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commit: 47592cb35c03ac6c245cf22a5883dd7e5ba7b69e |
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Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Sat Sep 2 12:45:48 2017 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Sat Sep 2 12:45:48 2017 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=47592cb3 |
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|
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sci-biology/samtools: Remove old |
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|
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.../samtools/files/samtools-1.0-buildsystem.patch | 59 ------- |
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.../samtools/files/samtools-1.0-rmdup.patch | 47 ----- |
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.../samtools/files/samtools-1.1-buildsystem.patch | 153 ---------------- |
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.../samtools/files/samtools-1.1-rmdup.patch | 47 ----- |
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.../samtools/files/samtools-1.2-buildsystem.patch | 193 --------------------- |
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.../samtools/files/samtools-1.2-rmdup.patch | 47 ----- |
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.../files/samtools-1.3.1-buildsystem.patch | 75 -------- |
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sci-biology/samtools/metadata.xml | 11 -- |
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sci-biology/samtools/samtools-1.0-r2.ebuild | 73 -------- |
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sci-biology/samtools/samtools-1.1-r1.ebuild | 83 --------- |
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sci-biology/samtools/samtools-1.2-r1.ebuild | 83 --------- |
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sci-biology/samtools/samtools-1.3.1.ebuild | 83 --------- |
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sci-biology/samtools/samtools-1.5.ebuild | 82 --------- |
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13 files changed, 1036 deletions(-) |
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|
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diff --git a/sci-biology/samtools/files/samtools-1.0-buildsystem.patch b/sci-biology/samtools/files/samtools-1.0-buildsystem.patch |
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deleted file mode 100644 |
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index 53a8b66f9..000000000 |
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--- a/sci-biology/samtools/files/samtools-1.0-buildsystem.patch |
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+++ /dev/null |
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@@ -1,59 +0,0 @@ |
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- Makefile | 26 ++++++++++++++++++-------- |
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- 1 file changed, 18 insertions(+), 8 deletions(-) |
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- |
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-diff --git a/Makefile b/Makefile |
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-index ae59abf..0d2788c 100644 |
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---- a/Makefile |
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-+++ b/Makefile |
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-@@ -21,11 +21,12 @@ |
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- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER |
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- # DEALINGS IN THE SOFTWARE. |
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- |
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--CC = gcc |
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--CPPFLAGS = $(DFLAGS) $(INCLUDES) |
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--CFLAGS = -g -Wall -O2 |
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--LDFLAGS = |
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--LDLIBS = |
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-+CC ?= gcc |
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-+CPPFLAGS += $(DFLAGS) $(INCLUDES) |
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-+CFLAGS ?= -g -Wall -O2 |
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-+LDFLAGS += |
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-+LDLIBS += |
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-+BAMLIB ?= libbam.a |
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- DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 |
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- LOBJS= bam_aux.o bam.o bam_import.o sam.o \ |
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- sam_header.o bam_plbuf.o |
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-@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses |
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- prefix = /usr/local |
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- exec_prefix = $(prefix) |
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- bindir = $(exec_prefix)/bin |
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-+bindir = $(exec_prefix)/lib |
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- mandir = $(prefix)/share/man |
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- man1dir = $(mandir)/man1 |
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- |
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-@@ -115,14 +117,22 @@ version.h: |
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- .c.o: |
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- $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $< |
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- |
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-+$(LOBJS): |
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-+ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< |
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- |
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--lib:libbam.a |
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-+ |
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-+lib:libbam.a libbam.so.1.0 |
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- |
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- libbam.a:$(LOBJS) |
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- $(AR) -csru $@ $(LOBJS) |
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- |
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--samtools: $(AOBJS) libbam.a $(HTSLIB) |
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-- $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz |
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-+libbam.so.1.0:$(LOBJS) |
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-+ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz |
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-+ ln -sf $@ libbam.so.0 |
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-+ ln -sf $@ libbam.so |
