], |
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-- [enable_optim=3]) |
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- |
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--AS_IF([test "x$enable_optim" != xno], [ext_CFLAGS="$ext_CFLAGS -O$enable_optim"]) |
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- AS_IF([test "x$enable_debug" = xyes], |
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- [debug_CFLAGS="-DDEBUG"], |
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- [debug_CFLAGS="-DNDEBUG"]) |
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- |
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- CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}" |
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- CXXFLAGS="$CFLAGS" |
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--CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS -I./SeqAn-1.4.2" |
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-+CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS" |
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- LDFLAGS="$BAM_LDFLAGS $BOOST_LDFLAGS $user_LDFLAGS" |
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- |
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- AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign]) |
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-@@ -122,7 +102,7 @@ |
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- -- ${PACKAGE_STRING} Configuration Results -- |
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- C++ compiler: ${CXX} ${CXXFLAGS} |
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- Linker flags: ${LDFLAGS} |
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-- BOOST libraries: ${BOOST_THREAD_LIBS}" |
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-+ BOOST libraries: ${BOOST_THREAD_LIB}" |
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- |
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- if test x"${GCC}" = x"yes" ; then |
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- gcc_version=`${CC} --version | head -n 1` |
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---- a/src/Makefile.am |
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-+++ b/src/Makefile.am |
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-@@ -683,17 +683,12 @@ |
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- SeqAn-1.4.2/seqan/system/system_thread.h \ |
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- SeqAn-1.4.2/seqan/version.h |
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- |
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--SAMDIR = ./samtools-0.1.18 |
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--SAMLIB = libbam.a |
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--SAMPROG = samtools_0.1.18 |
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--BAM_LIB = -lbam |
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--BAM_CPPFLAGS = -I$(SAMDIR) |
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--BAM_LDFLAGS = -L$(SAMDIR) |
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-+BAM_LIB = -lbam-0.1-legacy |
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-+AM_CPPFLAGS = -I/usr/include/bam-0.1-legacy/ |
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- |
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- #-- progs to be installed in $prefix/bin |
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- |
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- bin_PROGRAMS = \ |
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-- $(SAMPROG) \ |
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- prep_reads \ |
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- gtf_to_fasta \ |
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- fix_map_ordering \ |
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-@@ -722,9 +717,6 @@ |
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- tophat2 \ |
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- tophat |
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- |
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--clean-local: |
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-- cd $(SAMDIR) && make clean |
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-- |
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- tophat2: tophat2.sh |
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- cp tophat2.sh tophat2 && chmod 755 tophat2 |
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- |
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-@@ -732,7 +724,7 @@ |
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- sed -e 's|__VERSION__|$(VERSION)|' tophat.py > tophat && chmod 755 tophat |
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- |
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- #-- tophat library for linking convienence |
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--noinst_LIBRARIES = $(SAMLIB) libgc.a libtophat.a |
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-+noinst_LIBRARIES = libgc.a libtophat.a |
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- |
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- noinst_HEADERS = \ |
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- reads.h \ |
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-@@ -801,11 +793,11 @@ |
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- prep_reads_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) |
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- |
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- segment_juncs_SOURCES = segment_juncs.cpp |
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--segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB) |
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-+segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) |
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- segment_juncs_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS) |
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- |
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- long_spanning_reads_SOURCES = long_spanning_reads.cpp |
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--long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB) |
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-+long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) |
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- long_spanning_reads_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS) |
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- |
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- gtf_juncs_SOURCES = gtf_juncs.cpp |
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-@@ -817,7 +809,7 @@ |
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- juncs_db_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) |
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- |
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- tophat_reports_SOURCES = tophat_reports.cpp |
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--tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB) |
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-+tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) |
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- tophat_reports_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS) |
