1 |
commit: d401db74e7e270ab7e38d955308cd8d2dbc20a48 |
2 |
Author: David Seifert <soap <AT> gentoo <DOT> org> |
3 |
AuthorDate: Sat Sep 2 09:30:07 2017 +0000 |
4 |
Commit: David Seifert <soap <AT> gentoo <DOT> org> |
5 |
CommitDate: Sat Sep 2 09:32:42 2017 +0000 |
6 |
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d401db74 |
7 |
|
8 |
sci-biology/samtools: Version bump to 1.5 |
9 |
|
10 |
Package-Manager: Portage-2.3.8, Repoman-2.3.3 |
11 |
|
12 |
sci-biology/samtools/Manifest | 1 + |
13 |
.../samtools/files/samtools-1.5-buildsystem.patch | 413 +++++++++++++++++++++ |
14 |
sci-biology/samtools/samtools-1.5.ebuild | 61 +++ |
15 |
3 files changed, 475 insertions(+) |
16 |
|
17 |
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest |
18 |
index d25774fee86..791e2050ee7 100644 |
19 |
--- a/sci-biology/samtools/Manifest |
20 |
+++ b/sci-biology/samtools/Manifest |
21 |
@@ -5,3 +5,4 @@ DIST samtools-1.0.tar.bz2 4459669 SHA256 7340b843663c3f54a902a06f2f73c68198f3a62 |
22 |
DIST samtools-1.1.tar.bz2 4495373 SHA256 c24d26c303153d72b5bf3cc11f72c6c375a4ca1140cc485648c8c5473414b7f8 SHA512 a5552a6c8c4b0808b725b39ddb2fafa36c4f6623bfc7f84faadae7690223e4eec8d722af09c77145796ad9b3f01e04115dd0207207ccfafbb52ffc22d5fc09f0 WHIRLPOOL ed3131b2a8d8b4dab40b53d35a9b00b657670a949dc1597c91fbcd00392c1c1715a85a1d1e49bf0c73ae082738ccfb13d2c6809dbbeba17ff3028f6023ebc449 |
23 |
DIST samtools-1.2.tar.bz2 4547126 SHA256 420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa SHA512 4849c3274e732267516b63799f5430c5415d575d46eddf6b704dac51053281094b03b90dd9f5367bcd14c22fb0fb1bd6a412f7d4225f7be5f5385437c5d2101d WHIRLPOOL 273185764a807365a20c381769f987ef02d14ae8e20a3a7fd5af4344769c5fab68d7155523e8c0c8c3cc86092898c2c8454cce8f1560d415bc2b41549cdf04f4 |
24 |
DIST samtools-1.3.tar.bz2 3978333 SHA256 beea4003c795a0a25224656815b4036f6864b8753053ed30c590bb052b70b60e SHA512 72920d4f0f10aa7b54ef448e03e6e769e1e07abd07388a2307d0e52548fa2909c03ca2c7eec5c63cf5b67724b2356833accb0079ce1486bb2ac66a45963a24ea WHIRLPOOL 3f798078100b4ed164f6c89d18cc8f62159437e2cfb2a228ac00f8d08313f7c39ef546214c0796c25a419c0a1065dc21d14b966fed769726b9b1975ec07e3b3e |
25 |
+DIST samtools-1.5.tar.bz2 4190142 SHA256 8542da26832ee08c1978713f5f6188ff750635b50d8ab126a0c7bb2ac1ae2df6 SHA512 ff3e39ba867ecbd88f3363b038508c1557e349ea4223483f8f4ecb17ff8864fb53cd193bc2059a147e30f07395bbf53c8518d0f70219e454375c8bffe56e3059 WHIRLPOOL 1a88c9617857f1f6d146df179aef5b5c6bb83de8c9d127c405e5756842ced84c194a3f09f69a4757a8adf6ca623c9fdc972f4bf609649d3e991dda8f616e3582 |
26 |
|
27 |
diff --git a/sci-biology/samtools/files/samtools-1.5-buildsystem.patch b/sci-biology/samtools/files/samtools-1.5-buildsystem.patch |
28 |
new file mode 100644 |
29 |
index 00000000000..248089e09fc |
30 |
--- /dev/null |
31 |
+++ b/sci-biology/samtools/files/samtools-1.5-buildsystem.patch |
32 |
@@ -0,0 +1,413 @@ |
33 |
+--- a/config.mk.in |
34 |
++++ b/config.mk.in |
35 |
+@@ -28,27 +28,26 @@ |
36 |
+ # in the Makefile to reflect your configuration choices. If you don't run |
37 |
+ # configure, the main Makefile contains suitable conservative defaults. |
38 |
+ |
39 |