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-+ |
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-+samtools: $(AOBJS) $(HTSLIB) lib |
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-+ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz |
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- |
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- bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) |
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- bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h |
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|
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diff --git a/sci-biology/samtools/files/samtools-1.0-rmdup.patch b/sci-biology/samtools/files/samtools-1.0-rmdup.patch |
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deleted file mode 100644 |
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index 023b5d73d..000000000 |
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--- a/sci-biology/samtools/files/samtools-1.0-rmdup.patch |
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+++ /dev/null |
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@@ -1,47 +0,0 @@ |
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-From 05fb5c2e17576b1d0ea5a0b8203b9eba236f2455 Mon Sep 17 00:00:00 2001 |
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-From: kirkmcclure <kirkmcclure@××××××××××××××××××××.com> |
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-Date: Mon, 23 Mar 2015 05:35:00 -0800 |
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-Subject: [PATCH] Update bam.c |
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- |
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- For issue #138 - Samtools view -l no longer works. |
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-Implement bam_get_library() |
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---- |
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- bam.c | 23 ++++++++++++----------- |
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- 1 file changed, 12 insertions(+), 11 deletions(-) |
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- |
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-diff --git a/bam.c b/bam.c |
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-index f909b7e..864d3f0 100644 |
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---- a/bam.c |
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-+++ b/bam.c |
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-@@ -61,19 +61,20 @@ int bam_validate1(const bam_header_t *header, const bam1_t *b) |
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- return 1; |
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- } |
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- |
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--// FIXME: we should also check the LB tag associated with each alignment |
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- const char *bam_get_library(bam_header_t *h, const bam1_t *b) |
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- { |
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--#if 0 |
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-- const uint8_t *rg; |
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-- if (h->dict == 0) h->dict = sam_header_parse2(h->text); |
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-- if (h->rg2lib == 0) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB"); |
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-- rg = bam_aux_get(b, "RG"); |
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-- return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1)); |
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--#else |
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-- fprintf(stderr, "Samtools-htslib-API: bam_get_library() not yet implemented\n"); |
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-- abort(); |
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--#endif |
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-+ const uint8_t *rg = 0; |
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-+ const uint8_t *pLibName, *pDict; |
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-+ if ( b != 0 && h != 0 ) { |
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-+ if ( (rg = bam_aux_get(b, "RG") ) != 0 |
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-+ && (pDict = sam_header_parse2(h->text)) != 0 ) { |
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-+ pLibName = sam_header2tbl(pDict, "RG", "ID", "LB"); |
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-+ if ( pLibName && strlen( (char*)pLibName ) > 0 ) { |
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-+ return sam_tbl_get((void*)pLibName, (const char*)(rg + 1)); |
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-+ } |
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-+ } |
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-+ } |
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-+ return 0; |
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- } |
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- |
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- int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func) |
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|
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diff --git a/sci-biology/samtools/files/samtools-1.1-buildsystem.patch b/sci-biology/samtools/files/samtools-1.1-buildsystem.patch |
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deleted file mode 100644 |
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index b9ae77de6..000000000 |
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--- a/sci-biology/samtools/files/samtools-1.1-buildsystem.patch |
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+++ /dev/null |
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@@ -1,153 +0,0 @@ |
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- Makefile | 76 ++++++++++++++++++++++++++++++++++++---------------------------- |
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- 1 file changed, 43 insertions(+), 33 deletions(-) |
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- |
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-diff --git a/Makefile b/Makefile |
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-index 43cefc3..743dd07 100644 |
156 |
---- a/Makefile |
157 |
-+++ b/Makefile |
158 |
-@@ -21,11 +21,12 @@ |
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- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER |
160 |
- # DEALINGS IN THE SOFTWARE. |
161 |
- |
162 |
--CC = gcc |
163 |
--CPPFLAGS = $(DFLAGS) $(INCLUDES) |
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--CFLAGS = -g -Wall -O2 |
165 |
--LDFLAGS = |
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--LDLIBS = |
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-+CC ?= gcc |
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-+CPPFLAGS += $(DFLAGS) $(INCLUDES) |