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- |
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- fix_map_ordering_SOURCES = fix_map_ordering.cpp |
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-@@ -844,15 +836,5 @@ |
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- gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB) |
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- gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) |
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- |
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-- |
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--libbam_a_SOURCES = |
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--samtools_0_1_18_SOURCES = |
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-- |
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--$(SAMPROG): $(SAMLIB) |
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-- |
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-- |
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--$(SAMLIB): |
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-- cd $(SAMDIR) && make $(SAMPROG) && cp $(SAMLIB) $(SAMPROG) .. |
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-- |
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- install-data-hook: |
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- cp -r intervaltree sortedcontainers $(DESTDIR)$(bindir) |
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|
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diff --git a/sci-biology/tophat/metadata.xml b/sci-biology/tophat/metadata.xml |
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deleted file mode 100644 |
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index 959160fe46b..00000000000 |
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--- a/sci-biology/tophat/metadata.xml |
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+++ /dev/null |
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@@ -1,8 +0,0 @@ |
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-<?xml version="1.0" encoding="UTF-8"?> |
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-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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-<pkgmetadata> |
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- <maintainer type="project"> |
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- <email>sci-biology@g.o</email> |
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- <name>Gentoo Biology Project</name> |
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- </maintainer> |
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-</pkgmetadata> |
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|
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diff --git a/sci-biology/tophat/tophat-2.1.1-r5.ebuild b/sci-biology/tophat/tophat-2.1.1-r5.ebuild |
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deleted file mode 100644 |
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index 75318877138..00000000000 |
285 |
--- a/sci-biology/tophat/tophat-2.1.1-r5.ebuild |
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+++ /dev/null |
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@@ -1,83 +0,0 @@ |
288 |
-# Copyright 1999-2020 Gentoo Authors |
289 |
-# Distributed under the terms of the GNU General Public License v2 |
290 |
- |
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-EAPI=6 |
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- |
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-PYTHON_COMPAT=( python2_7 ) |
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- |
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-inherit autotools eutils flag-o-matic python-single-r1 toolchain-funcs |
296 |
- |
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-DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie2" |
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-HOMEPAGE="https://ccb.jhu.edu/software/tophat/" |
299 |
-SRC_URI="https://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz" |
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- |
301 |
-LICENSE="Artistic" |
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-SLOT="0" |
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-KEYWORDS="~amd64 ~x86" |
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-IUSE="debug" |
305 |
-REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
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- |
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-RDEPEND="${PYTHON_DEPS} |
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- dev-libs/boost:=[threads] |
309 |
- $(python_gen_cond_dep ' |
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- dev-python/intervaltree[${PYTHON_MULTI_USEDEP}] |
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- dev-python/sortedcontainers[${PYTHON_MULTI_USEDEP}] |
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- ') |
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- sci-biology/samtools:0.1-legacy |
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- sci-biology/bowtie:2" |
315 |
-DEPEND="${RDEPEND} |
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- virtual/pkgconfig |
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- sci-biology/seqan:1.4 |
318 |
- >=sys-devel/autoconf-archive-2016.09.16" |
319 |
- |
320 |
-PATCHES=( |
321 |
- "${FILESDIR}"/${P}-unbundle-seqan-samtools.patch |
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- "${FILESDIR}"/${P}-fix-c++14.patch |
323 |
- "${FILESDIR}"/${P}-python2-shebangs.patch |
324 |
-) |
325 |
- |
326 |
-src_prepare() { |
327 |
- default |
328 |
- |
329 |
- # remove bundled libs |
330 |
- rm -rf src/samtools-0.1.18/ src/SeqAn-1.4.2/ || die |
331 |
- |
332 |
- sed -e "s:samtools_0.1.18:${EPREFIX}/usr/bin/samtools-0.1-legacy/samtools:" \ |
333 |
- -i src/tophat.py src/common.cpp || die |
334 |
- |
335 |
- sed -e "s:/usr/include/bam-0.1-legacy/:${EPREFIX}/usr/include/bam-0.1-legacy/:" \ |
336 |
- -e '/^samtools-0\.1\.18\//d' \ |
337 |
- -e '/^SeqAn-1\.4\.2\//d' \ |
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- -e 's:sortedcontainers/sortedset.py \\:sortedcontainers/sortedset.py:' \ |
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- -e 's:\$(top_builddir)\/src\/::' \ |
340 |
- -i src/Makefile.am || die |
341 |
- sed -e 's:\$(top_builddir)\/src\/::' -i src/Makefile.am || die |
342 |
- |
343 |
- # innocuous non-security flags, prevent log pollution |
344 |
- append-cflags -Wno-unused-but-set-variable -Wno-unused-variable |
345 |
- append-cppflags "$($(tc-getPKG_CONFIG) --cflags seqan-1.4)" |
346 |
- |
347 |
- # remove ancient autoconf archive macros, wreaking havoc, |
348 |
- # depend on sys-devel/autoconf-archive instead, bug #594810 |
349 |
- rm {ax_boost_thread,ax_boost_base}.m4 || die |
350 |
- |
351 |
- eautoreconf |
352 |
-} |
353 |
- |
354 |
-src_configure() { |
355 |
- econf $(use_enable debug) |
356 |
-} |
357 |
- |
358 |
-src_install() { |
359 |
- default |
360 |
- |
361 |
- # delete bundled python modules |
362 |
- local i |
363 |
- for i in intervaltree sortedcontainers; do |
364 |
- rm -r "${ED%/}"/usr/bin/${i} || die |
365 |
- done |
366 |
-} |
367 |
- |
368 |
-pkg_postinst() { |
369 |
- optfeature "ABI SOLiD colorspace reads" sci-biology/bowtie:1 |
370 |
-} |