commit: 767b616524e6b171ed4775fe35ecd068f58abc22 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Mon Mar 28 19:59:02 2016 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Mon Mar 28 19:59:24 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=767b6165
sci-biology/samtools: version bump to 1.3, to match htslib * EAPI=6 * Added modern AX_WITH_CURSES that works with pkg-config * Fixed incorrect symlinks for libbam.so Package-Manager: portage-2.2.28 sci-biology/samtools/Manifest | 1 + .../samtools/files/samtools-1.3-buildsystem.patch | 174 +++++ .../samtools/files/samtools-1.3-ncurses.patch | 737 +++++++++++++++++++++ sci-biology/samtools/samtools-1.3.ebuild | 86 +++ 4 files changed, 998 insertions(+) diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest index fd88ba4..d25774f 100644 --- a/sci-biology/samtools/Manifest +++ b/sci-biology/samtools/Manifest @@ -4,3 +4,4 @@ DIST samtools-0.1.20.tar.gz 566387 SHA256 500019b4d1886ad995513d5ce8b413b14b51f1 DIST samtools-1.0.tar.bz2 4459669 SHA256 7340b843663c3f54a902a06f2f73c68198f3a62d29a2ed20671139957f7fd7c0 SHA512 5b80995c522d08b06a4c559f60a5e200d9085be7f44c3c9618db91e3de85e36c1473e42715eae8175520d7da3df8245bafa82e625d2fc08e0197adb395851693 WHIRLPOOL 2aa0f8639da9b0b828ca7296969e5c600b0e5452ad3231b914e4a7be418700906a4d695c928eaf837b643255567ec82cfadf0b53007e0f1e3a956856f6c4c832 DIST samtools-1.1.tar.bz2 4495373 SHA256 c24d26c303153d72b5bf3cc11f72c6c375a4ca1140cc485648c8c5473414b7f8 SHA512 a5552a6c8c4b0808b725b39ddb2fafa36c4f6623bfc7f84faadae7690223e4eec8d722af09c77145796ad9b3f01e04115dd0207207ccfafbb52ffc22d5fc09f0 WHIRLPOOL ed3131b2a8d8b4dab40b53d35a9b00b657670a949dc1597c91fbcd00392c1c1715a85a1d1e49bf0c73ae082738ccfb13d2c6809dbbeba17ff3028f6023ebc449 DIST samtools-1.2.tar.bz2 4547126 SHA256 420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa SHA512 4849c3274e732267516b63799f5430c5415d575d46eddf6b704dac51053281094b03b90dd9f5367bcd14c22fb0fb1bd6a412f7d4225f7be5f5385437c5d2101d WHIRLPOOL 273185764a807365a20c381769f987ef02d14ae8e20a3a7fd5af4344769c5fab68d7155523e8c0c8c3cc86092898c2c8454cce8f1560d415bc2b41549cdf04f4 +DIST samtools-1.3.tar.bz2 3978333 SHA256 beea4003c795a0a25224656815b4036f6864b8753053ed30c590bb052b70b60e SHA512 72920d4f0f10aa7b54ef448e03e6e769e1e07abd07388a2307d0e52548fa2909c03ca2c7eec5c63cf5b67724b2356833accb0079ce1486bb2ac66a45963a24ea WHIRLPOOL 3f798078100b4ed164f6c89d18cc8f62159437e2cfb2a228ac00f8d08313f7c39ef546214c0796c25a419c0a1065dc21d14b966fed769726b9b1975ec07e3b3e diff --git a/sci-biology/samtools/files/samtools-1.3-buildsystem.patch b/sci-biology/samtools/files/samtools-1.3-buildsystem.patch new file mode 100644 index 0000000..61f6b03 --- /dev/null +++ b/sci-biology/samtools/files/samtools-1.3-buildsystem.patch @@ -0,0 +1,174 @@ +--- samtools-1.3/Makefile ++++ samtools-1.3/Makefile +@@ -21,11 +21,12 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc +-CPPFLAGS = +-CFLAGS = -g -Wall -O2 +-LDFLAGS = +-LIBS = ++CC ?= gcc ++CPPFLAGS += ++CFLAGS ?= -g -Wall -O2 ++LDFLAGS += ++LIBS += ++BAMLIB ?= libbam.a + + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE + LOBJS= bam_aux.o bam.o bam_import.o sam.o \ +@@ -42,6 +43,7 @@ + prefix = /usr/local + exec_prefix = $(prefix) + bindir = $(exec_prefix)/bin ++libdir ?= $(exec_prefix)/lib + datarootdir = $(prefix)/share + mandir = $(datarootdir)/man + man1dir = $(mandir)/man1 +@@ -129,67 +131,74 @@ + .c.o: + $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $< + ++$(LOBJS): ++ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< + +-lib:libbam.a ++lib:libbam.a libbam.so.1.0 + + libbam.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) + +-samtools: $(AOBJS) libbam.a $(HTSLIB) +- $(CC) -pthread $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) ++libbam.so.1.0:$(LOBJS) ++ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz ++ ln -sf $@ libbam.so.1 ++ ln -sf $@ libbam.so ++ ++samtools: $(AOBJS) lib ++ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz + + bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) + bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h + bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) + bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) +-bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(htslib_khash_h) $(bam_lpileup_h) ++bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(bam_lpileup_h) + sam_h = sam.h $(htslib_sam_h) $(bam_h) + sam_opts_h = sam_opts.h $(htslib_hts_h) +-sample_h = sample.h $(htslib_kstring_h) ++sample_h = sample.h + + bam.o: bam.c $(bam_h) $(htslib_kstring_h) sam_header.h +-bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) errmod.h ++bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(bam2bcf_h) errmod.h + bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(htslib_khash_h) $(htslib_ksort_h) + bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h $(sam_opts_h) + bam_addrprg.o: bam_addrprg.c $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h) + bam_aux.o: bam_aux.c $(bam_h) + bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) + bam_color.o: bam_color.c $(bam_h) +-bam_import.o: bam_import.c $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h) +-bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h +-bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h) ++bam_import.o: bam_import.c $(bam_h) ++bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) ++bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) + bam_mate.o: bam_mate.c $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) + bam_md.o: bam_md.