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-+CFLAGS ?= -g -Wall -O2 |
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-+LDFLAGS += |
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-+LDLIBS += |
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-+BAMLIB ?= libbam.a |
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- DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 |
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- LOBJS= bam_aux.o bam.o bam_import.o sam.o \ |
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- sam_header.o bam_plbuf.o |
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-@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses |
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- prefix = /usr/local |
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- exec_prefix = $(prefix) |
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- bindir = $(exec_prefix)/bin |
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-+libdir = $(exec_prefix)/lib |
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- mandir = $(prefix)/share/man |
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- man1dir = $(mandir)/man1 |
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- |
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-@@ -115,63 +117,71 @@ version.h: |
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- .c.o: |
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- $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $< |
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- |
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-+$(LOBJS): |
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-+ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< |
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- |
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--lib:libbam.a |
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-+ |
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-+lib:libbam.a libbam.so.1.0 |
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- |
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- libbam.a:$(LOBJS) |
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- $(AR) -csru $@ $(LOBJS) |
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- |
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--samtools: $(AOBJS) libbam.a $(HTSLIB) |
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-- $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz |
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-+libbam.so.1.0:$(LOBJS) |
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-+ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz |
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-+ ln -sf $@ libbam.so.0 |
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-+ ln -sf $@ libbam.so |
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-+ |
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-+samtools: $(AOBJS) lib |
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-+ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz |
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- |
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- bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) |
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- bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h |
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- bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) |
211 |
- bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) |
212 |
--bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(HTSDIR)/htslib/khash.h $(bam_lpileup_h) |
213 |
-+bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(bam_lpileup_h) |
214 |
- sam_h = sam.h $(htslib_sam_h) $(bam_h) |
215 |
--sample_h = sample.h $(HTSDIR)/htslib/kstring.h |
216 |
-+sample_h = sample.h |
217 |
- |
218 |
- bam.o: bam.c $(bam_h) sam_header.h |
219 |
--bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kfunc.h $(bam2bcf_h) errmod.h |
220 |
-+bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(bam2bcf_h) errmod.h |
221 |
- bam2bcf_indel.o: bam2bcf_indel.c bam2bcf.h |
222 |
- bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h |
223 |
- bam_aux.o: bam_aux.c |
224 |
- bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(bam_h) |
225 |
- bam_color.o: bam_color.c $(bam_h) |
226 |
--bam_import.o: bam_import.c $(HTSDIR)/htslib/kstring.h $(bam_h) $(HTSDIR)/htslib/kseq.h |
227 |
--bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(HTSDIR)/htslib/khash.h |
228 |
--bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(HTSDIR)/htslib/ksort.h |
229 |
-+bam_import.o: bam_import.c $(bam_h) |
230 |
-+bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) |
231 |
-+bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) |
232 |
- bam_mate.o: bam_mate.c $(bam_h) |
233 |
- bam_md.o: bam_md.c $(htslib_faidx_h) $(sam_h) kaln.h kprobaln.h |
234 |
- bam_pileup.o: bam_pileup.c $(sam_h) |
235 |
- bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) |
236 |
--bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash_str2int.h sam_header.h samtools.h $(bam2bcf_h) $(sample_h) |
237 |
-+bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) sam_header.h samtools.h $(bam2bcf_h) $(sample_h) |
238 |
- bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(bam_h) |
239 |
--bam_rmdup.o: bam_rmdup.c $(sam_h) $(HTSDIR)/htslib/khash.h |
240 |
--bam_rmdupse.o: bam_rmdupse.c $(sam_h) $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h |
241 |
--bam_sort.o: bam_sort.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) |
242 |
-+bam_rmdup.o: bam_rmdup.c $(sam_h) |
243 |
-+bam_rmdupse.o: bam_rmdupse.c $(sam_h) |
244 |
-+bam_sort.o: bam_sort.c $(htslib_sam_h) |
245 |
- bam_stat.o: bam_stat.c $(bam_h) samtools.h |
246 |
- bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) |
247 |
- bam_tview_curses.o: bam_tview_curses.c $(bam_tview_h) |
248 |
- bam_tview_html.o: bam_tview_html.c $(bam_tview_h) |
249 |
- bam_flags.o: bam_flags.c $(sam_h) |
250 |
--bamshuf.o: bamshuf.c $(htslib_sam_h) $(HTSDIR)/htslib/ksort.h samtools.h |
251 |
-+bamshuf.o: bamshuf.c $(htslib_sam_h) samtools.h |
252 |
- bamtk.o: bamtk.c $(bam_h) version.h samtools.h |
253 |
--bedcov.o: bedcov.c $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) $(HTSDIR)/htslib/kseq.h |
254 |
--bedidx.o: bedidx.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h |
255 |
-+bedcov.o: bedcov.c $(htslib_sam_h) |
256 |
-+bedidx.o: bedidx.c |
257 |
- cut_target.o: cut_target.c $(bam_h) errmod.h $(htslib_faidx_h) |
258 |
--errmod.o: errmod.c errmod.h $(HTSDIR)/htslib/ksort.h |
259 |
-+errmod.o: errmod.c errmod.h |
260 |
- kaln.o: kaln.c kaln.h |
261 |
- kprobaln.o: kprobaln.c kprobaln.h |
262 |
- padding.o: padding.c sam_header.h $(sam_h) $(bam_h) $(htslib_faidx_h) |
263 |
--phase.o: phase.c $(htslib_sam_h) errmod.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h |
264 |
-+phase.o: phase.c $(htslib_sam_h) errmod.h |
265 |
- sam.o: sam.c $(htslib_faidx_h) $(sam_h) |