+-prefix = @prefix@ |
40 |
+-exec_prefix = @exec_prefix@ |
41 |
+-bindir = @bindir@ |
42 |
+-datarootdir = @datarootdir@ |
43 |
+-mandir = @mandir@ |
44 |
++prefix = @prefix@ |
45 |
++exec_prefix = @exec_prefix@ |
46 |
++bindir = @bindir@ |
47 |
++libdir = @libdir@ |
48 |
++datarootdir = @datarootdir@ |
49 |
++mandir = @mandir@ |
50 |
++man1dir = $(mandir)/man1 |
51 |
+ |
52 |
+ CC = @CC@ |
53 |
++AR = @AR@ |
54 |
+ CPPFLAGS = @CPPFLAGS@ |
55 |
+ CFLAGS = @CFLAGS@ |
56 |
+ LDFLAGS = @LDFLAGS@ |
57 |
+ LIBS = @LIBS@ |
58 |
+ |
59 |
+-@Hsource@HTSDIR = @HTSDIR@ |
60 |
+-@Hsource@include $(HTSDIR)/htslib.mk |
61 |
+-@Hsource@include $(HTSDIR)/htslib_static.mk |
62 |
+-@Hsource@HTSLIB = $(HTSDIR)/libhts.a |
63 |
+-@Hsource@HTSLIB_LIB = $(HTSLIB) $(HTSLIB_static_LIBS) |
64 |
+-@Hsource@HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS) |
65 |
+-@Hsource@BGZIP = $(HTSDIR)/bgzip |
66 |
+-HTSLIB_CPPFLAGS = @HTSLIB_CPPFLAGS@ |
67 |
+-@Hinstall@HTSLIB_LDFLAGS = @HTSLIB_LDFLAGS@ |
68 |
+-@Hinstall@HTSLIB_LIB = -lhts |
69 |
++HTSLIB_CFLAGS = @HTSLIB_CFLAGS@ |
70 |
++HTSLIB_LIBS = @HTSLIB_LIBS@ |
71 |
+ |
72 |
+-CURSES_LIB = @CURSES_LIB@ |
73 |
++NCURSES_CFLAGS = @NCURSES_CFLAGS@ |
74 |
++NCURSES_LIBS = @NCURSES_LIBS@ |
75 |
++ |
76 |
++ZLIB_CFLAGS = @ZLIB_CFLAGS@ |
77 |
++ZLIB_LIBS = @ZLIB_LIBS@ |
78 |
+--- a/configure.ac |
79 |
++++ b/configure.ac |
80 |
+@@ -29,9 +29,6 @@ |
81 |
+ AC_CONFIG_SRCDIR([bamtk.c]) |
82 |
+ AC_CONFIG_HEADERS([config.h]) |
83 |
+ |
84 |
+-m4_include([m4/ax_with_curses.m4]) |
85 |
+-m4_include([m4/ax_with_htslib.m4]) |
86 |
+- |
87 |
+ dnl Copyright notice to be copied into the generated configure script |
88 |
+ AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd. |
89 |
+ |
90 |
+@@ -39,73 +36,27 @@ |
91 |
+ redistribute it. There is NO WARRANTY, to the extent permitted by law.]) |
92 |
+ |
93 |
+ AC_PROG_CC |
94 |
++AM_PROG_AR |
95 |
+ |
96 |
+ AC_SYS_LARGEFILE |
97 |
+ |
98 |
+-AX_WITH_HTSLIB |
99 |
+-if test "$ax_cv_htslib" != yes; then |
100 |
+- AC_MSG_ERROR([HTSlib development files not found |
101 |
+- |
102 |
+-Samtools uses HTSlib to parse bioinformatics file formats etc. Building it |
103 |
+-requires an unpacked HTSlib source tree (which will be built in conjunction |
104 |
+-with samtools) or a previously-installed HTSlib. In either case you may |
105 |
+-need to configure --with-htslib=DIR to locate the appropriate HTSlib. |
106 |
+- |
107 |
+-FAILED. You must supply an HTSlib in order to build samtools successfully.]) |
108 |
+-fi |
109 |
+- |
110 |
+-if test "$ax_cv_htslib_which" = source; then |
111 |
+- Hsource= |
112 |
+- Hinstall='#' |
113 |
+-else |
114 |
+- Hsource='#' |
115 |
+- Hinstall= |
116 |
+-fi |
117 |
+-AC_SUBST([Hsource]) |
118 |
+-AC_SUBST([Hinstall]) |
119 |
++dnl htslib |
120 |
++PKG_CHECK_MODULES([HTSLIB], [htslib]) |
121 |
+ |
122 |
++dnl ncurses |
123 |
+ AC_ARG_WITH([curses], |
124 |
+ [AS_HELP_STRING([--without-curses], |
125 |
+ [omit curses support, so no curses library needed])]) |
126 |
+ |
127 |
+-if test "$with_curses" != no; then |
128 |
+- AX_WITH_CURSES |
129 |
+- if test "$ax_cv_curses" != yes; then |
130 |
