Gentoo Archives: gentoo-commits

From: David Seifert <soap@g.o>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/hmmer/files/, sci-biology/hmmer/
Date: Sun, 09 Oct 2016 15:14:46
Message-Id: 1476026058.c0a145c569b658ac97b0addecdee386768d4bb16.soap@gentoo
1 commit: c0a145c569b658ac97b0addecdee386768d4bb16
2 Author: David Seifert <soap <AT> gentoo <DOT> org>
3 AuthorDate: Sun Oct 9 12:44:16 2016 +0000
4 Commit: David Seifert <soap <AT> gentoo <DOT> org>
5 CommitDate: Sun Oct 9 15:14:18 2016 +0000
6 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c0a145c5
7
8 sci-biology/hmmer: Version bump to 3.1_beta2
9
10 * EAPI=6
11 * Make perl shebangs portable
12 * Install headers into 'hmmer3' subdir
13
14 Package-Manager: portage-2.3.1
15
16 sci-biology/hmmer/Manifest | 1 +
17 .../hmmer-3.1_beta2-fix-header-install-path.patch | 89 ++++++
18 .../files/hmmer-3.1_beta2-fix-perl-shebangs.patch | 331 +++++++++++++++++++++
19 sci-biology/hmmer/hmmer-3.1_beta2.ebuild | 49 +++
20 4 files changed, 470 insertions(+)
21
22 diff --git a/sci-biology/hmmer/Manifest b/sci-biology/hmmer/Manifest
23 index 7fef69f..dada007 100644
24 --- a/sci-biology/hmmer/Manifest
25 +++ b/sci-biology/hmmer/Manifest
26 @@ -1,2 +1,3 @@
27 DIST hmmer-2.3.2.tar.gz 1024933 SHA256 d20e1779fcdff34ab4e986ea74a6c4ac5c5f01da2993b14e92c94d2f076828b4 SHA512 5abf9c304de38b183a5beab7a5cfc75c3774ff6e161b7b8e55a0eae9fd156dbb7ed95d216c16d3c585c494bb69e3a9fdfabfb5dc729b7050a4d1be95c74df7d7 WHIRLPOOL 604cc3f532d6eae3fbca893d991d0714a5a897fbac3059d63fdbebc6221e9321c2b444db2700e7068a11c043c0a7f9f3935617a3aa1878ca06ba18c558d55d40
28 DIST hmmer-3.0.tar.gz 3952015 SHA256 6977e6473fcb554b1d5a86dc9edffffa53918c1bd88d7fd20d7499f1ba719e83 SHA512 752f06b0494a87ccd2cf6aa93e622fd02173eaa0df60df0527b3361dcaa2baf2b45a2daf0123217c0029bc9d95e505a92f1e97039eb8b7218b4c4b65ddad1db5 WHIRLPOOL a181ce8ddb016bf1209c83fa754163e9ac653acb51fed13dee8598565d2f058a118fca04229aef7e4e5a79aae86712639b8e43bf7e12c50a8bf22e32be9df658
29 +DIST hmmer-3.1b2.tar.gz 5965253 SHA256 dd16edf4385c1df072c9e2f58c16ee1872d855a018a2ee6894205277017b5536 SHA512 64c8a840cb62160a1c13a20e64f42d297edb7969425d5047eefd8ee9f992d66612d62843523e8f33a2c38568ce1b0a9df23dd1d3ecf6773007f6db12d4cc4771 WHIRLPOOL 0b6d17b5f5efe31873cde93ff33cc5b01c53de8e1daf1ed473ef92d6585f34abcbb31e35e4d02537fbbc2c808131b70a0f51a3832ee332e23246cbc75edc354a
30
31 diff --git a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch
32 new file mode 100644
33 index 00000000..b9ff5b9
34 --- /dev/null
35 +++ b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch
36 @@ -0,0 +1,89 @@
37 +Install headers into 'hmmer3' subdir and not into global includedir.