266 |
--sam_header.o: sam_header.c sam_header.h $(HTSDIR)/htslib/khash.h |
267 |
--sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash.h samtools.h |
268 |
--sample.o: sample.c $(sample_h) $(HTSDIR)/htslib/khash.h |
269 |
--stats_isize.o: stats_isize.c stats_isize.h $(HTSDIR)/htslib/khash.h |
270 |
--stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/khash_str2int.h $(htslib_faidx_h) |
271 |
-+sam_header.o: sam_header.c sam_header.h |
272 |
-+sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) samtools.h |
273 |
-+sample.o: sample.c $(sample_h) |
274 |
-+stats_isize.o: stats_isize.c stats_isize.h |
275 |
-+stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(htslib_faidx_h) |
276 |
- |
277 |
- |
278 |
- # test programs |
279 |
-@@ -179,8 +189,8 @@ stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib |
280 |
- # For tests that might use it, set $REF_PATH explicitly to use only reference |
281 |
- # areas within the test suite (or set it to ':' to use no reference areas). |
282 |
- # (regression.sh sets $REF_PATH to a subdirectory itself.) |
283 |
--check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) |
284 |
-- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) |
285 |
-+check test: samtools $(BUILT_TEST_PROGRAMS) |
286 |
-+ REF_PATH=: test/test.pl --exec bgzip=bgzip |
287 |
- test/merge/test_bam_translate test/merge/test_bam_translate.tmp |
288 |
- test/merge/test_pretty_header |
289 |
- test/merge/test_rtrans_build |
290 |
-@@ -253,10 +263,10 @@ misc/md5sum-lite: misc/md5sum-lite.o |
291 |
- misc/wgsim: misc/wgsim.o |
292 |
- $(CC) $(LDFLAGS) -o $@ misc/wgsim.o $(LDLIBS) -lm -lz |
293 |
- |
294 |
--misc/ace2sam.o: misc/ace2sam.c $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h |
295 |
-+misc/ace2sam.o: misc/ace2sam.c |
296 |
- misc/md5.o: misc/md5.c misc/md5.h |
297 |
--misc/md5fa.o: misc/md5fa.c misc/md5.h $(HTSDIR)/htslib/kseq.h |
298 |
--misc/wgsim.o: misc/wgsim.c $(HTSDIR)/htslib/kseq.h |
299 |
-+misc/md5fa.o: misc/md5fa.c misc/md5.h |
300 |
-+misc/wgsim.o: misc/wgsim.c |
301 |
- |
302 |
- misc/maq2sam-short.o: misc/maq2sam.c |
303 |
- $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ misc/maq2sam.c |
304 |
|
305 |
diff --git a/sci-biology/samtools/files/samtools-1.1-rmdup.patch b/sci-biology/samtools/files/samtools-1.1-rmdup.patch |
306 |
deleted file mode 100644 |
307 |
index 023b5d73d..000000000 |
308 |
--- a/sci-biology/samtools/files/samtools-1.1-rmdup.patch |
309 |
+++ /dev/null |
310 |
@@ -1,47 +0,0 @@ |
311 |
-From 05fb5c2e17576b1d0ea5a0b8203b9eba236f2455 Mon Sep 17 00:00:00 2001 |
312 |
-From: kirkmcclure <kirkmcclure@××××××××××××××××××××.com> |
313 |
-Date: Mon, 23 Mar 2015 05:35:00 -0800 |
314 |
-Subject: [PATCH] Update bam.c |
315 |
- |
316 |
- For issue #138 - Samtools view -l no longer works. |
317 |
-Implement bam_get_library() |
318 |
---- |
319 |
- bam.c | 23 ++++++++++++----------- |
320 |
- 1 file changed, 12 insertions(+), 11 deletions(-) |
321 |
- |
322 |
-diff --git a/bam.c b/bam.c |
323 |
-index f909b7e..864d3f0 100644 |
324 |
---- a/bam.c |
325 |
-+++ b/bam.c |
326 |
-@@ -61,19 +61,20 @@ int bam_validate1(const bam_header_t *header, const bam1_t *b) |
327 |
- return 1; |
328 |
- } |
329 |
- |
330 |
--// FIXME: we should also check the LB tag associated with each alignment |
331 |
- const char *bam_get_library(bam_header_t *h, const bam1_t *b) |
332 |
- { |
333 |
--#if 0 |
334 |
-- const uint8_t *rg; |
335 |
-- if (h->dict == 0) h->dict = sam_header_parse2(h->text); |
336 |
-- if (h->rg2lib == 0) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB"); |
337 |
-- rg = bam_aux_get(b, "RG"); |
338 |
-- return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1)); |
339 |
--#else |
340 |
-- fprintf(stderr, "Samtools-htslib-API: bam_get_library() not yet implemented\n"); |
341 |
-- abort(); |
342 |
--#endif |
343 |
-+ const uint8_t *rg = 0; |
344 |
-+ const uint8_t *pLibName, *pDict; |
345 |
-+ if ( b != 0 && h != 0 ) { |
346 |
-+ if ( (rg = bam_aux_get(b, "RG") ) != 0 |
347 |
-+ && (pDict = sam_header_parse2(h->text)) != 0 ) { |
348 |
-+ pLibName = sam_header2tbl(pDict, "RG", "ID", "LB"); |
349 |
-+ if ( pLibName && strlen( (char*)pLibName ) > 0 ) { |
350 |
-+ return sam_tbl_get((void*)pLibName, (const char*)(rg + 1)); |
351 |
-+ } |
352 |
-+ } |
353 |
-+ } |
354 |
-+ return 0; |
355 |
- } |
356 |
- |
357 |
- int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func) |
358 |
|
359 |
diff --git a/sci-biology/samtools/files/samtools-1.2-buildsystem.patch b/sci-biology/samtools/files/samtools-1.2-buildsystem.patch |
360 |
deleted file mode 100644 |
361 |
index 2343b2245..000000000 |
362 |
--- a/sci-biology/samtools/files/samtools-1.2-buildsystem.patch |
363 |
+++ /dev/null |
364 |
@@ -1,193 +0,0 @@ |
365 |
- Makefile | 94 +++++++++++++++++++++++++++++++++++----------------------------- |
366 |
- 1 file changed, 52 insertions(+), 42 deletions(-) |
367 |
- |
368 |
-diff --git a/Makefile b/Makefile |
369 |
-index e368cee..9054526 100644 |
370 |
---- a/Makefile |
371 |
-+++ b/Makefile |
372 |
-@@ -21,11 +21,12 @@ |
373 |
- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER |
374 |
- # DEALINGS IN THE SOFTWARE. |
375 |
- |
376 |
--CC = gcc |
377 |
--CPPFLAGS = $(DFLAGS) $(INCLUDES) |
378 |
--CFLAGS = -g -Wall -O2 |
379 |
--LDFLAGS = |
380 |
--LDLIBS = |
381 |
-+CC ?= gcc |
382 |
-+CPPFLAGS += $(DFLAGS) $(INCLUDES) |
383 |
-+CFLAGS ?= -g -Wall -O2 |
384 |
-+LDFLAGS += |
385 |
-+LDLIBS += |
386 |
-+BAMLIB ?= libbam.a |
387 |
- DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 |
388 |
- LOBJS= bam_aux.o bam.o bam_import.o sam.o \ |
389 |
- sam_header.o bam_plbuf.o |
390 |
-@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses |
391 |
- prefix = /usr/local |
392 |
- exec_prefix = $(prefix) |
393 |
- bindir = $(exec_prefix)/bin |
394 |
-+libdir = $(exec_prefix)/lib |
395 |
- mandir = $(prefix)/share/man |
396 |
- man1dir = $(mandir)/man1 |
397 |
- |
398 |
-@@ -115,62 +117,70 @@ version.h: |
399 |
- .c.o: |
400 |
- $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $< |
401 |
- |
402 |
-+$(LOBJS): |
403 |
-+ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< |
404 |
- |
405 |
--lib:libbam.a |
406 |
-+ |
407 |
-+lib:libbam.a libbam.so.1.0 |
408 |
- |
409 |
- libbam.a:$(LOBJS) |
410 |
- $(AR) -csru $@ $(LOBJS) |
411 |
- |
412 |
--samtools: $(AOBJS) libbam.a $(HTSLIB) |
413 |
-- $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz |
414 |
-+libbam.so.1.0:$(LOBJS) |
415 |
-+ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz |
416 |
-+ ln -sf $@ libbam.so.0 |
417 |
-+ ln -sf $@ libbam.so |
418 |
-+ |
419 |
-+samtools: $(AOBJS) lib |
420 |
-+ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz |
421 |
- |
422 |
- bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) |
423 |
- bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h |
424 |
- bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) |
425 |
- bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) |
426 |
--bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(HTSDIR)/htslib/khash.h $(bam_lpileup_h) |