+- AC_MSG_ERROR([curses development files not found |
131 |
+- |
132 |
+-The 'samtools tview' command uses the curses text user interface library. |
133 |
+-Building samtools with tview requires curses/ncurses/etc development files |
134 |
+-to be installed on the build machine; you may need to ensure a package such |
135 |
+-as libncurses5-dev (on Debian or Ubuntu Linux) or ncurses-devel (on RPM-based |
136 |
+-Linux distributions) is installed. |
137 |
+- |
138 |
+-FAILED. Either configure --without-curses or resolve this error to build |
139 |
+-samtools successfully.]) |
140 |
+- fi |
141 |
+-else |
142 |
+- CURSES_LIB= |
143 |
+- CURSES_CPPFLAGS= |
144 |
+- AC_SUBST([CURSES_LIB]) |
145 |
+- AC_SUBST([CURSES_CPPFLAGS]) |
146 |
+-fi |
147 |
+- |
148 |
+-save_LIBS=$LIBS |
149 |
+-zlib_devel=ok |
150 |
+-dnl Set a trivial non-empty INCLUDES to avoid excess default includes tests |
151 |
+-AC_CHECK_HEADER([zlib.h], [], [zlib_devel=missing], [;]) |
152 |
+-AC_CHECK_LIB(z, inflate, [], [zlib_devel=missing]) |
153 |
+-LIBS=$save_LIBS |
154 |
+- |
155 |
+-if test $zlib_devel != ok; then |
156 |
+- AC_MSG_ERROR([zlib development files not found |
157 |
+- |
158 |
+-Samtools uses compression routines from the zlib library <http://zlib.net>. |
159 |
+-Building samtools requires zlib development files to be installed on the build |
160 |
+-machine; you may need to ensure a package such as zlib1g-dev (on Debian or |
161 |
+-Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions) is installed. |
162 |
++AS_IF([test "x$with_curses" != "xno"], [ |
163 |
++ PKG_CHECK_MODULES([NCURSES], [ncurses]) |
164 |
++ |
165 |
++ AC_DEFINE([HAVE_CURSES], [1]) |
166 |
++ AC_DEFINE([HAVE_NCURSES_H], [1]) |
167 |
++]) |
168 |
+ |
169 |
+-FAILED. This error must be resolved in order to build samtools successfully.]) |
170 |
+-fi |
171 |
++dnl zlib |
172 |
++PKG_CHECK_MODULES([ZLIB], [zlib]) |
173 |
+ |
174 |
+ AC_CONFIG_FILES([config.mk]) |
175 |
+ AC_OUTPUT |
176 |
+--- a/Makefile |
177 |
++++ b/Makefile |
178 |
+@@ -21,14 +21,6 @@ |
179 |
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER |
180 |
+ # DEALINGS IN THE SOFTWARE. |
181 |
+ |
182 |
+-CC = gcc |
183 |
+-AR = ar |
184 |
+-CPPFLAGS = |
185 |
+-#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 |
186 |
+-CFLAGS = -g -Wall -O2 |
187 |
+-LDFLAGS = |
188 |
+-LIBS = |
189 |
+- |
190 |
+ LOBJS= bam_aux.o bam.o bam_import.o sam.o \ |
191 |
+ sam_header.o bam_plbuf.o |
192 |
+ AOBJS= bam_index.o bam_plcmd.o sam_view.o \ |
193 |
+@@ -40,13 +32,6 @@ |
194 |
+ bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \ |
195 |
+ bam_quickcheck.o bam_addrprg.o |
196 |
+ |
197 |
+-prefix = /usr/local |
198 |
+-exec_prefix = $(prefix) |
199 |
+-bindir = $(exec_prefix)/bin |
200 |
+-datarootdir = $(prefix)/share |
201 |
+-mandir = $(datarootdir)/man |
202 |
+-man1dir = $(mandir)/man1 |
203 |
+- |
204 |
+ # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS) |
205 |
+ misc_bindir = $(bindir) |
206 |
+ |
207 |
+@@ -85,15 +70,14 @@ |
208 |
+ |
209 |
+ all: $(PROGRAMS) $(MISC_PROGRAMS) $(TEST_PROGRAMS) |
210 |
+ |
211 |
+-ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) |