38 +
39 +--- a/easel/Makefile.in
40 ++++ b/easel/Makefile.in
41 +@@ -465,11 +465,12 @@
42 + ${INSTALL} -d ${DESTDIR}${bindir}
43 + ${INSTALL} -d ${DESTDIR}${libdir}
44 + ${INSTALL} -d ${DESTDIR}${includedir}
45 ++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
46 + ${INSTALL} -m 0644 libeasel.a ${DESTDIR}${libdir}/
47 + for file in ${HDRS}; do\
48 +- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
49 ++ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
50 + done
51 +- ${INSTALL} -m 0644 esl_config.h ${DESTDIR}${includedir}/
52 ++ ${INSTALL} -m 0644 esl_config.h ${DESTDIR}${includedir}/hmmer3/
53 + ${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} install
54 +
55 + # "make uninstall" reverses the steps of "make install"
56 +--- a/Makefile.in
57 ++++ b/Makefile.in
58 +@@ -143,6 +143,7 @@
59 + ${INSTALL} -d ${DESTDIR}${bindir}
60 + ${INSTALL} -d ${DESTDIR}${libdir}
61 + ${INSTALL} -d ${DESTDIR}${includedir}
62 ++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
63 + ${INSTALL} -d ${DESTDIR}${man1dir}
64 + ${INSTALL} -d ${DESTDIR}${pdfdir}
65 + ${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} install
66 +--- a/src/impl_dummy/Makefile.in
67 ++++ b/src/impl_dummy/Makefile.in
68 +@@ -152,8 +152,9 @@
69 + ${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
70 +
71 + install:
72 ++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
73 + for file in ${HDRS}; do \
74 +- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
75 ++ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
76 + done
77 +
78 + uninstall:
79 +--- a/src/impl_sse/Makefile.in
80 ++++ b/src/impl_sse/Makefile.in
81 +@@ -155,8 +155,9 @@
82 +
83 +
84 + install:
85 ++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
86 + for file in ${HDRS}; do \
87 +- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
88 ++ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
89 + done
90 +
91 + uninstall:
92 +--- a/src/impl_vmx/Makefile.in
93 ++++ b/src/impl_vmx/Makefile.in
94 +@@ -152,8 +152,9 @@
95 + ${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
96 +
97 + install:
98 ++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
99 + for file in ${HDRS}; do \
100 +- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
101 ++ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
102 + done
103 +
104 + uninstall:
105 +--- a/src/Makefile.in
106 ++++ b/src/Makefile.in
107 +@@ -322,15 +322,16 @@
108 + ${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
109 +
110 + install:
111 ++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
112 + ${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} install
113 + for file in ${PROGS}; do \
114 + ${INSTALL} -m 0755 $$file ${DESTDIR}${bindir}/ ;\
115 + done
116 + ${INSTALL} -m 0755 libhmmer.a ${DESTDIR}${libdir}/
117 + for file in ${HDRS}; do \
118 +- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
119 ++ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
120 + done
121 +- ${INSTALL} -m 0644 p7_config.h ${DESTDIR}${includedir}/ ;\
122 ++ ${INSTALL} -m 0644 p7_config.h ${DESTDIR}${includedir}/hmmer3/ ;\
123 +
124 + uninstall:
125 + ${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} uninstall
126
127 diff --git a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-perl-shebangs.patch b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-perl-shebangs.patch
128 new file mode 100644
129 index 00000000..39fdbd5
130 --- /dev/null
131 +++ b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-perl-shebangs.patch
132 @@ -0,0 +1,331 @@
133 +Fix perl shebangs to be portable and usable on Prefix.