427 |
-+bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(bam_lpileup_h) |
428 |
- sam_h = sam.h $(htslib_sam_h) $(bam_h) |
429 |
--sample_h = sample.h $(HTSDIR)/htslib/kstring.h |
430 |
-+sample_h = sample.h |
431 |
- |
432 |
- bam.o: bam.c $(bam_h) sam_header.h |
433 |
--bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kfunc.h $(bam2bcf_h) errmod.h |
434 |
-+bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(bam2bcf_h) errmod.h |
435 |
- bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h |
436 |
- bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h |
437 |
- bam_aux.o: bam_aux.c |
438 |
- bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(bam_h) |
439 |
- bam_color.o: bam_color.c $(bam_h) |
440 |
--bam_import.o: bam_import.c $(HTSDIR)/htslib/kstring.h $(bam_h) $(HTSDIR)/htslib/kseq.h |
441 |
--bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(HTSDIR)/htslib/khash.h |
442 |
--bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(HTSDIR)/htslib/ksort.h |
443 |
-+bam_import.o: bam_import.c $(bam_h) |
444 |
-+bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) |
445 |
-+bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) |
446 |
- bam_mate.o: bam_mate.c $(bam_h) |
447 |
- bam_md.o: bam_md.c $(htslib_faidx_h) $(sam_h) kprobaln.h |
448 |
- bam_pileup.o: bam_pileup.c $(sam_h) |
449 |
- bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) |
450 |
--bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash_str2int.h sam_header.h samtools.h $(bam2bcf_h) $(sample_h) |
451 |
-+bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) sam_header.h samtools.h $(bam2bcf_h) $(sample_h) |
452 |
- bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(bam_h) |
453 |
--bam_rmdup.o: bam_rmdup.c $(sam_h) $(HTSDIR)/htslib/khash.h |
454 |
--bam_rmdupse.o: bam_rmdupse.c $(sam_h) $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h |
455 |
--bam_sort.o: bam_sort.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) |
456 |
-+bam_rmdup.o: bam_rmdup.c $(sam_h) |
457 |
-+bam_rmdupse.o: bam_rmdupse.c $(sam_h) |
458 |
-+bam_sort.o: bam_sort.c $(htslib_sam_h) |
459 |
- bam_stat.o: bam_stat.c $(bam_h) samtools.h |
460 |
- bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) |
461 |
- bam_tview_curses.o: bam_tview_curses.c $(bam_tview_h) |
462 |
- bam_tview_html.o: bam_tview_html.c $(bam_tview_h) |
463 |
- bam_flags.o: bam_flags.c $(sam_h) |
464 |
--bamshuf.o: bamshuf.c $(htslib_sam_h) $(HTSDIR)/htslib/ksort.h samtools.h |
465 |
-+bamshuf.o: bamshuf.c $(htslib_sam_h) samtools.h |
466 |
- bamtk.o: bamtk.c $(htslib_hts_h) version.h samtools.h |
467 |
--bedcov.o: bedcov.c $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) $(HTSDIR)/htslib/kseq.h |
468 |
--bedidx.o: bedidx.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h |
469 |
-+bedcov.o: bedcov.c $(htslib_sam_h) |
470 |
-+bedidx.o: bedidx.c |
471 |
- cut_target.o: cut_target.c $(bam_h) errmod.h $(htslib_faidx_h) |
472 |
--errmod.o: errmod.c errmod.h $(HTSDIR)/htslib/ksort.h |
473 |
-+errmod.o: errmod.c errmod.h |
474 |
- kprobaln.o: kprobaln.c kprobaln.h |
475 |
- padding.o: padding.c sam_header.h $(sam_h) $(bam_h) $(htslib_faidx_h) |
476 |
--phase.o: phase.c $(htslib_sam_h) errmod.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h |
477 |
-+phase.o: phase.c $(htslib_sam_h) errmod.h |
478 |
- sam.o: sam.c $(htslib_faidx_h) $(sam_h) |
479 |
--sam_header.o: sam_header.c sam_header.h $(HTSDIR)/htslib/khash.h |
480 |
--sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash.h samtools.h |
481 |
--sample.o: sample.c $(sample_h) $(HTSDIR)/htslib/khash.h |
482 |
--stats_isize.o: stats_isize.c stats_isize.h $(HTSDIR)/htslib/khash.h |
483 |
--stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/khash_str2int.h $(htslib_faidx_h) |
484 |
-+sam_header.o: sam_header.c sam_header.h |
485 |
-+sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) samtools.h |
486 |
-+sample.o: sample.c $(sample_h) |
487 |
-+stats_isize.o: stats_isize.c stats_isize.h |
488 |
-+stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(htslib_faidx_h) |
489 |
- |
490 |
- |
491 |
- # test programs |
492 |
-@@ -178,8 +188,8 @@ stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib |
493 |
- # For tests that might use it, set $REF_PATH explicitly to use only reference |
494 |
- # areas within the test suite (or set it to ':' to use no reference areas). |
495 |
- # (regression.sh sets $REF_PATH to a subdirectory itself.) |
496 |
--check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) |
497 |
-- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) |
498 |
-+check test: samtools $(BUILT_TEST_PROGRAMS) |
499 |
-+ REF_PATH=: test/test.pl --exec bgzip=bgzip |
500 |
- test/merge/test_bam_translate test/merge/test_bam_translate.tmp |
501 |
- test/merge/test_pretty_header |
502 |
- test/merge/test_rtrans_build |
503 |
-@@ -191,31 +201,31 @@ check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) |
504 |
- test/split/test_parse_args |
505 |
- |
506 |
- |
507 |
--test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o $(HTSLIB) |
508 |
-+test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o |
509 |
- $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o $(HTSLIB) $(LDLIBS) -lz |
510 |
- |
511 |
--test/merge/test_pretty_header: test/merge/test_pretty_header.o $(HTSLIB) |
512 |
-+test/merge/test_pretty_header: test/merge/test_pretty_header.o |
513 |
- $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_pretty_header.o $(HTSLIB) $(LDLIBS) -lz |
514 |
- |
515 |
--test/merge/test_rtrans_build: test/merge/test_rtrans_build.o $(HTSLIB) |
516 |
-+test/merge/test_rtrans_build: test/merge/test_rtrans_build.o |
517 |
- $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o $(HTSLIB) $(LDLIBS) -lz |
518 |
- |
519 |
--test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o $(HTSLIB) |
520 |
-+test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o |
521 |
- $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o $(HTSLIB) $(LDLIBS) -lz |
522 |
- |
523 |
--test/split/test_count_rg: test/split/test_count_rg.o test/test.o $(HTSLIB) |
524 |
-+test/split/test_count_rg: test/split/test_count_rg.o test/test.o |
525 |
- $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz |
526 |
- |
527 |
--test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o $(HTSLIB) |
528 |
-+test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o |
529 |
- $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o $(HTSLIB) $(LDLIBS) -lz |
530 |
- |
531 |
--test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o $(HTSLIB) |
532 |
-+test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o |
533 |
- $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz |
534 |
- |
535 |
--test/split/test_parse_args: test/split/test_parse_args.o test/test.o $(HTSLIB) |
536 |
-+test/split/test_parse_args: test/split/test_parse_args.o test/test.o |
537 |
- $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o $(HTSLIB) $(LDLIBS) -lz |
538 |
- |
539 |
--test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) |
540 |