212 |
+-ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS) |
213 |
+-ALL_LIBS = -lz $(LIBS) |
214 |
++ALL_CPPFLAGS = -I. $(HTSLIB_CFLAGS) $(CPPFLAGS) |
215 |
++ALL_LIBS = $(ZLIB_LIBS) $(LIBS) |
216 |
+ |
217 |
+ # Usually config.mk and config.h are generated by running configure |
218 |
+ # or config.status, but if those aren't used create defaults here. |
219 |
+ |
220 |
+ config.mk: |
221 |
+- @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.5#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@ |
222 |
++ @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.5#g;s/@HTSLIB_CFLAGS@/-I$$(HTSDIR)/g;s/@NCURSES_LIBS@/-lcurses/g' config.mk.in > $@ |
223 |
+ |
224 |
+ config.h: |
225 |
+ echo '/* Basic config.h generated by Makefile */' > $@ |
226 |
+@@ -133,17 +117,22 @@ |
227 |
+ .c.o: |
228 |
+ $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $< |
229 |
+ |
230 |
++$(LOBJS): |
231 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< |
232 |
++ |
233 |
+ |
234 |
+ LIBST_OBJS = sam_opts.o sam_utils.o |
235 |
+ |
236 |
+ |
237 |
+-lib:libbam.a |
238 |
++lib: libbam.so.1.0 |
239 |
+ |
240 |
+-libbam.a:$(LOBJS) |
241 |
+- $(AR) -csru $@ $(LOBJS) |
242 |
++libbam.so.1.0:$(LOBJS) |
243 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) |
244 |
++ ln -sf $@ libbam.so.1 |
245 |
++ ln -sf $@ libbam.so |
246 |
+ |
247 |
+-samtools: $(AOBJS) libbam.a libst.a $(HTSLIB) |
248 |
+- $(CC) $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a libst.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) -lpthread |
249 |
++samtools: $(AOBJS) libbam.so.1.0 libst.a |
250 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) libbam.so.1.0 libst.a $(HTSLIB_LIBS) $(NCURSES_LIBS) -lm $(ALL_LIBS) -lpthread |
251 |
+ |
252 |
+ # For building samtools and its test suite only: NOT to be installed. |
253 |
+ libst.a: $(LIBST_OBJS) |
254 |
+@@ -151,58 +140,58 @@ |
255 |
+ $(AR) -rcs $@ $(LIBST_OBJS) |
256 |
+ |
257 |
+ |
258 |
+-bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) |
259 |
+-bam2bcf_h = bam2bcf.h $(htslib_hts_h) $(htslib_vcf_h) |
260 |
+-bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) |
261 |
+-bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) |
262 |
+-bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(htslib_khash_h) $(bam_lpileup_h) |
263 |
+-sam_h = sam.h $(htslib_sam_h) $(bam_h) |
264 |
+-sam_opts_h = sam_opts.h $(htslib_hts_h) |
265 |
+-sample_h = sample.h $(htslib_kstring_h) |
266 |
+- |
267 |
+-bam.o: bam.c config.h $(bam_h) $(htslib_kstring_h) sam_header.h |
268 |
+-bam2bcf.o: bam2bcf.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) |
269 |
+-bam2bcf_indel.o: bam2bcf_indel.c config.h $(htslib_hts_h) $(htslib_sam_h) $(bam2bcf_h) $(htslib_khash_h) $(htslib_ksort_h) |
270 |
+-bam2depth.o: bam2depth.c config.h $(htslib_sam_h) samtools.h $(sam_opts_h) |
271 |
+-bam_addrprg.o: bam_addrprg.c config.h $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h) |
272 |
++bam_h = bam.h |
273 |
++bam2bcf_h = bam2bcf.h |
274 |
++bam_lpileup_h = bam_lpileup.h |
275 |
++bam_plbuf_h = bam_plbuf.h |
276 |