134 +See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/
135 +
136 +--- a/easel/demotic/infernal_tab2gff.pl
137 ++++ b/easel/demotic/infernal_tab2gff.pl
138 +@@ -1,4 +1,4 @@
139 +-#!/usr/bin/perl -w -I/groups/eddy/home/jonest/Demotic
140 ++#!/usr/bin/env perl
141 +
142 + # TAJ 6/23/08 last mod 7/10/08
143 + # Purpose: flexibly convert "cmsearch --tabfile TAB.out" output to GFF format
144 +--- a/easel/demotic/test.pl
145 ++++ b/easel/demotic/test.pl
146 +@@ -1,4 +1,4 @@
147 +-#! /usr/bin/perl
148 ++#!/usr/bin/env perl
149 +
150 + use demotic_blast;
151 +
152 +--- a/easel/devkit/rmanprocess.pl
153 ++++ b/easel/devkit/rmanprocess.pl
154 +@@ -1,4 +1,4 @@
155 +-#! /usr/bin/perl
156 ++#!/usr/bin/env perl
157 +
158 + # rmanprocess.pl <rman LaTeX2e output>
159 + #
160 +--- a/easel/miniapps/esl-afetch.itest.pl
161 ++++ b/easel/miniapps/esl-afetch.itest.pl
162 +@@ -1,4 +1,4 @@
163 +-#! /usr/bin/perl
164 ++#!/usr/bin/env perl
165 +
166 + # Testing the esl-afetch miniapp
167 + #
168 +--- a/easel/miniapps/esl-alimanip.itest.pl
169 ++++ b/easel/miniapps/esl-alimanip.itest.pl
170 +@@ -1,4 +1,4 @@
171 +-#! /usr/bin/perl
172 ++#!/usr/bin/env perl
173 +
174 + # Integrated test of the esl-alimanip miniapp.
175 + #
176 +--- a/easel/miniapps/esl-alimap.itest.pl
177 ++++ b/easel/miniapps/esl-alimap.itest.pl
178 +@@ -1,4 +1,4 @@
179 +-#! /usr/bin/perl
180 ++#!/usr/bin/env perl
181 +
182 + # Integrated test of the esl-alimap miniapp.
183 + #
184 +--- a/easel/miniapps/esl-alimask.itest.pl
185 ++++ b/easel/miniapps/esl-alimask.itest.pl
186 +@@ -1,4 +1,4 @@
187 +-#! /usr/bin/perl
188 ++#!/usr/bin/env perl
189 +
190 + # Integrated test of esl-alimask miniapp.
191 + #
192 +--- a/easel/miniapps/esl-alimerge.itest.pl
193 ++++ b/easel/miniapps/esl-alimerge.itest.pl
194 +@@ -1,4 +1,4 @@
195 +-#! /usr/bin/perl
196 ++#!/usr/bin/env perl
197 +
198 + # Integrated test of esl-alimerge miniapp.
199 + #
200 +--- a/easel/miniapps/esl-alistat.itest.pl
201 ++++ b/easel/miniapps/esl-alistat.itest.pl
202 +@@ -1,4 +1,4 @@
203 +-#! /usr/bin/perl
204 ++#!/usr/bin/env perl
205 +
206 + # Integrated test of the esl-alistat miniapp.
207 + #
208 +--- a/easel/miniapps/esl-compalign.itest.pl
209 ++++ b/easel/miniapps/esl-compalign.itest.pl
210 +@@ -1,4 +1,4 @@
211 +-#! /usr/bin/perl
212 ++#!/usr/bin/env perl
213 +
214 + # Integrated test of the esl-compalign miniapp.
215 + #
216 +--- a/easel/miniapps/esl-construct.itest.pl
217 ++++ b/easel/miniapps/esl-construct.itest.pl
218 +@@ -1,4 +1,4 @@
219 +-#! /usr/bin/perl
220 ++#!/usr/bin/env perl
221 +
222 + # Integrated test of the esl-construct miniapp.
223 + #
224 +--- a/easel/miniapps/esl-mask.itest.pl
225 ++++ b/easel/miniapps/esl-mask.itest.pl
226 +@@ -1,4 +1,4 @@
227 +-#! /usr/bin/perl
228 ++#!/usr/bin/env perl
229 +
230 + # Integrated test of esl-mask miniapp.
231 + #
232 +--- a/easel/miniapps/esl-seqrange.itest.pl
233 ++++ b/easel/miniapps/esl-seqrange.itest.pl
234 +@@ -1,4 +1,4 @@
235 +-#! /usr/bin/perl
236 ++#!/usr/bin/env perl
237 +
238 + # Integrated test of the esl-seqrange miniapp.