-+test/vcf-miniview: test/vcf-miniview.o |
541 |
- $(CC) -pthread $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB) $(LDLIBS) -lz |
542 |
- |
543 |
- test_test_h = test/test.h $(htslib_sam_h) |
544 |
-@@ -252,10 +262,10 @@ misc/md5sum-lite: misc/md5sum-lite.o |
545 |
- misc/wgsim: misc/wgsim.o |
546 |
- $(CC) $(LDFLAGS) -o $@ misc/wgsim.o $(LDLIBS) -lm -lz |
547 |
- |
548 |
--misc/ace2sam.o: misc/ace2sam.c $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h |
549 |
-+misc/ace2sam.o: misc/ace2sam.c |
550 |
- misc/md5.o: misc/md5.c misc/md5.h |
551 |
--misc/md5fa.o: misc/md5fa.c misc/md5.h $(HTSDIR)/htslib/kseq.h |
552 |
--misc/wgsim.o: misc/wgsim.c $(HTSDIR)/htslib/kseq.h |
553 |
-+misc/md5fa.o: misc/md5fa.c misc/md5.h |
554 |
-+misc/wgsim.o: misc/wgsim.c |
555 |
- |
556 |
- misc/maq2sam-short.o: misc/maq2sam.c |
557 |
- $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ misc/maq2sam.c |
558 |
|
559 |
diff --git a/sci-biology/samtools/files/samtools-1.2-rmdup.patch b/sci-biology/samtools/files/samtools-1.2-rmdup.patch |
560 |
deleted file mode 100644 |
561 |
index 023b5d73d..000000000 |
562 |
--- a/sci-biology/samtools/files/samtools-1.2-rmdup.patch |
563 |
+++ /dev/null |
564 |
@@ -1,47 +0,0 @@ |
565 |
-From 05fb5c2e17576b1d0ea5a0b8203b9eba236f2455 Mon Sep 17 00:00:00 2001 |
566 |
-From: kirkmcclure <kirkmcclure@××××××××××××××××××××.com> |
567 |
-Date: Mon, 23 Mar 2015 05:35:00 -0800 |
568 |
-Subject: [PATCH] Update bam.c |
569 |
- |
570 |
- For issue #138 - Samtools view -l no longer works. |
571 |
-Implement bam_get_library() |
572 |
---- |
573 |
- bam.c | 23 ++++++++++++----------- |
574 |
- 1 file changed, 12 insertions(+), 11 deletions(-) |
575 |
- |
576 |
-diff --git a/bam.c b/bam.c |
577 |
-index f909b7e..864d3f0 100644 |
578 |
---- a/bam.c |
579 |
-+++ b/bam.c |
580 |
-@@ -61,19 +61,20 @@ int bam_validate1(const bam_header_t *header, const bam1_t *b) |
581 |
- return 1; |
582 |
- } |
583 |
- |
584 |
--// FIXME: we should also check the LB tag associated with each alignment |
585 |
- const char *bam_get_library(bam_header_t *h, const bam1_t *b) |
586 |
- { |
587 |
--#if 0 |
588 |
-- const uint8_t *rg; |
589 |
-- if (h->dict == 0) h->dict = sam_header_parse2(h->text); |
590 |
-- if (h->rg2lib == 0) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB"); |
591 |
-- rg = bam_aux_get(b, "RG"); |
592 |
-- return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1)); |
593 |
--#else |
594 |
-- fprintf(stderr, "Samtools-htslib-API: bam_get_library() not yet implemented\n"); |
595 |
-- abort(); |
596 |
--#endif |
597 |
-+ const uint8_t *rg = 0; |
598 |
-+ const uint8_t *pLibName, *pDict; |
599 |
-+ if ( b != 0 && h != 0 ) { |
600 |
-+ if ( (rg = bam_aux_get(b, "RG") ) != 0 |
601 |
-+ && (pDict = sam_header_parse2(h->text)) != 0 ) { |
602 |
-+ pLibName = sam_header2tbl(pDict, "RG", "ID", "LB"); |
603 |
-+ if ( pLibName && strlen( (char*)pLibName ) > 0 ) { |
604 |
-+ return sam_tbl_get((void*)pLibName, (const char*)(rg + 1)); |
605 |
-+ } |
606 |
-+ } |
607 |
-+ } |
608 |
-+ return 0; |
609 |
- } |
610 |
- |
611 |
- int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func) |
612 |
|
613 |
diff --git a/sci-biology/samtools/files/samtools-1.3.1-buildsystem.patch b/sci-biology/samtools/files/samtools-1.3.1-buildsystem.patch |
614 |
deleted file mode 100644 |
615 |
index bd0f20c7c..000000000 |
616 |
--- a/sci-biology/samtools/files/samtools-1.3.1-buildsystem.patch |
617 |
+++ /dev/null |
618 |
@@ -1,75 +0,0 @@ |
619 |
---- samtools-1.3.1/Makefile.ori 2016-04-22 11:51:16.000000000 +0200 |
620 |
-+++ samtools-1.3.1/Makefile 2017-02-16 23:41:19.819951687 +0100 |
621 |
-@@ -21,9 +21,9 @@ |
622 |
- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER |
623 |
- # DEALINGS IN THE SOFTWARE. |
624 |
- |
625 |
--CC = gcc |
626 |
-+CC ?= gcc |
627 |
- CPPFLAGS = |
628 |
--CFLAGS = -g -Wall -O2 |
629 |
-+CFLAGS ?= -g -Wall -O2 |
630 |
- LDFLAGS = |
631 |
- LIBS = |
632 |
- |
633 |
-@@ -197,8 +203,8 @@ |
634 |
- # For tests that might use it, set $REF_PATH explicitly to use only reference |
635 |
- # areas within the test suite (or set it to ':' to use no reference areas). |
636 |
- # (regression.sh sets $REF_PATH to a subdirectory itself.) |
637 |
--check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) |
638 |
-- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) |
639 |
-+check test: samtools $(BUILT_TEST_PROGRAMS) |
640 |
-+ REF_PATH=: test/test.pl --exec bgzip=bgzip |
641 |
- test/merge/test_bam_translate test/merge/test_bam_translate.tmp |
642 |
- test/merge/test_rtrans_build |
643 |
- test/merge/test_trans_tbl_init |
644 |
-@@ -210,28 +216,28 @@ |
645 |
- test/split/test_parse_args |
646 |
- |
647 |
- |
648 |
--test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB) |
649 |
-+test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o sam_opts.o |
650 |
- $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) |
651 |
- |
652 |
--test/merge/test_rtrans_build: test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB) |
653 |
-+test/merge/test_rtrans_build: test/merge/test_rtrans_build.o sam_opts.o |
654 |
- $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) |
655 |
- |
656 |
--test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB) |
657 |
-+test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o sam_opts.o |
658 |
- $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) |
659 |
- |
660 |
--test/split/test_count_rg: test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB) |
661 |
-+test/split/test_count_rg: test/split/test_count_rg.o test/test.o sam_opts.o |
662 |
- $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) |
663 |
- |
664 |
--test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB) |
665 |
-+test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o sam_opts.o |
666 |
- $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) |
667 |
- |
668 |
--test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB) |
669 |
-+test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o sam_opts.o |
670 |
- $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) |
671 |
- |
672 |
--test/split/test_parse_args: test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB) |
673 |
-+test/split/test_parse_args: test/split/test_parse_args.o test/test.o sam_opts.o |
674 |
- $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) |
675 |
- |
676 |
--test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) |
677 |
-+test/vcf-miniview: test/vcf-miniview.o |
678 |
- $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) |
679 |
- |
680 |
- test_test_h = test/test.h $(htslib_sam_h) |
681 |
-@@ -258,10 +264,10 @@ |
682 |
- misc/maq2sam-long: misc/maq2sam-long.o |
683 |
- $(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS) |
684 |
- |
685 |
--misc/md5fa: misc/md5fa.o $(HTSLIB) |
686 |
-+misc/md5fa: misc/md5fa.o |
687 |
- $(CC) $(ALL_LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIB) $(ALL_LIBS) |
688 |
- |
689 |
--misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB) |
690 |
-+misc/md5sum-lite: misc/md5sum-lite.o |