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) kprobaln.h $(sam_opts_h) + bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) +-bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h) ++bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) sam_header.h samtools.h $(bam2bcf_h) $(sample_h) + bam_quickcheck.o: bam_quickcheck.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_bgzf_h) + bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h +-bam_rmdup.o: bam_rmdup.c $(htslib_sam_h) $(sam_opts_h) $(bam_h) $(htslib_khash_h) +-bam_rmdupse.o: bam_rmdupse.c $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) +-bam_sort.o: bam_sort.c $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) ++bam_rmdup.o: bam_rmdup.c $(sam_h) ++bam_rmdupse.o: bam_rmdupse.c $(sam_h) ++bam_sort.o: bam_sort.c $(htslib_sam_h) + bam_split.o: bam_split.c $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(sam_opts_h) + bam_stat.o: bam_stat.c $(htslib_sam_h) samtools.h + bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) $(sam_opts_h) + bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h) + bam_tview_html.o: bam_tview_html.c $(bam_tview_h) + bam_flags.o: bam_flags.c $(htslib_sam_h) +-bamshuf.o: bamshuf.c $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h) ++bamshuf.o: bamshuf.c $(htslib_sam_h) samtools.h + bamtk.o: bamtk.c $(htslib_hts_h) samtools.h version.h +-bedcov.o: bedcov.c $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h) +-bedidx.o: bedidx.c $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h) ++bedcov.o: bedcov.c $(htslib_sam_h) ++bedidx.o: bedidx.c + cut_target.o: cut_target.c $(htslib_sam_h) errmod.h $(htslib_faidx_h) $(sam_opts_h) + dict.o: dict.c $(htslib_kseq_h) $(htslib_hts_h) +-errmod.o: errmod.c errmod.h $(htslib_ksort_h) ++errmod.o: errmod.c errmod.h + kprobaln.o: kprobaln.c kprobaln.h + padding.o: padding.c $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) +-phase.o: phase.c $(htslib_sam_h) errmod.h $(sam_opts_h) $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h) ++phase.o: phase.c $(htslib_sam_h) errmod.h + sam.o: sam.c $(htslib_faidx_h) $(sam_h) +-sam_header.o: sam_header.c sam_header.h $(htslib_khash_h) ++sam_header.o: sam_header.c sam_header.h + sam_opts.o: sam_opts.c $(sam_opts_h) +-sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h) +-sample.o: sample.c $(sample_h) $(htslib_khash_h) +-stats_isize.o: stats_isize.c stats_isize.h $(htslib_khash_h) +-stats.o: stats.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) stats_isize.h $(sam_opts_h) ++sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) samtools.h ++sample.o: sample.c $(sample_h) ++stats_isize.o: stats_isize.c stats_isize.h ++stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(htslib_faidx_h) + + + # test programs +@@ -197,8 +206,8 @@ + # For tests that might use it, set $REF_PATH explicitly to use only reference + # areas within the test suite (or set it to ':' to use no reference areas). + # (regression.sh sets $REF_PATH to a subdirectory itself.) +-check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) +- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) ++check test: samtools $(BUILT_TEST_PROGRAMS) ++ REF_PATH=: test/test.pl --exec bgzip=bgzip + test/merge/test_bam_translate test/merge/test_bam_translate.tmp + test/merge/test_rtrans_build + test/merge/test_trans_tbl_init +@@ -210,28 +219,28 @@ + test/split/test_parse_args + + +-test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB) ++test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +-test/merge/test_rtrans_build: test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB) ++test/merge/test_rtrans_build: test/merge/test_rtrans_build.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +-test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB) ++test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +-test/split/test_count_rg: test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB) ++test/split/test_count_rg: test/split/test_count_rg.o test/test.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +-test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB) ++test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +-test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB) ++test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +-test/split/test_parse_args: test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB) ++test/split/test_parse_args: test/split/test_parse_args.o test/test.