239 + #
240 +--- a/easel/miniapps/esl-shuffle.itest.pl
241 ++++ b/easel/miniapps/esl-shuffle.itest.pl
242 +@@ -1,4 +1,4 @@
243 +-#! /usr/bin/perl
244 ++#!/usr/bin/env perl
245 +
246 + # Integrated test of esl-shuffle miniapp
247 + #
248 +--- a/easel/miniapps/esl-ssdraw.itest.pl
249 ++++ b/easel/miniapps/esl-ssdraw.itest.pl
250 +@@ -1,4 +1,4 @@
251 +-#! /usr/bin/perl
252 ++#!/usr/bin/env perl
253 +
254 + # Integrated test of the esl-ssdraw miniapp.
255 + #
256 +--- a/easel/testsuite/coverage_report.pl
257 ++++ b/easel/testsuite/coverage_report.pl
258 +@@ -1,4 +1,4 @@
259 +-#! /usr/bin/perl
260 ++#!/usr/bin/env perl
261 +
262 + # Measures testsuite coverage (as percentage of source lines),
263 + # using gcov.
264 +--- a/easel/testsuite/driver_report.pl
265 ++++ b/easel/testsuite/driver_report.pl
266 +@@ -1,4 +1,4 @@
267 +-#! /usr/bin/perl
268 ++#!/usr/bin/env perl
269 +
270 + # Make sure that all drivers compile.
271 + # (Eventually, we should also make sure they run! But that
272 +--- a/easel/testsuite/i1-degen-residues.pl
273 ++++ b/easel/testsuite/i1-degen-residues.pl
274 +@@ -1,4 +1,4 @@
275 +-#! /usr/bin/perl
276 ++#!/usr/bin/env perl
277 +
278 + # Integration tests of reading all valid protein sequence residue characters.
279 + #
280 +--- a/easel/testsuite/i2-ncbi-indices.pl
281 ++++ b/easel/testsuite/i2-ncbi-indices.pl
282 +@@ -1,4 +1,4 @@
283 +-#! /usr/bin/perl
284 ++#!/usr/bin/env perl
285 +
286 + # Testing that we can read FASTA files, even if they have NCBI
287 + # formatted BLAST databases in the same directory.
288 +--- a/easel/testsuite/i3-blank-gf.pl
289 ++++ b/easel/testsuite/i3-blank-gf.pl
290 +@@ -1,4 +1,4 @@
291 +-#! /usr/bin/perl
292 ++#!/usr/bin/env perl
293 +
294 + # Bug #e5: blank text line following #=GF <tag> handled improperly.
295 + #
296 +--- a/easel/testsuite/valgrind_report.pl
297 ++++ b/easel/testsuite/valgrind_report.pl
298 +@@ -1,4 +1,4 @@
299 +-#! /usr/bin/perl
300 ++#!/usr/bin/env perl
301 +
302 + # Run the testsuite under Valgrind, to check for memory leakage.
303 + #
304 +--- a/profmark/pmark-master.pl
305 ++++ b/profmark/pmark-master.pl
306 +@@ -1,4 +1,4 @@
307 +-#! /usr/bin/perl -w
308 ++#!/usr/bin/env perl
309 +
310 + # The top level script that runs a pmark benchmark.
311 + #
312 +--- a/profmark/rocplot.pl
313 ++++ b/profmark/rocplot.pl
314 +@@ -1,4 +1,4 @@
315 +-#! /usr/bin/perl
316 ++#!/usr/bin/env perl
317 +
318 + $nsearches = 2809;
319 +
320 +--- a/src/hmmpress.itest.pl
321 ++++ b/src/hmmpress.itest.pl
322 +@@ -1,4 +1,4 @@
323 +-#! /usr/bin/perl
324 ++#!/usr/bin/env perl
325 +
326 + # Integrated test of hmmpress
327 + #
328 +--- a/testsuite/i10-duplicate-names.pl
329 ++++ b/testsuite/i10-duplicate-names.pl
330 +@@ -1,4 +1,4 @@
331 +-#! /usr/bin/perl
332 ++#!/usr/bin/env perl
333 +
334 + # Check that we can deal with profiles and sequences that contain
335 + # duplicate names, both as queries and targets.