++bam_tview_h = bam_tview.h $(bam2bcf_h) $(bam_lpileup_h) |
277 |
++sam_h = sam.h $(bam_h) |
278 |
++sam_opts_h = sam_opts.h |
279 |
++sample_h = sample.h |
280 |
++ |
281 |
++bam.o: bam.c config.h $(bam_h) sam_header.h |
282 |
++bam2bcf.o: bam2bcf.c config.h $(bam2bcf_h) |
283 |
++bam2bcf_indel.o: bam2bcf_indel.c config.h $(bam2bcf_h) |
284 |
++bam2depth.o: bam2depth.c config.h samtools.h $(sam_opts_h) |
285 |
++bam_addrprg.o: bam_addrprg.c config.h samtools.h $(sam_opts_h) |
286 |
+ bam_aux.o: bam_aux.c config.h $(bam_h) |
287 |
+-bam_cat.o: bam_cat.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) samtools.h |
288 |
++bam_cat.o: bam_cat.c config.h samtools.h |
289 |
+ bam_color.o: bam_color.c config.h $(bam_h) |
290 |
+-bam_import.o: bam_import.c config.h $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h) |
291 |
+-bam_index.o: bam_index.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h |
292 |
+-bam_lpileup.o: bam_lpileup.c config.h $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h) |
293 |
+-bam_mate.o: bam_mate.c config.h $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) samtools.h |
294 |
+-bam_md.o: bam_md.c config.h $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) $(sam_opts_h) samtools.h |
295 |
+-bam_plbuf.o: bam_plbuf.c config.h $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) |
296 |
+-bam_plcmd.o: bam_plcmd.c config.h $(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) |
297 |
+-bam_quickcheck.o: bam_quickcheck.c config.h $(htslib_hts_h) $(htslib_sam_h) |
298 |
+-bam_reheader.o: bam_reheader.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h |
299 |
+-bam_rmdup.o: bam_rmdup.c config.h $(htslib_sam_h) $(sam_opts_h) samtools.h $(bam_h) $(htslib_khash_h) |
300 |
+-bam_rmdupse.o: bam_rmdupse.c config.h $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) samtools.h |
301 |
+-bam_sort.o: bam_sort.c config.h $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) samtools.h |
302 |
+-bam_split.o: bam_split.c config.h $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(htslib_cram_h) $(sam_opts_h) samtools.h |
303 |
+-bam_stat.o: bam_stat.c config.h $(htslib_sam_h) samtools.h |
304 |
+-bam_tview.o: bam_tview.c config.h $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) samtools.h $(sam_opts_h) |
305 |
++bam_import.o: bam_import.c config.h $(bam_h) |
306 |
++bam_index.o: bam_index.c config.h samtools.h |
307 |
++bam_lpileup.o: bam_lpileup.c config.h $(bam_plbuf_h) $(bam_lpileup_h) |
308 |
++bam_mate.o: bam_mate.c config.h $(sam_opts_h) samtools.h |
309 |
++bam_md.o: bam_md.c config.h $(sam_opts_h) samtools.h |
310 |
++bam_plbuf.o: bam_plbuf.c config.h $(bam_plbuf_h) |
311 |
++bam_plcmd.o: bam_plcmd.c config.h sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h) |
312 |
++bam_quickcheck.o: bam_quickcheck.c config.h |
313 |
++bam_reheader.o: bam_reheader.c config.h samtools.h |
314 |
++bam_rmdup.o: bam_rmdup.c config.h $(sam_opts_h) samtools.h $(bam_h) |
315 |
++bam_rmdupse.o: bam_rmdupse.c config.h $(bam_h) samtools.h |
316 |
++bam_sort.o: bam_sort.c config.h $(sam_opts_h) samtools.h |
317 |