691 |
- $(CC) $(ALL_LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIB) $(ALL_LIBS) |
692 |
- |
693 |
- misc/wgsim: misc/wgsim.o |
694 |
|
695 |
diff --git a/sci-biology/samtools/metadata.xml b/sci-biology/samtools/metadata.xml |
696 |
deleted file mode 100644 |
697 |
index 5b953af48..000000000 |
698 |
--- a/sci-biology/samtools/metadata.xml |
699 |
+++ /dev/null |
700 |
@@ -1,11 +0,0 @@ |
701 |
-<?xml version="1.0" encoding="UTF-8"?> |
702 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
703 |
-<pkgmetadata> |
704 |
- <maintainer type="project"> |
705 |
- <email>sci-biology@g.o</email> |
706 |
- <name>Gentoo Biology Project</name> |
707 |
- </maintainer> |
708 |
- <upstream> |
709 |
- <remote-id type="sourceforge">samtools</remote-id> |
710 |
- </upstream> |
711 |
-</pkgmetadata> |
712 |
|
713 |
diff --git a/sci-biology/samtools/samtools-1.0-r2.ebuild b/sci-biology/samtools/samtools-1.0-r2.ebuild |
714 |
deleted file mode 100644 |
715 |
index 6be28b674..000000000 |
716 |
--- a/sci-biology/samtools/samtools-1.0-r2.ebuild |
717 |
+++ /dev/null |
718 |
@@ -1,73 +0,0 @@ |
719 |
-# Copyright 1999-2017 Gentoo Foundation |
720 |
-# Distributed under the terms of the GNU General Public License v2 |
721 |
- |
722 |
-EAPI=5 |
723 |
- |
724 |
-PYTHON_COMPAT=( python2_7 ) |
725 |
- |
726 |
-inherit eutils multilib python-r1 toolchain-funcs |
727 |
- |
728 |
-DESCRIPTION="Utilities for SAM (Sequence Alignment/Map)" |
729 |
-HOMEPAGE="http://www.htslib.org/" |
730 |
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" |
731 |
- |
732 |
-LICENSE="MIT" |
733 |
-SLOT="0" |
734 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
735 |
-IUSE="examples" |
736 |
- |
737 |
-REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
738 |
- |
739 |
-CDEPEND=" |
740 |
- sys-libs/ncurses:0= |
741 |
- sci-libs/htslib:0=" |
742 |
- |
743 |
-RDEPEND="${CDEPEND} |
744 |
- dev-lang/lua |
745 |
- dev-lang/perl" |
746 |
-DEPEND="${CDEPEND} |
747 |
- virtual/pkgconfig" |
748 |
- |
749 |
-src_prepare() { |
750 |
- find htslib-1.0 -delete || die |
751 |
- |
752 |
- sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die |
753 |
- |
754 |
- epatch \ |
755 |
- "${FILESDIR}"/${P}-buildsystem.patch \ |
756 |
- "${FILESDIR}"/${P}-rmdup.patch |
757 |
- |
758 |
- tc-export CC AR |
759 |
- |
760 |
- sed \ |
761 |
- -e '/htslib.mk/d' \ |
762 |
- -i Makefile || die |
763 |
-} |
764 |
- |
765 |
-src_compile() { |
766 |
- local mymakeargs=( |
767 |
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" |
768 |
- HTSDIR="${EPREFIX}/usr/include" |
769 |
- HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) |
770 |
- BAMLIB="libbam.so" |
771 |
- ) |
772 |
- emake "${mymakeargs[@]}" |
773 |
-} |
774 |
- |
775 |
-src_install() { |
776 |
- dobin samtools $(find misc -type f -executable) |
777 |
- |
778 |
- python_replicate_script "${ED}"/usr/bin/varfilter.py |
779 |
- dolib.so libbam.so* |
780 |
- |
781 |
- insinto /usr/include/bam |
782 |
- doins *.h |
783 |
- |
784 |
- doman ${PN}.1 |
785 |
- dodoc AUTHORS NEWS README |
786 |
- |
787 |
- if use examples; then |
788 |
- insinto /usr/share/${PN} |
789 |
- doins -r examples |
790 |
- fi |
791 |
-} |
792 |
|
793 |
diff --git a/sci-biology/samtools/samtools-1.1-r1.ebuild b/sci-biology/samtools/samtools-1.1-r1.ebuild |
794 |
deleted file mode 100644 |
795 |
index 19cada025..000000000 |
796 |
--- a/sci-biology/samtools/samtools-1.1-r1.ebuild |
797 |
+++ /dev/null |
798 |
@@ -1,83 +0,0 @@ |
799 |
-# Copyright 1999-2017 Gentoo Foundation |
800 |
-# Distributed under the terms of the GNU General Public License v2 |
801 |
- |
802 |
-EAPI=5 |
803 |
- |
804 |
-PYTHON_COMPAT=( python2_7 ) |
805 |
- |
806 |
-inherit eutils multilib python-r1 toolchain-funcs |
807 |
- |
808 |
-DESCRIPTION="Utilities for SAM (Sequence Alignment/Map)" |
809 |
-HOMEPAGE="http://www.htslib.org/" |
810 |
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" |
811 |
- |
812 |
-LICENSE="MIT" |
813 |
-SLOT="0" |
814 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
815 |
-IUSE="examples" |
816 |
- |
817 |
-REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
818 |
- |
819 |
-CDEPEND=" |
820 |
- sys-libs/ncurses:0= |
821 |
- ~sci-libs/htslib-${PV}:0=" |
822 |
- |
823 |
-RDEPEND="${CDEPEND} |
824 |
- dev-lang/lua |
825 |
- dev-lang/perl" |
826 |
-DEPEND="${CDEPEND} |
827 |
- virtual/pkgconfig" |
828 |
- |
829 |
-src_prepare() { |
830 |
- find htslib-* -delete || die |
831 |
- |
832 |
- sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die |
833 |
- |
834 |
- epatch \ |
835 |
- "${FILESDIR}"/${P}-buildsystem.patch \ |
836 |
- "${FILESDIR}"/${P}-rmdup.patch |
837 |
- |
838 |
- tc-export CC AR |
839 |
- |
840 |
- sed \ |
841 |
- -e '/htslib.mk/d' \ |
842 |
- -i Makefile || die |
843 |
-} |
844 |
- |
845 |
-src_compile() { |
846 |
- local mymakeargs=( |
847 |
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" |
848 |
- HTSDIR="${EPREFIX}/usr/include" |
849 |
- HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) |
850 |
- BAMLIB="libbam.so" |
851 |
- ) |
852 |
- emake "${mymakeargs[@]}" |
853 |
-} |
854 |
- |
855 |
-src_test() { |
856 |
- local mymakeargs=( |
857 |
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" |
858 |
- HTSDIR="${EPREFIX}/usr/include" |
859 |
- HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) |
860 |
- BAMLIB="libbam.so" |
861 |
- ) |
862 |
- emake "${mymakeargs[@]}" test |
863 |
-} |
864 |
- |
865 |
-src_install() { |
866 |
- dobin samtools $(find misc -type f -executable) |
867 |
- |
868 |
- python_replicate_script "${ED}"/usr/bin/varfilter.py |
869 |
- dolib.so libbam.so* |
870 |
- |
871 |
- insinto /usr/include/bam |
872 |
- doins *.h |
873 |
- |
874 |
- doman ${PN}.1 |
875 |
- dodoc AUTHORS NEWS README |
876 |
- |
877 |
- if use examples; then |
878 |
- insinto /usr/share/${PN} |
879 |
- doins -r examples |
880 |
- fi |
881 |
-} |
882 |
|
883 |
diff --git a/sci-biology/samtools/samtools-1.2-r1.ebuild b/sci-biology/samtools/samtools-1.2-r1.ebuild |
884 |
deleted file mode 100644 |
885 |
index 702d9bcb9..000000000 |
886 |
--- a/sci-biology/samtools/samtools-1.2-r1.ebuild |
887 |
+++ /dev/null |
888 |
@@ -1,83 +0,0 @@ |
889 |
-# Copyright 1999-2017 Gentoo Foundation |
890 |
-# Distributed under the terms of the GNU General Public License v2 |
891 |
- |
892 |
-EAPI=5 |
893 |
- |
894 |
-PYTHON_COMPAT=( python2_7 ) |
895 |
- |
896 |
-inherit eutils multilib python-r1 toolchain-funcs |
897 |
- |
898 |
-DESCRIPTION="Utilities for SAM (Sequence Alignment/Map)" |
899 |
-HOMEPAGE="http://www.htslib.org/" |
900 |
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" |
901 |
- |
902 |
-LICENSE="MIT" |
903 |
-SLOT="0" |
904 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
905 |
-IUSE="examples" |
906 |
- |
907 |
-REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
908 |
- |
909 |
-CDEPEND=" |
910 |
- sys-libs/ncurses:0= |
911 |
- >=sci-libs/htslib-${PV}:0=" |
912 |
- |
913 |
-RDEPEND="${CDEPEND} |
914 |
- dev-lang/lua |
915 |
- dev-lang/perl" |
916 |
-DEPEND="${CDEPEND} |
917 |
- virtual/pkgconfig" |
918 |