336 +--- a/testsuite/i11-hmmalign-mapali.pl
337 ++++ b/testsuite/i11-hmmalign-mapali.pl
338 +@@ -1,4 +1,4 @@
339 +-#! /usr/bin/perl
340 ++#!/usr/bin/env perl
341 +
342 + # Another test of the hmmalign --mapali option, after Elena reports
343 + # bug #h73 in bad interaction of checksum calculation and marking
344 +--- a/testsuite/i12-delete-corruption.pl
345 ++++ b/testsuite/i12-delete-corruption.pl
346 +@@ -1,4 +1,4 @@
347 +-#! /usr/bin/perl
348 ++#!/usr/bin/env perl
349 +
350 + # Bug #h77: hmmalign corrupts column preceding an all-delete column
351 + #
352 +--- a/testsuite/i13-msa-integrity.pl
353 ++++ b/testsuite/i13-msa-integrity.pl
354 +@@ -1,4 +1,4 @@
355 +-#! /usr/bin/perl
356 ++#!/usr/bin/env perl
357 +
358 + # Look for any problems in hmmalign that corrupt the input sequences.
359 + #
360 +--- a/testsuite/i14-hmmemit-consensus.pl
361 ++++ b/testsuite/i14-hmmemit-consensus.pl
362 +@@ -1,4 +1,4 @@
363 +-#! /usr/bin/perl
364 ++#!/usr/bin/env perl
365 +
366 + # Tests hmmemit -c and hmmemit -C consensus-generating options.
367 + #
368 +--- a/testsuite/i15-hmmconvert.pl
369 ++++ b/testsuite/i15-hmmconvert.pl
370 +@@ -1,4 +1,4 @@
371 +-#! /usr/bin/perl
372 ++#!/usr/bin/env perl
373 +
374 + # Bug #h80: hmmconvert can't read H2 Nucleic files
375 + #
376 +--- a/testsuite/i16-build-allins.pl
377 ++++ b/testsuite/i16-build-allins.pl
378 +@@ -1,4 +1,4 @@
379 +-#! /usr/bin/perl
380 ++#!/usr/bin/env perl
381 +
382 + # Bug #h82: hmmbuild corrupts resave alignment on all-insert seq
383 + #
384 +--- a/testsuite/i17-stdin.pl
385 ++++ b/testsuite/i17-stdin.pl
386 +@@ -1,4 +1,4 @@
387 +-#! /usr/bin/perl
388 ++#!/usr/bin/env perl
389 +
390 + # Test that programs accept and reject argument of '-' (for reading
391 + # data from stdin, rather than from files) as they're supposed to.
392 +--- a/testsuite/i18-nhmmer-generic.pl
393 ++++ b/testsuite/i18-nhmmer-generic.pl
394 +@@ -1,4 +1,4 @@
395 +-#! /usr/bin/perl
396 ++#!/usr/bin/env perl
397 +
398 + # Test of hmmbuild/nhmmer as used to build a DNA model, then query a
399 + # a database of long (1MB).
400 +--- a/testsuite/i19-hmmpgmd-ga.pl
401 ++++ b/testsuite/i19-hmmpgmd-ga.pl
402 +@@ -1,4 +1,4 @@
403 +-#! /usr/bin/perl
404 ++#!/usr/bin/env perl
405 +
406 + # Test that hmmpgmd is correctly applying bit score thresholds;
407 + # in this case, the --cut_ga threshold, using an example that
408 +--- a/testsuite/i20-fmindex-core.pl
409 ++++ b/testsuite/i20-fmindex-core.pl
410 +@@ -1,4 +1,4 @@
411 +-#! /usr/bin/perl
412 ++#!/usr/bin/env perl
413 +
414 + # Test of makenhmmerdb and the core fm-index search functionality, using extactmatch
415 + #
416 +--- a/testsuite/i5-hmmbuild-naming.pl
417 ++++ b/testsuite/i5-hmmbuild-naming.pl
418 +@@ -1,4 +1,4 @@
419 +-#! /usr/bin/perl
420 ++#!/usr/bin/env perl
421 +
422 + # Test that HMM naming in hmmbuild works as advertised.