++bam_split.o: bam_split.c config.h $(sam_opts_h) samtools.h |
318 |
++bam_stat.o: bam_stat.c config.h samtools.h |
319 |
++bam_tview.o: bam_tview.c config.h $(bam_tview_h) samtools.h $(sam_opts_h) |
320 |
+ bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h) |
321 |
+ bam_tview_html.o: bam_tview_html.c config.h $(bam_tview_h) |
322 |
+-bam_flags.o: bam_flags.c config.h $(htslib_sam_h) |
323 |
+-bamshuf.o: bamshuf.c config.h $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h) |
324 |
+-bamtk.o: bamtk.c config.h $(htslib_hts_h) samtools.h version.h |
325 |
+-bedcov.o: bedcov.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h) |
326 |
+-bedidx.o: bedidx.c config.h $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h) |
327 |
+-cut_target.o: cut_target.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) samtools.h $(sam_opts_h) |
328 |
+-dict.o: dict.c config.h $(htslib_kseq_h) $(htslib_hts_h) |
329 |
+-faidx.o: faidx.c config.h $(htslib_faidx_h) samtools.h |
330 |
+-padding.o: padding.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) samtools.h |
331 |
+-phase.o: phase.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(sam_opts_h) samtools.h $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h) |
332 |
+-sam.o: sam.c config.h $(htslib_faidx_h) $(sam_h) |
333 |
+-sam_header.o: sam_header.c config.h sam_header.h $(htslib_khash_h) |
334 |
++bam_flags.o: bam_flags.c config.h |
335 |
++bamshuf.o: bamshuf.c config.h samtools.h $(sam_opts_h) |
336 |
++bamtk.o: bamtk.c config.h samtools.h version.h |
337 |
++bedcov.o: bedcov.c config.h $(sam_opts_h) |
338 |
++bedidx.o: bedidx.c config.h |
339 |
++cut_target.o: cut_target.c config.h samtools.h $(sam_opts_h) |
340 |
++dict.o: dict.c config.h |
341 |
++faidx.o: faidx.c config.h samtools.h |
342 |
++padding.o: padding.c config.h sam_header.h $(sam_opts_h) samtools.h |
343 |
++phase.o: phase.c config.h $(sam_opts_h) samtools.h |
344 |
++sam.o: sam.c config.h $(sam_h) |
345 |
++sam_header.o: sam_header.c config.h sam_header.h |
346 |
+ sam_opts.o: sam_opts.c config.h $(sam_opts_h) |
347 |
+ sam_utils.o: sam_utils.c config.h samtools.h |
348 |
+-sam_view.o: sam_view.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h) |
349 |
+-sample.o: sample.c config.h $(sample_h) $(htslib_khash_h) |
350 |
+-stats_isize.o: stats_isize.c config.h stats_isize.h $(htslib_khash_h) |
351 |
+-stats.o: stats.c config.h $(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) |
352 |
++sam_view.o: sam_view.c config.h samtools.h $(sam_opts_h) |
353 |
++sample.o: sample.c config.h $(sample_h) |
354 |
++stats_isize.o: stats_isize.c config.h stats_isize.h |
355 |
++stats.o: stats.c config.h sam_header.h samtools.h stats_isize.h $(sam_opts_h) |
356 |
+ |
357 |
+ |
358 |
+ # test programs |
359 |
+@@ -224,30 +213,30 @@ |
360 |
+ |
361 |
+ |
362 |
+ test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB) |
363 |
+- $(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread |
364 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread |
365 |
+ |
366 |
+ test/merge/test_rtrans_build: test/merge/test_rtrans_build.o libst.a $(HTSLIB) |
367 |