- |
919 |
-src_prepare() { |
920 |
- find htslib-* -delete || die |
921 |
- |
922 |
- sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die |
923 |
- |
924 |
- epatch \ |
925 |
- "${FILESDIR}"/${P}-buildsystem.patch \ |
926 |
- "${FILESDIR}"/${P}-rmdup.patch |
927 |
- |
928 |
- tc-export CC AR |
929 |
- |
930 |
- sed \ |
931 |
- -e '/htslib.mk/d' \ |
932 |
- -i Makefile || die |
933 |
-} |
934 |
- |
935 |
-src_compile() { |
936 |
- local mymakeargs=( |
937 |
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" |
938 |
- HTSDIR="${EPREFIX}/usr/include" |
939 |
- HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) |
940 |
- BAMLIB="libbam.so" |
941 |
- ) |
942 |
- emake "${mymakeargs[@]}" |
943 |
-} |
944 |
- |
945 |
-src_test() { |
946 |
- local mymakeargs=( |
947 |
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" |
948 |
- HTSDIR="${EPREFIX}/usr/include" |
949 |
- HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) |
950 |
- BAMLIB="libbam.so" |
951 |
- ) |
952 |
- LD_LIBRARY_PATH="${S}" emake "${mymakeargs[@]}" test |
953 |
-} |
954 |
- |
955 |
-src_install() { |
956 |
- dobin samtools $(find misc -type f -executable) |
957 |
- |
958 |
- python_replicate_script "${ED}"/usr/bin/varfilter.py |
959 |
- dolib.so libbam.so* |
960 |
- |
961 |
- insinto /usr/include/bam |
962 |
- doins *.h |
963 |
- |
964 |
- doman ${PN}.1 |
965 |
- dodoc AUTHORS NEWS README |
966 |
- |
967 |
- if use examples; then |
968 |
- insinto /usr/share/${PN} |
969 |
- doins -r examples |
970 |
- fi |
971 |
-} |
972 |
|
973 |
diff --git a/sci-biology/samtools/samtools-1.3.1.ebuild b/sci-biology/samtools/samtools-1.3.1.ebuild |
974 |
deleted file mode 100644 |
975 |
index 98649e6ec..000000000 |
976 |
--- a/sci-biology/samtools/samtools-1.3.1.ebuild |
977 |
+++ /dev/null |
978 |
@@ -1,83 +0,0 @@ |
979 |
-# Copyright 1999-2017 Gentoo Foundation |
980 |
-# Distributed under the terms of the GNU General Public License v2 |
981 |
- |
982 |
-EAPI=5 |
983 |
- |
984 |
-PYTHON_COMPAT=( python2_7 ) |
985 |
- |
986 |
-inherit eutils multilib python-r1 toolchain-funcs |
987 |
- |
988 |
-DESCRIPTION="Utilities for SAM (Sequence Alignment/Map)" |
989 |
-HOMEPAGE="http://www.htslib.org/" |
990 |
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" |
991 |
- |
992 |
-LICENSE="MIT" |
993 |
-SLOT="0" |
994 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
995 |
-IUSE="examples" |
996 |
- |
997 |
-REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
998 |
- |
999 |
-CDEPEND=" |
1000 |
- sys-libs/ncurses:0= |
1001 |
- >=sci-libs/htslib-${PV}:0=" |
1002 |
- |
1003 |
-RDEPEND="${CDEPEND} |
1004 |
- dev-lang/lua |
1005 |
- dev-lang/perl" |
1006 |
-DEPEND="${CDEPEND} |
1007 |
- virtual/pkgconfig" |
1008 |
- |
1009 |
-src_prepare() { |
1010 |
- find htslib-* -delete || die |
1011 |
- |
1012 |
- sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die |
1013 |
- |
1014 |
- epatch \ |
1015 |
- "${FILESDIR}"/${P}-buildsystem.patch |
1016 |
- |
1017 |
- tc-export CC AR |
1018 |
- |
1019 |
- sed \ |
1020 |
- -e '/htslib.mk/d' \ |
1021 |
- -i Makefile || die |
1022 |
-} |
1023 |
- |
1024 |
-src_compile() { |
1025 |
- local mymakeargs=( |
1026 |
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" |
1027 |
- HTSDIR="${EPREFIX}/usr/include" |
1028 |
- HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) |
1029 |
- BAMLIB="libbam.so" |
1030 |
- ) |
1031 |
- emake "${mymakeargs[@]}" |
1032 |
-} |
1033 |
- |
1034 |
-src_test() { |
1035 |
- local mymakeargs=( |
1036 |
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" |
1037 |
- HTSDIR="${EPREFIX}/usr/include" |
1038 |
- HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) |
1039 |
- BAMLIB="libbam.so" |
1040 |
- ) |
1041 |
- LD_LIBRARY_PATH="${S}" emake "${mymakeargs[@]}" test |
1042 |
-} |
1043 |
- |
1044 |
-src_install() { |
1045 |
- dobin samtools $(find misc -type f -executable) |
1046 |
- |
1047 |
- python_replicate_script "${ED}"/usr/bin/varfilter.py |
1048 |
- #dolib.so libbam.so* |
1049 |
- dolib libbam.a |
1050 |
- |
1051 |
- insinto /usr/include/bam |
1052 |
- doins *.h |
1053 |
- |
1054 |
- doman ${PN}.1 |
1055 |
- dodoc AUTHORS NEWS README |
1056 |
- |
1057 |
- if use examples; then |
1058 |
- insinto /usr/share/${PN} |
1059 |
- doins -r examples |
1060 |
- fi |
1061 |
-} |
1062 |
|
1063 |
diff --git a/sci-biology/samtools/samtools-1.5.ebuild b/sci-biology/samtools/samtools-1.5.ebuild |
1064 |
deleted file mode 100644 |
1065 |
index 2a2d80423..000000000 |
1066 |
--- a/sci-biology/samtools/samtools-1.5.ebuild |
1067 |
+++ /dev/null |
1068 |
@@ -1,82 +0,0 @@ |
1069 |
-# Copyright 1999-2017 Gentoo Foundation |
1070 |
-# Distributed under the terms of the GNU General Public License v2 |
1071 |
- |
1072 |
-EAPI=5 |
1073 |
- |
1074 |
-PYTHON_COMPAT=( python2_7 ) |
1075 |
- |
1076 |
-inherit eutils multilib python-r1 toolchain-funcs |
1077 |
- |
1078 |
-DESCRIPTION="Utilities for SAM (Sequence Alignment/Map) and BAM files" |
1079 |
-HOMEPAGE="http://www.htslib.org/" |
1080 |
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" |
1081 |
- |
1082 |
-LICENSE="MIT" |
1083 |
-SLOT="0" |
1084 |
-KEYWORDS="" |
1085 |
-# KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
1086 |
-IUSE="examples" |
1087 |
- |
1088 |
-REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
1089 |
- |
1090 |
-CDEPEND=" |
1091 |
- sys-libs/ncurses:0= |
1092 |
- >=sci-libs/htslib-${PV}:2=" |
1093 |
- |
1094 |
-RDEPEND="${CDEPEND} |
1095 |
- dev-lang/lua |
1096 |
- dev-lang/perl" |
1097 |
-DEPEND="${CDEPEND} |
1098 |
- virtual/pkgconfig" |
1099 |
- |
1100 |
-src_prepare() { |
1101 |
- find htslib-* -delete || die |
1102 |
- |
1103 |
- sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die |
1104 |
- |
1105 |
- tc-export CC AR |
1106 |
- |
1107 |
- sed \ |
1108 |
- -e '/htslib.mk/d' \ |
1109 |
- -i Makefile || die |
1110 |
-} |
1111 |
- |
1112 |
-src_compile() { |
1113 |
- local mymakeargs=( |
1114 |
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" |
1115 |
- HTSDIR="${EPREFIX}/usr/include" |
1116 |
- HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) |
1117 |
- BAMLIB="libbam.so" |
1118 |
- CC=$(tc-getCC) CFLAGS="${CFLAGS}" |
1119 |
- ) |
1120 |
- emake "${mymakeargs[@]}" |
1121 |
-} |
1122 |
- |
1123 |
-src_test() { |
1124 |
- local mymakeargs=( |
1125 |
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" |
1126 |
- HTSDIR="${EPREFIX}/usr/include" |
1127 |
- HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) |
1128 |
- BAMLIB="libbam.so" |
1129 |
- ) |
1130 |
- LD_LIBRARY_PATH="${S}" emake "${mymakeargs[@]}" test |
1131 |
-} |
1132 |
- |
1133 |
-src_install() { |
1134 |
- dobin samtools $(find misc -type f -executable) |
1135 |
- |
1136 |
- python_replicate_script "${ED}"/usr/bin/varfilter.py |
1137 |
- #dolib.so libbam.so* |
1138 |
- dolib libbam.a |
1139 |
- |
1140 |
- insinto /usr/include/bam |
1141 |
- doins *.h |
1142 |
- |
1143 |
- doman ${PN}.1 |
1144 |
- dodoc AUTHORS NEWS README |
1145 |
- |
1146 |
- if use examples; then |
1147 |
- insinto /usr/share/${PN} |
1148 |
- doins -r examples |
1149 |
- fi |
1150 |
-} |