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +-test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) ++test/vcf-miniview: test/vcf-miniview.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) + + test_test_h = test/test.h $(htslib_sam_h) diff --git a/sci-biology/samtools/files/samtools-1.3-ncurses.patch b/sci-biology/samtools/files/samtools-1.3-ncurses.patch new file mode 100644 index 0000000..baeb670 --- /dev/null +++ b/sci-biology/samtools/files/samtools-1.3-ncurses.patch @@ -0,0 +1,737 @@ +* Add modern AX_WITH_CURSES that prefers using pkg-config for detecting ncurses +* Change macro structure by moving AX_WITH_HTSLIB into its own file + +--- samtools-1.3/configure.ac ++++ samtools-1.3/configure.ac +@@ -28,6 +28,7 @@ + AC_PREREQ([2.63]) dnl This version introduced 4-argument AC_CHECK_HEADER + AC_CONFIG_SRCDIR([bamtk.c]) + AC_CONFIG_HEADERS([config.h]) ++AC_CONFIG_MACRO_DIR([m4]) + + dnl Copyright notice to be copied into the generated configure script + AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd. +--- samtools-1.3/m4/ax_with_curses.m4 ++++ samtools-1.3/m4/ax_with_curses.m4 +@@ -0,0 +1,578 @@ ++# =========================================================================== ++# http://www.gnu.org/software/autoconf-archive/ax_with_curses.html ++# =========================================================================== ++# ++# SYNOPSIS ++# ++# AX_WITH_CURSES ++# ++# DESCRIPTION ++# ++# This macro checks whether a SysV or X/Open-compatible Curses library is ++# present, along with the associated header file. The NcursesW ++# (wide-character) library is searched for first, followed by Ncurses, ++# then the system-default plain Curses. The first library found is the ++# one returned. Finding libraries will first be attempted by using ++# pkg-config, and should the pkg-config files not be available, will ++# fallback to combinations of known flags itself. ++# ++# The following options are understood: --with-ncursesw, --with-ncurses, ++# --without-ncursesw, --without-ncurses. The "--with" options force the ++# macro to use that particular library, terminating with an error if not ++# found. The "--without" options simply skip the check for that library. ++# The effect on the search pattern is: ++# ++# (no options) - NcursesW, Ncurses, Curses ++# --with-ncurses --with-ncursesw - NcursesW only [*] ++# --without-ncurses --with-ncursesw - NcursesW only [*] ++# --with-ncursesw - NcursesW only [*] ++# --with-ncurses --without-ncursesw - Ncurses only [*] ++# --with-ncurses - NcursesW, Ncurses [**] ++# --without-ncurses --without-ncursesw - Curses only ++# --without-ncursesw - Ncurses, Curses ++# --without-ncurses - NcursesW, Curses ++# ++# [*] If the library is not found, abort the configure script. ++# ++# [**] If the second library (Ncurses) is not found, abort configure. ++# ++# The following preprocessor symbols may be defined by this macro if the ++# appropriate conditions are met: ++# ++# HAVE_CURSES - if any SysV or X/Open Curses library found ++# HAVE_CURSES_ENHANCED - if library supports X/Open Enhanced functions ++# HAVE_CURSES_COLOR - if library supports color (enhanced functions) ++# HAVE_CURSES_OBSOLETE - if library supports certain obsolete features ++# HAVE_NCURSESW - if NcursesW (wide char) library is to be used ++# HAVE_NCURSES - if the Ncurses library is to be used ++# ++# HAVE_CURSES_H - if <curses.h> is present and should be used ++# HAVE_NCURSESW_H - if <ncursesw.h> should be used ++# HAVE_NCURSES_H - if <ncurses.h> should be used ++# HAVE_NCURSESW_CURSES_H - if <ncursesw/curses.h> should be used ++# HAVE_NCURSES_CURSES_H - if <ncurses/curses.h> should be used ++# ++# (These preprocessor symbols are discussed later in this document.) ++# ++# The following output variables are defined by this macro; they are ++# precious and may be overridden on the ./configure command line: ++# ++# CURSES_LIB - library to add to xxx_LDADD ++# CURSES_CPPFLAGS - include paths to add to xxx_CPPFLAGS ++# ++# Neither the library listed in CURSES_LIB, nor the flags in ++# CURSES_CPPFLAGS are added to LIBS, respectively CPPFLAGS, by default. ++# You need to add both to the appropriate xxx_LDADD/xxx_CPPFLAGS line in ++# your Makefile.am. For example: ++# ++# prog_LDADD = @CURSES_LIB@ ++# prog_CPPFLAGS = @CURSES_CPPFLAGS@ ++# ++# If CURSES_LIB is set on the configure command line (such as by running ++# "./configure CURSES_LIB=-lmycurses"), then the only header searched for ++# is <curses.h>. If the user needs to specify an alternative path for a ++# library (such as for a non-standard NcurseW), the user should use the ++# LDFLAGS variable. ++# ++# The following shell variables may be defined by this macro: ++# ++# ax_cv_curses - set to "yes" if any Curses library found ++# ax_cv_curses_enhanced - set to "yes" if Enhanced functions present ++# ax_cv_curses_color - set to "yes" if color functions present ++# ax_cv_curses_obsolete - set to "yes" if obsolete features present ++# ++# ax_cv_ncursesw - set to "yes" if NcursesW library found ++# ax_cv_ncurses - set to "yes" if Ncurses library found ++# ax_cv_plaincurses - set to "yes" if plain Curses library found ++# ax_cv_curses_which - set to "ncursesw", "ncurses", "plaincurses" or "no" ++# ++# These variables can be used in your configure.ac to determine the level ++# of support you need from the Curses library. For example, if you must ++# have either Ncurses or NcursesW, you could include: ++# ++# AX_WITH_CURSES ++# if test "x$ax_cv_ncursesw" != xyes && test "x$ax_cv_ncurses" != xyes; then ++# AC_MSG_ERROR([requires either NcursesW or Ncurses library]) ++# fi ++# ++# If any Curses library will do (but one must be present and must support ++# color), you could use: ++# ++# AX_WITH_CURSES ++# if test "x$ax_cv_curses" != xyes || test "x$ax_cv_curses_color" != xyes; then ++# AC_MSG_ERROR([requires an X/Open-compatible Curses library with color]) ++# fi ++# ++# Certain preprocessor symbols and shell variables defined by this macro ++# can be used to determine various features of the Curses library. In ++# particular, HAVE_CURSES and ax_cv_curses are defined if the Curses ++# library found conforms to the traditional SysV and/or X/Open Base Curses ++# definition. Any working Curses library conforms to this level. ++# ++# HAVE_CURSES_ENHANCED and ax_cv_curses_enhanced are defined if the ++# library supports the X/Open Enhanced Curses definition. In particular, ++# the wide-character types attr_t, cchar_t and wint_t, the functions ++# wattr_set() and wget_wch() and the macros WA_NORMAL and _XOPEN_CURSES ++# are checked. The Ncurses library does NOT conform to this definition, ++# although NcursesW does. ++# ++# HAVE_CURSES_COLOR and ax_cv_curses_color are defined if the library ++# supports color functions and macros such as COLOR_PAIR, A_COLOR, ++# COLOR_WHITE, COLOR_RED and init_pair(). These are NOT part of the ++# X/Open Base Curses definition, but are part of the Enhanced set of ++# functions. The Ncurses library DOES support these functions, as does ++# NcursesW. ++# ++# HAVE_CURSES_OBSOLETE and ax_cv_curses_obsolete are defined if the ++# library supports certain features present in SysV and BSD Curses but not ++# defined in the X/Open definition. In particular, the functions ++# getattrs(), getcurx() and getmaxx() are checked. ++# ++# To use the HAVE_xxx_H preprocessor symbols, insert the following into ++# your system.h (or equivalent) header file: ++# ++# #if defined HAVE_NCURSESW_CURSES_H ++# # include <ncursesw/curses.h> ++# #elif defined HAVE_NCURSESW_H ++# # include <ncursesw.h> ++# #elif defined HAVE_NCURSES_CURSES_H ++# # include <ncurses/curses.h> ++# #elif defined HAVE_NCURSES_H ++# # include <ncurses.h> ++# #elif defined HAVE_CURSES_H ++# # include <curses.h> ++# #else ++# # error "SysV or X/Open-compatible Curses header file required" ++# #endif ++# ++# For previous users of this macro: you should not need to change anything ++# in your configure.ac or Makefile.am, as the previous (serial 10) ++# semantics are still valid. However, you should update your system.h (or ++# equivalent) header file to the fragment shown above. You are encouraged ++# also to make use of the extended functionality provided by this version ++# of AX_WITH_CURSES, as well as in the additional macros ++# AX_WITH_CURSES_PANEL, AX_WITH_CURSES_MENU and AX_WITH_CURSES_FORM. ++# ++# LICENSE ++# ++# Copyright (c) 2009 Mark Pulford <m...@kyne.com.au> ++# Copyright (c) 2009 Damian Pietras <da...@daper.net> ++# Copyright (c) 2012 Reuben Thomas <r...@sc3d.org> ++# Copyright (c) 2011 John Zaitseff <j.zaits...@zap.org.au> ++# ++# This program is free software: you can redistribute it and/or modify it ++# under the terms of the GNU General Public License as published by the ++# Free Software Foundation, either version 3 of the License, or (at your ++# option) any later version. ++# ++# This program is distributed in the hope that it will be useful, but ++# WITHOUT ANY WARRANTY; without even the implied warranty of ++# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General ++# Public License for more details. ++# ++# You should have received a copy of the GNU General Public License along ++# with this program. If not, see <http://www.gnu.org/licenses/>. ++# ++# As a special exception, the respective Autoconf Macro's copyright owner ++# gives unlimited permission to copy, distribute and modify the configure ++# scripts that are the output of Autoconf when processing the Macro. You ++# need not follow the terms of the GNU General Public License when using ++# or distributing such scripts, even though portions of the text of the ++# Macro appear in them. The GNU General Public License (GPL) does govern ++# all other use of the material that constitutes the Autoconf Macro. ++# ++# This special exception to the GPL applies to versions of the Autoconf ++# Macro released by the Autoconf Archive. When you make and distribute a ++# modified version of the Autoconf Macro, you may extend this special ++# exception to the GPL to apply to your modified version as well. ++ ++#serial 16 ++ ++# internal function to factorize common code that is used by both ncurses ++# and ncursesw ++AC_DEFUN([_FIND_CURSES_FLAGS], [ ++ AC_MSG_CHECKING([for $1 via pkg-config]) ++ ++ _PKG_CONFIG([_ax_cv_$1_lib], [libs], [$1]) ++ _PKG_CONFIG([_ax_cv_$1_cppflags], [cflags], [$1]) ++ ++ AS_IF([test "x$pkg_failed" = "xyes" || test "x$pkg_failed" = "xuntried"],[ ++ AC_MSG_RESULT([no]) ++ # No suitable .pc file found, have to find flags via fallback ++ AC_CACHE_CHECK([for $1 via fallback], [ax_cv_$1], [ ++ AS_ECHO() ++ pkg_cv__ax_cv_$1_lib="-l$1" ++ pkg_cv__ax_cv_$1_cppflags="$CURSES_CPPFLAGS" ++ LIBS="$ax_saved_LIBS $pkg_cv__ax_cv_$1_lib" ++ CPPFLAGS="$ax_saved_CPPFLAGS $pkg_cv__ax_cv_$1_cppflags" ++ ++ AC_MSG_CHECKING([for initscr() with $pkg_cv__ax_cv_$1_lib]) ++ AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])], ++ [ ++ AC_MSG_RESULT([yes]) ++ AC_MSG_CHECKING([for nodelay() with $pkg_cv__ax_cv_$1_lib]) ++ AC_LINK_IFELSE([AC_LANG_CALL([], [nodelay])],[ ++ ax_cv_$1=yes ++ ],[ ++ AC_MSG_RESULT([no]) ++ m4_if( ++ [$1],[ncursesw],[pkg_cv__ax_cv_$1_lib="$pkg_cv__ax_cv_$1_lib -ltinfow"], ++ [$1],[ncurses],[pkg_cv__ax_cv_$1_lib="$pkg_cv__ax_cv_$1_lib -ltinfo"] ++ ) ++ LIBS="$ax_saved_LIBS $pkg_cv__ax_cv_$1_lib" ++ ++ AC_MSG_CHECKING([for nodelay() with $pkg_cv__ax_cv_$1_lib]) ++ AC_LINK_IFELSE([AC_LANG_CALL([], [nodelay])],[ ++ ax_cv_$1=yes ++ ],[ ++ ax_cv_$1=no ++ ]) ++ ]) ++ ],[ ++ ax_cv_$1=no ++ ]) ++ ]) ++ ],[ ++ AC_MSG_RESULT([yes]) ++ # Found .pc file, using its information ++ LIBS="$ax_saved_LIBS $pkg_cv__ax_cv_$1_lib" ++ CPPFLAGS="$ax_saved_CPPFLAGS $pkg_cv__ax_cv_$1_cppflags" ++ ax_cv_$1=yes ++ ]) ++]) ++ ++AU_ALIAS([MP_WITH_CURSES], [AX_WITH_CURSES]) ++AC_DEFUN([AX_WITH_CURSES], [ ++ AC_ARG_VAR([CURSES_LIB], [linker library for Curses, e.g. -lcurses]) ++ AC_ARG_VAR([CURSES_CPPFLAGS], [preprocessor flags for Curses, e.g. -I/usr/include/ncursesw]) ++ AC_ARG_WITH([ncurses], [AS_HELP_STRING([--with-ncurses], ++ [force the use of Ncurses or NcursesW])], ++ [], [with_ncurses=check]) ++ AC_ARG_WITH([ncursesw], [AS_HELP_STRING([--without-ncursesw], ++ [do not use NcursesW (wide character support)])], ++ [], [with_ncursesw=check]) ++ AC_REQUIRE([PKG_PROG_PKG_CONFIG]) ++ ++ ax_saved_LIBS=$LIBS ++ ax_saved_CPPFLAGS=$CPPFLAGS ++ ++ AS_IF([test "x$with_ncurses" = xyes || test "x$with_ncursesw" = xyes], ++ [ax_with_plaincurses=no], [ax_with_plaincurses=check]) ++ ++ ax_cv_curses_which=no ++ ++ # Test for NcursesW ++ AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncursesw" != xno], [ ++ _FIND_CURSES_FLAGS([ncursesw]) ++ ++ AS_IF([test "x$ax_cv_ncursesw" = xno && test "x$with_ncursesw" = xyes], [ ++ AC_MSG_ERROR([--with-ncursesw specified but could not find NcursesW library]) ++ ]) ++ ++ AS_IF([test "x$ax_cv_ncursesw" = xyes], [ ++ ax_cv_curses=yes ++ ax_cv_curses_which=ncursesw ++ CURSES_LIB="$pkg_cv__ax_cv_ncursesw_lib" ++ CURSES_CPPFLAGS="$pkg_cv__ax_cv_ncursesw_cppflags" ++ AC_DEFINE([HAVE_NCURSESW], [1], [Define to 1 if the NcursesW library is present]) ++ AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present]) ++ ++ AC_CACHE_CHECK([for working ncursesw/curses.h], [ax_cv_header_ncursesw_curses_h], [ ++ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ ++ @%:@define _XOPEN_SOURCE_EXTENDED 1 ++ @%:@include <ncursesw/curses.h> ++ ]], [[ ++ chtype a = A_BOLD; ++ int b = KEY_LEFT; ++ chtype c = COLOR_PAIR(1) & A_COLOR; ++ attr_t d = WA_NORMAL; ++ cchar_t e; ++ wint_t f; ++ int g = getattrs(stdscr); ++ int h = getcurx(stdscr) + getmaxx(stdscr); ++ initscr(); ++ init_pair(1, COLOR_WHITE, COLOR_RED); ++ wattr_set(stdscr, d, 0, NULL); ++ wget_wch(stdscr, &f); ++ ]])], ++ [ax_cv_header_ncursesw_curses_h=yes], ++ [ax_cv_header_ncursesw_curses_h=no]) ++ ]) ++ AS_IF([test "x$ax_cv_header_ncursesw_curses_h" = xyes], [ ++ ax_cv_curses_enhanced=yes ++ ax_cv_curses_color=yes ++ ax_cv_curses_obsolete=yes ++ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) ++ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) ++ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) ++ AC_DEFINE([HAVE_NCURSESW_CURSES_H], [1], [Define to 1 if <ncursesw/curses.h> is present]) ++ ]) ++ ++ AC_CACHE_CHECK([for working ncursesw.h], [ax_cv_header_ncursesw_h], [ ++ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ ++ @%:@define _XOPEN_SOURCE_EXTENDED 1 ++ @%:@include <ncursesw.h> ++ ]], [[ ++ chtype a = A_BOLD; ++ int b = KEY_LEFT; ++ chtype c = COLOR_PAIR(1) & A_COLOR; ++ attr_t d = WA_NORMAL; ++ cchar_t e; ++ wint_t f; ++ int g = getattrs(stdscr); ++ int h = getcurx(stdscr) + getmaxx(stdscr); ++ initscr(); ++ init_pair(1, COLOR_WHITE, COLOR_RED); ++ wattr_set(stdscr, d, 0, NULL); ++ wget_wch(stdscr, &f); ++ ]])], ++ [ax_cv_header_ncursesw_h=yes], ++ [ax_cv_header_ncursesw_h=no]) ++ ]) ++ AS_IF([test "x$ax_cv_header_ncursesw_h" = xyes], [ ++ ax_cv_curses_enhanced=yes ++ ax_cv_curses_color=yes ++ ax_cv_curses_obsolete=yes ++ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) ++ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) ++ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) ++ AC_DEFINE([HAVE_NCURSESW_H], [1], [Define to 1 if <ncursesw.h> is present]) ++ ]) ++ ++ AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h_with_ncursesw], [ ++ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ ++ @%:@define _XOPEN_SOURCE_EXTENDED 1 ++ @%:@include <ncurses.h> ++ ]], [[ ++ chtype a = A_BOLD; ++ int b = KEY_LEFT; ++ chtype c = COLOR_PAIR(1) & A_COLOR; ++ attr_t d = WA_NORMAL; ++ cchar_t e; ++ wint_t f; ++ int g = getattrs(stdscr); ++ int h = getcurx(stdscr) + getmaxx(stdscr); ++ initscr(); ++ init_pair(1, COLOR_WHITE, COLOR_RED); ++ wattr_set(stdscr, d, 0, NULL); ++ wget_wch(stdscr, &f); ++ ]])], ++ [ax_cv_header_ncurses_h_with_ncursesw=yes], ++ [ax_cv_header_ncurses_h_with_ncursesw=no]) ++ ]) ++ AS_IF([test "x$ax_cv_header_ncurses_h_with_ncursesw" = xyes], [ ++ ax_cv_curses_enhanced=yes ++ ax_cv_curses_color=yes ++ ax_cv_curses_obsolete=yes ++ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) ++ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) ++ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) ++ AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if <ncurses.h> is present]) ++ ]) ++ ++ AS_IF([test "x$ax_cv_header_ncursesw_curses_h" = xno && test "x$ax_cv_header_ncursesw_h" = xno && test "x$ax_cv_header_ncurses_h_with_ncursesw" = xno], [ ++ AC_MSG_WARN([could not find a working ncursesw/curses.h, ncursesw.h or ncurses.h]) ++ ]) ++ ]) ++ ]) ++ unset pkg_cv__ax_cv_ncursesw_lib ++ unset pkg_cv__ax_cv_ncursesw_cppflags ++ ++ # Test for Ncurses ++ AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncurses" != xno && test "x$ax_cv_curses_which" = xno], [ ++ _FIND_CURSES_FLAGS([ncurses]) ++ ++ AS_IF([test "x$ax_cv_ncurses" = xno && test "x$with_ncurses" = xyes], [ ++ AC_MSG_ERROR([--with-ncurses specified but could not find Ncurses library]) ++ ]) ++ ++ AS_IF([test "x$ax_cv_ncurses" = xyes], [ ++ ax_cv_curses=yes ++ ax_cv_curses_which=ncurses ++ CURSES_LIB="$pkg_cv__ax_cv_ncurses_lib" ++ CURSES_CPPFLAGS="$pkg_cv__ax_cv_ncurses_cppflags" ++ AC_DEFINE([HAVE_NCURSES], [1], [Define to 1 if the Ncurses library is present]) ++ AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present]) ++ ++ AC_CACHE_CHECK([for working ncurses/curses.h], [ax_cv_header_ncurses_curses_h], [ ++ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ ++ @%:@include <ncurses/curses.h> ++ ]], [[ ++ chtype a = A_BOLD; ++ int b = KEY_LEFT; ++ chtype c = COLOR_PAIR(1) & A_COLOR; ++ int g = getattrs(stdscr); ++ int h = getcurx(stdscr) + getmaxx(stdscr); ++ initscr(); ++ init_pair(1, COLOR_WHITE, COLOR_RED); ++ ]])], ++ [ax_cv_header_ncurses_curses_h=yes], ++ [ax_cv_header_ncurses_curses_h=no]) ++ ]) ++ AS_IF([test "x$ax_cv_header_ncurses_curses_h" = xyes], [ ++ ax_cv_curses_color=yes ++ ax_cv_curses_obsolete=yes ++ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) ++ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) ++ AC_DEFINE([HAVE_NCURSES_CURSES_H], [1], [Define to 1 if <ncurses/curses.h> is present]) ++ ]) ++ ++ AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h], [ ++ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ ++ @%:@include <ncurses.h> ++ ]], [[ ++ chtype a = A_BOLD; ++ int b = KEY_LEFT; ++ chtype c = COLOR_PAIR(1) & A_COLOR; ++ int g = getattrs(stdscr); ++ int h = getcurx(stdscr) + getmaxx(stdscr); ++ initscr(); ++ init_pair(1, COLOR_WHITE, COLOR_RED); ++ ]])], ++ [ax_cv_header_ncurses_h=yes], ++ [ax_cv_header_ncurses_h=no]) ++ ]) ++ AS_IF([test "x$ax_cv_header_ncurses_h" = xyes], [ ++ ax_cv_curses_color=yes ++ ax_cv_curses_obsolete=yes ++ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) ++ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) ++ AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if <ncurses.h> is present]) ++ ]) ++ ++ AS_IF([test "x$ax_cv_header_ncurses_curses_h" = xno && test "x$ax_cv_header_ncurses_h" = xno], [ ++ AC_MSG_WARN([could not find a working ncurses/curses.h or ncurses.h]) ++ ]) ++ ]) ++ ]) ++ unset pkg_cv__ax_cv_ncurses_lib ++ unset pkg_cv__ax_cv_ncurses_cppflags ++ ++ # Test for plain Curses (or if CURSES_LIB was set by user) ++ AS_IF([test "x$with_plaincurses" != xno && test "x$ax_cv_curses_which" = xno], [ ++ AS_IF([test "x$CURSES_LIB" != x], [ ++ LIBS="$ax_saved_LIBS $CURSES_LIB" ++ ], [ ++ LIBS="$ax_saved_LIBS -lcurses" ++ ]) ++ ++ AC_CACHE_CHECK([for Curses library], [ax_cv_plaincurses], [ ++ AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])], ++ [ax_cv_plaincurses=yes], [ax_cv_plaincurses=no]) ++ ]) ++ ++ AS_IF([test "x$ax_cv_plaincurses" = xyes], [ ++ ax_cv_curses=yes ++ ax_cv_curses_which=plaincurses ++ AS_IF([test "x$CURSES_LIB" = x], [ ++ CURSES_LIB="-lcurses" ++ ]) ++ AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present]) ++ ++ # Check for base conformance (and header file) ++ ++ AC_CACHE_CHECK([for working curses.h], [ax_cv_header_curses_h], [ ++ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ ++ @%:@include <curses.h> ++ ]], [[ ++ chtype a = A_BOLD; ++ int b = KEY_LEFT; ++ initscr(); ++ ]])], ++ [ax_cv_header_curses_h=yes], ++ [ax_cv_header_curses_h=no]) ++ ]) ++ AS_IF([test "x$ax_cv_header_curses_h" = xyes], [ ++ AC_DEFINE([HAVE_CURSES_H], [1], [Define to 1 if <curses.h> is present]) ++ ++ # Check for X/Open Enhanced conformance ++ ++ AC_CACHE_CHECK([for X/Open Enhanced Curses conformance], [ax_cv_plaincurses_enhanced], [ ++ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ ++ @%:@define _XOPEN_SOURCE_EXTENDED 1 ++ @%:@include <curses.h> ++ @%:@ifndef _XOPEN_CURSES ++ @%:@error "this Curses library is not enhanced" ++ "this Curses library is not enhanced" ++ @%:@endif ++ ]], [[ ++ chtype a = A_BOLD; ++ int b = KEY_LEFT; ++ chtype c = COLOR_PAIR(1) & A_COLOR; ++ attr_t d = WA_NORMAL; ++ cchar_t e; ++ wint_t f; ++ initscr(); ++ init_pair(1, COLOR_WHITE, COLOR_RED); ++ wattr_set(stdscr, d, 0, NULL); ++ wget_wch(stdscr, &f); ++ ]])], ++ [ax_cv_plaincurses_enhanced=yes], ++ [ax_cv_plaincurses_enhanced=no]) ++ ]) ++ AS_IF([test "x$ax_cv_plaincurses_enhanced" = xyes], [ ++ ax_cv_curses_enhanced=yes ++ ax_cv_curses_color=yes ++ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) ++ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) ++ ]) ++ ++ # Check for color functions ++ ++ AC_CACHE_CHECK([for Curses color functions], [ax_cv_plaincurses_color], [ ++ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ ++ @%:@define _XOPEN_SOURCE_EXTENDED 1 ++ @%:@include <curses.h> ++ ]], [[ ++ chtype a = A_BOLD; ++ int b = KEY_LEFT; ++ chtype c = COLOR_PAIR(1) & A_COLOR; ++ initscr(); ++ init_pair(1, COLOR_WHITE, COLOR_RED); ++ ]])], ++ [ax_cv_plaincurses_color=yes], ++ [ax_cv_plaincurses_color=no]) ++ ]) ++ AS_IF([test "x$ax_cv_plaincurses_color" = xyes], [ ++ ax_cv_curses_color=yes ++ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) ++ ]) ++ ++ # Check for obsolete functions ++ ++ AC_CACHE_CHECK([for obsolete Curses functions], [ax_cv_plaincurses_obsolete], [ ++ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ ++ @%:@include <curses.h> ++ ]], [[ ++ chtype a = A_BOLD; ++ int b = KEY_LEFT; ++ int g = getattrs(stdscr); ++ int h = getcurx(stdscr) + getmaxx(stdscr); ++ initscr(); ++ ]])], ++ [ax_cv_plaincurses_obsolete=yes], ++ [ax_cv_plaincurses_obsolete=no]) ++ ]) ++ AS_IF([test "x$ax_cv_plaincurses_obsolete" = xyes], [ ++ ax_cv_curses_obsolete=yes ++ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) ++ ]) ++ ]) ++ ++ AS_IF([test "x$ax_cv_header_curses_h" = xno], [ ++ AC_MSG_WARN([could not find a working curses.h]) ++ ]) ++ ]) ++ ]) ++ ++ AS_IF([test "x$ax_cv_curses" != xyes], [ax_cv_curses=no]) ++ AS_IF([test "x$ax_cv_curses_enhanced" != xyes], [ax_cv_curses_enhanced=no]) ++ AS_IF([test "x$ax_cv_curses_color" != xyes], [ax_cv_curses_color=no]) ++ AS_IF([test "x$ax_cv_curses_obsolete" != xyes], [ax_cv_curses_obsolete=no]) ++ ++ LIBS=$ax_saved_LIBS ++ CPPFLAGS=$ax_saved_CPPFLAGS ++ ++ unset ax_saved_LIBS ++ unset ax_saved_CPPFLAGS ++])dnl +--- samtools-1.3/m4/ax_with_htslib.m4 ++++ samtools-1.3/m4/ax_with_htslib.m4 +@@ -0,0 +1,140 @@ ++# =========================================================================== ++# http://www.gnu.org/software/autoconf-archive/ax_with_htslib.html ++# =========================================================================== ++# ++# SYNOPSIS ++# ++# AX_WITH_HTSLIB ++# ++# DESCRIPTION ++# ++# This macro checks whether HTSlib <http://www.htslib.org/> is installed ++# or nearby, and adds a --with-htslib=DIR option to the configure script ++# for specifying the location. It locates either an installation prefix ++# (with 'include' and 'lib' subdirectories) or an HTSlib source tree, as ++# HTSlib is fast-moving and users may wish to use an in-development tree. ++# ++# Different checks occur depending on the --with-htslib argument given: ++# ++# With --with-htslib=DIR, checks whether DIR is a source tree or contains ++# a working installation. ++# By default, searches for a source tree (with a name matching htslib*) ++# within or alongside $srcdir. Produces AC_MSG_ERROR if there are ++# several equally-likely candidates. If there are none, checks for ++# a working default installation. ++# With --with-htslib=system, checks for a working default installation. ++# ++# If a source tree is found or specified, it is added to AC_CONFIG_SUBDIRS ++# (which unfortunately may cause a "you should use literals" warning when ++# autoconf is