+- $(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread |
368 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread |
369 |
+ |
370 |
+ test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o libst.a $(HTSLIB) |
371 |
+- $(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread |
372 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread |
373 |
+ |
374 |
+ test/split/test_count_rg: test/split/test_count_rg.o test/test.o libst.a $(HTSLIB) |
375 |
+- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread |
376 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread |
377 |
+ |
378 |
+ test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB) |
379 |
+- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread |
380 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread |
381 |
+ |
382 |
+ test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB) |
383 |
+- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread |
384 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread |
385 |
+ |
386 |
+ test/split/test_parse_args: test/split/test_parse_args.o test/test.o libst.a $(HTSLIB) |
387 |
+- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread |
388 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread |
389 |
+ |
390 |
+ test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) |
391 |
+- $(CC) $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) -lpthread |
392 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread |
393 |
+ |
394 |
+-test_test_h = test/test.h $(htslib_sam_h) |
395 |
++test_test_h = test/test.h |
396 |
+ |
397 |
+ test/merge/test_bam_translate.o: test/merge/test_bam_translate.c config.h bam_sort.o $(test_test_h) |
398 |
+ test/merge/test_rtrans_build.o: test/merge/test_rtrans_build.c config.h bam_sort.o |
399 |
+@@ -256,34 +245,34 @@ |
400 |
+ test/split/test_expand_format_string.o: test/split/test_expand_format_string.c config.h bam_split.o $(test_test_h) |
401 |
+ test/split/test_filter_header_rg.o: test/split/test_filter_header_rg.c config.h bam_split.o $(test_test_h) |
402 |
+ test/split/test_parse_args.o: test/split/test_parse_args.c config.h bam_split.o $(test_test_h) |
403 |
+-test/test.o: test/test.c config.h $(htslib_sam_h) $(test_test_h) |
404 |
+-test/vcf-miniview.o: test/vcf-miniview.c config.h $(htslib_vcf_h) |
405 |
++test/test.o: test/test.c config.h $(test_test_h) |
406 |
++test/vcf-miniview.o: test/vcf-miniview.c config.h |
407 |
+ |
408 |
+ |
409 |
+ # misc programs |
410 |
+ |
411 |
+ misc/ace2sam: misc/ace2sam.o |
412 |
+- $(CC) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS) |
413 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS) |
414 |
+ |
415 |
+ misc/maq2sam-short: misc/maq2sam-short.o |
416 |
+- $(CC) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS) |
417 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS) |
418 |
+ |
419 |
+ misc/maq2sam-long: misc/maq2sam-long.o |
420 |
+- $(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS) |
421 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS) |
422 |
+ |
423 |
+ misc/md5fa: misc/md5fa.o $(HTSLIB) |
424 |