423 + # Written to test for #h50.
424 +--- a/testsuite/i6-hmmalign-mapali.pl
425 ++++ b/testsuite/i6-hmmalign-mapali.pl
426 +@@ -1,4 +1,4 @@
427 +-#! /usr/bin/perl
428 ++#!/usr/bin/env perl
429 +
430 + # Test the hmmalign --mapali option.
431 + #
432 +--- a/testsuite/i7-hmmbuild-fragments.pl
433 ++++ b/testsuite/i7-hmmbuild-fragments.pl
434 +@@ -1,4 +1,4 @@
435 +-#! /usr/bin/perl
436 ++#!/usr/bin/env perl
437 +
438 + # Test the ability of hmmbuild to deal with crappy alignments
439 + # of lots of sequence fragments.
440 +--- a/testsuite/i8-nonresidues.pl
441 ++++ b/testsuite/i8-nonresidues.pl
442 +@@ -1,4 +1,4 @@
443 +-#! /usr/bin/perl
444 ++#!/usr/bin/env perl
445 +
446 + # Regression test of handling a nonresidue '*' character. By design,
447 + # '*' residues score 0 in insert states and N,C,J; and -inf in match
448 +--- a/testsuite/i9-optional-annotation.pl
449 ++++ b/testsuite/i9-optional-annotation.pl
450 +@@ -1,4 +1,4 @@
451 +-#! /usr/bin/perl
452 ++#!/usr/bin/env perl
453 +
454 + # Check that we can deal with HMMs with no optional annotation, in either
455 + # hmmscan or hmmsearch mode.
456 +--- a/testsuite/test-make.pl
457 ++++ b/testsuite/test-make.pl
458 +@@ -1,4 +1,4 @@
459 +-#! /usr/bin/perl -w
460 ++#!/usr/bin/env perl
461 +
462 + # Usage: test-make.pl <builddir> <srcdir> <tmppfx>
463 + #
464
465 diff --git a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild b/sci-biology/hmmer/hmmer-3.1_beta2.ebuild
466 new file mode 100644
467 index 00000000..d893cb3
468 --- /dev/null
469 +++ b/sci-biology/hmmer/hmmer-3.1_beta2.ebuild
470 @@ -0,0 +1,49 @@
471 +# Copyright 1999-2016 Gentoo Foundation
472 +# Distributed under the terms of the GNU General Public License v2
473 +# $Id$
474 +
475 +EAPI=6
476 +
477 +MY_PV="${PV/_beta/b}"
478 +
479 +DESCRIPTION="Sequence analysis using profile hidden Markov models"
480 +HOMEPAGE="http://hmmer.org/"
481 +SRC_URI="http://eddylab.org/software/${PN}3/${MY_PV}/hmmer-${MY_PV}.tar.gz"
482 +
483 +LICENSE="GPL-3"
484 +SLOT="0"
485 +IUSE="altivec cpu_flags_x86_sse gsl mpi test +threads"
486 +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
487 +
488 +RDEPEND="
489 + mpi? ( virtual/mpi )
490 + gsl? ( sci-libs/gsl:= )"
491 +DEPEND="${RDEPEND}
492 + test? ( dev-lang/perl )"
493 +
494 +S="${WORKDIR}/${PN}-${MY_PV}"
495 +PATCHES=(
496 + "${FILESDIR}/${PN}-3.1_beta2-fix-perl-shebangs.patch"
497 + "${FILESDIR}/${PN}-3.1_beta2-fix-header-install-path.patch"
498 +)
499 +
500 +src_configure() {
501 + # make build verbose, bug 429308
502 + export V=1
503 +
504 + econf \
505 + --disable-pic \
506 + $(use_enable altivec vmx) \
507 + $(use_enable cpu_flags_x86_sse sse) \
508 + $(use_enable mpi) \
509 + $(use_enable threads) \
510 + $(use_with gsl)
511 +}
512 +
513 +src_install() {
514 + default
515 + dodoc Userguide.pdf
516 +
517 + insinto /usr/share/${PN}
518 + doins -r tutorial
519 +}