run). ++# ++# The following output variables are set by this macro: ++# ++# HTSDIR Directory containing HTSlib source tree ++# HTSLIB_CPPFLAGS Preprocessor flags for compiling with HTSlib ++# HTSLIB_LDFLAGS Linker flags for linking with HTSlib ++# ++# The following shell variables may be defined: ++# ++# ax_cv_htslib Set to "yes" if HTSlib was found ++# ax_cv_htslib_which Set to "source", "install", or "none" ++# ++# LICENSE ++# ++# Copyright (C) 2015 Genome Research Ltd ++# ++# Copying and distribution of this file, with or without modification, are ++# permitted in any medium without royalty provided the copyright notice ++# and this notice are preserved. This file is offered as-is, without any ++# warranty. ++ ++#serial 1 ++ ++AC_DEFUN([AX_WITH_HTSLIB], ++[AC_ARG_WITH([htslib], ++ [AS_HELP_STRING([--with-htslib=DIR], ++ [use the HTSlib source tree or installation in DIR]) ++dnl Not indented, to avoid extra whitespace outwith AS_HELP_STRING() ++AS_HELP_STRING([--with-htslib=system], ++ [use only a system HTSlib installation])], ++ [], [with_htslib=search]) ++ ++case $with_htslib in ++yes|search) ++ AC_MSG_CHECKING([location of HTSlib source tree]) ++ case $srcdir in ++ .) srcp= ;; ++ *) srcp=$srcdir/ ;; ++ esac ++ found= ++ for dir in ${srcp}htslib* -- ${srcp}../htslib -- ${srcp}../htslib* ++ do ++ if test "$dir" = "--"; then ++ test -n "$found" && break ++ elif test -f "$dir/hts.c" && test -f "$dir/htslib/hts.h"; then ++ found="${found}1" ++ HTSDIR=$dir ++ fi ++ done ++ if test -z "$found"; then ++ AC_MSG_RESULT([none found]) ++ ax_cv_htslib_which=system ++ elif test "$found" = 1; then ++ AC_MSG_RESULT([$HTSDIR]) ++ ax_cv_htslib_which=source ++ else ++ AC_MSG_RESULT([several directories found]) ++ AC_MSG_ERROR([use --with-htslib=DIR to select which HTSlib to use]) ++ fi ++ ;; ++no) ax_cv_htslib_which=none ;; ++system) ax_cv_htslib_which=system ;; ++*) ++ HTSDIR=$with_htslib ++ if test -f "$HTSDIR/hts.c" && test -f "$HTSDIR/htslib/hts.h"; then ++ ax_cv_htslib_which=source ++ else ++ ax_cv_htslib_which=install ++ fi ++ ;; ++esac ++ ++case $ax_cv_htslib_which in ++source) ++ ax_cv_htslib=yes ++ HTSLIB_CPPFLAGS="-I$HTSDIR" ++ HTSLIB_LDFLAGS="-L$HTSDIR" ++ # We can't use a literal, because $HTSDIR is user-provided and variable ++ AC_CONFIG_SUBDIRS($HTSDIR) ++ ;; ++system) ++ AC_CHECK_HEADER([htslib/sam.h], ++ [AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])], ++ [ax_cv_htslib=no], [;]) ++ ax_cv_htslib_which=install ++ HTSDIR= ++ HTSLIB_CPPFLAGS= ++ HTSLIB_LDFLAGS= ++ ;; ++install) ++ ax_saved_CPPFLAGS=$CPPFLAGS ++ ax_saved_LDFLAGS=$LDFLAGS ++ HTSLIB_CPPFLAGS="-I$HTSDIR/include" ++ HTSLIB_LDFLAGS="-L$HTSDIR/lib" ++ CPPFLAGS="$CPPFLAGS $HTSLIB_CPPFLAGS" ++ LDFLAGS="$LDFLAGS $HTSLIB_LDFLAGS" ++ AC_CHECK_HEADER([htslib/sam.h], ++ [AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])], ++ [ax_cv_htslib=no], [;]) ++ HTSDIR= ++ CPPFLAGS=$ax_saved_CPPFLAGS ++ LDFLAGS=$ax_saved_LDFLAGS ++ ;; ++none) ++ ax_cv_htslib=no ++ ;; ++esac ++ ++AC_SUBST([HTSDIR]) ++AC_SUBST([HTSLIB_CPPFLAGS]) ++AC_SUBST([HTSLIB_LDFLAGS])]) diff --git a/sci-biology/samtools/samtools-1.3.ebuild b/sci-biology/samtools/samtools-1.3.ebuild new file mode 100644 index 0000000..ec510ec --- /dev/null +++ b/sci-biology/samtools/samtools-1.3.ebuild @@ -0,0 +1,86 @@ +# 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 python-r1 toolchain-funcs + +DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" +HOMEPAGE="http://www.htslib.org/"; +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" +IUSE="examples" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="sys-libs/ncurses:0= + >=sci-libs/htslib-${PV} + dev-lang/lua:0 + dev-lang/perl" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +PATCHES=( + "${FILESDIR}/${P}-buildsystem.patch" + "${FILESDIR}/${P}-ncurses.patch" +) + +src_prepare() { + default + + # unbundle libs + find htslib-* -delete || die + + sed -i -e 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die + sed -i -e '/htslib.mk/d' -i Makefile || die + + tc-export CC AR + + rm -f aclocal.m4 || die + eautoreconf +} + +src_compile() { + local mymakeargs=( + LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" + HTSDIR="${EPREFIX}/usr/include" + HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) + BAMLIB="libbam.so" + libdir=/usr/$(get_libdir) + ) + emake "${mymakeargs[@]}" +} + +src_test() { + local mymakeargs=( + LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" + HTSDIR="${EPREFIX}/usr/include" + HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) + BAMLIB="libbam.so" + ) + LD_LIBRARY_PATH="${S}" emake "${mymakeargs[@]}" test +} + +src_install() { + dobin samtools $(find misc -type f -executable) + + python_replicate_script "${ED}"/usr/bin/varfilter.py + dolib.so libbam.so* + + insinto /usr/include/bam + doins *.h + + doman ${PN}.1 + dodoc AUTHORS NEWS README + + if use examples; then + insinto /usr/share/${PN} + doins -r examples + fi +}