+- $(CC) $(ALL_LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIB) $(ALL_LIBS) |
425 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIBS) $(ALL_LIBS) |
426 |
+ |
427 |
+ misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB) |
428 |
+- $(CC) $(ALL_LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIB) $(ALL_LIBS) |
429 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIBS) $(ALL_LIBS) |
430 |
+ |
431 |
+ misc/wgsim: misc/wgsim.o |
432 |
+- $(CC) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS) |
433 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS) |
434 |
+ |
435 |
+-misc/ace2sam.o: misc/ace2sam.c config.h $(htslib_kstring_h) $(htslib_kseq_h) |
436 |
+-misc/md5fa.o: misc/md5fa.c config.h $(htslib_kseq_h) $(htslib_hts_h) |
437 |
+-misc/md5sum-lite.o: misc/md5sum-lite.c config.h $(htslib_hts_h) |
438 |
+-misc/wgsim.o: misc/wgsim.c config.h $(htslib_kseq_h) |
439 |
++misc/ace2sam.o: misc/ace2sam.c config.h |
440 |
++misc/md5fa.o: misc/md5fa.c config.h |
441 |
++misc/md5sum-lite.o: misc/md5sum-lite.c config.h |
442 |
++misc/wgsim.o: misc/wgsim.c config.h |
443 |
+ |
444 |
+ misc/maq2sam-short.o: misc/maq2sam.c config.h |
445 |
+ $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c |
446 |
|
447 |
diff --git a/sci-biology/samtools/samtools-1.5.ebuild b/sci-biology/samtools/samtools-1.5.ebuild |
448 |
new file mode 100644 |
449 |
index 00000000000..c2bc7ce89cf |
450 |
--- /dev/null |
451 |
+++ b/sci-biology/samtools/samtools-1.5.ebuild |
452 |
@@ -0,0 +1,61 @@ |
453 |
+# Copyright 1999-2017 Gentoo Foundation |
454 |
+# Distributed under the terms of the GNU General Public License v2 |
455 |
+ |
456 |
+EAPI=6 |
457 |
+ |
458 |
+PYTHON_COMPAT=( python2_7 ) |
459 |
+ |
460 |
+inherit autotools python-r1 toolchain-funcs |
461 |
+ |
462 |
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" |
463 |
+HOMEPAGE="http://www.htslib.org/" |
464 |
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" |
465 |
+ |
466 |
+LICENSE="MIT" |
467 |
+SLOT="0" |
468 |
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
469 |
+IUSE="examples" |
470 |
+REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
471 |
+ |
472 |
+RDEPEND=" |
473 |
+ dev-lang/perl |
474 |
+ =sci-libs/htslib-${PV}* |
475 |
+ sys-libs/ncurses:0= |
476 |
+ sys-libs/zlib |
477 |
+ ${PYTHON_DEPS}" |
478 |
+DEPEND="${RDEPEND} |
479 |
+ virtual/pkgconfig" |
480 |
+ |
481 |
+PATCHES=( "${FILESDIR}/${PN}-1.5-buildsystem.patch" ) |
482 |
+ |
483 |
+src_prepare() { |
484 |
+ default |
485 |
+ |
486 |
+ python_setup |
487 |
+ python_fix_shebang misc/varfilter.py |
488 |
+ |
489 |
+ # remove bundled htslib |
490 |
+ rm -r htslib-* || die |
491 |
+ |
492 |
+ eautoreconf |
493 |
+} |
494 |
+ |
495 |
+src_test() { |
496 |
+ local -x LD_LIBRARY_PATH="${S}" |
497 |
+ default |
498 |
+} |
499 |
+ |
500 |
+src_install() { |
501 |
+ default |
502 |
+ |
503 |
+ # install libbam and headers |
504 |
+ dolib.so libbam.so* |
505 |
+ |
506 |
+ insinto /usr/include/bam |
507 |
+ doins *.h |
508 |
+ |
509 |
+ if use examples; then |
510 |
+ dodoc -r examples |
511 |
+ docompress -x /usr/share/doc/${PF}/examples |
512 |
+ fi |
513 |
+} |