1 |
commit: 777780e24faa006c5883307c0dadd31cab8cecd8 |
2 |
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
3 |
AuthorDate: Fri Mar 29 16:24:12 2019 +0000 |
4 |
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
5 |
CommitDate: Fri Mar 29 16:24:12 2019 +0000 |
6 |
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=777780e2 |
7 |
|
8 |
sci-biology/repeatmasker: rewamp configuration code |
9 |
|
10 |
The changes are partly based on https://github.com/gentoo/sci/pull/580 |
11 |
from Michael Schubert but it seems we could figure out the paths |
12 |
to binaries automatically using `which`. |
13 |
|
14 |
Block between the USE options and allow only a single to be enabled, |
15 |
that is what configure requires, otherwise it enters a loop. |
16 |
|
17 |
The hmmer is the default in configure and preferred. |
18 |
|
19 |
Tested with `USE="hmmer -wublast -phrap -rmblast"` and other |
20 |
combinations while only one is allowed. |
21 |
|
22 |
If users have wublast/abblast/rmblast/crossmatch in the PATHS we just |
23 |
pick it. |
24 |
|
25 |
`which` returns a '.' (dot) if a binary was not found, we need to zap it |
26 |
otherwise configure enters a loop. |
27 |
|
28 |
In the end, one can get: |
29 |
|
30 |
Add a Search Engine: |
31 |
1. CrossMatch: [ Configured ] |
32 |
2. RMBlast - NCBI Blast with RepeatMasker extensions: [ Configured ] |
33 |
3. WUBlast/ABBlast (required by DupMasker): [ Un-configured ] |
34 |
4. HMMER3.1 & DFAM: [ Configured, Default ] |
35 |
|
36 |
5. Done |
37 |
|
38 |
properly written into |
39 |
|
40 |
/usr/lib64/perl5/vendor_perl/5.28.0/RepeatMaskerConfig.pm |
41 |
|
42 |
Package-Manager: Portage-2.3.62, Repoman-2.3.12 |
43 |
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz> |
44 |
|
45 |
.../files/repeatmasker-4.0.6__configure.patch | 4 +- |
46 |
sci-biology/repeatmasker/metadata.xml | 6 + |
47 |
.../repeatmasker/repeatmasker-4.0.6-r3.ebuild | 111 ---------------- |
48 |
.../repeatmasker/repeatmasker-4.0.6-r4.ebuild | 142 +++++++++++++++++++++ |
49 |
.../repeatmasker/repeatmasker-4.0.8-r1.ebuild | 111 ---------------- |
50 |
.../repeatmasker/repeatmasker-4.0.8-r2.ebuild | 142 +++++++++++++++++++++ |
51 |
6 files changed, 292 insertions(+), 224 deletions(-) |
52 |
|
53 |
diff --git a/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch b/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch |
54 |
index e4042190f..c1e0cfb55 100644 |
55 |
--- a/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch |
56 |
+++ b/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch |
57 |
@@ -1,5 +1,5 @@ |
58 |
---- configure.ori 2015-11-24 20:56:46.000000000 +0100 |
59 |
-+++ configure 2015-11-24 20:59:58.000000000 +0100 |
60 |
+--- RepeatMasker/configure.ori 2015-11-24 20:56:46.000000000 +0100 |
61 |
++++ RepeatMasker/configure 2015-11-24 20:59:58.000000000 +0100 |
62 |
@@ -253,17 +253,16 @@ |
63 |
close INVERS; |
64 |
} |
65 |
|
66 |
diff --git a/sci-biology/repeatmasker/metadata.xml b/sci-biology/repeatmasker/metadata.xml |
67 |
index 8417d1580..de382fa16 100644 |
68 |
--- a/sci-biology/repeatmasker/metadata.xml |
69 |
+++ b/sci-biology/repeatmasker/metadata.xml |
70 |
@@ -5,4 +5,10 @@ |
71 |
<email>sci-biology@g.o</email> |
72 |
<name>Gentoo Biology Project</name> |
73 |
</maintainer> |
74 |
+ <use> |
75 |
+ <flag name="phrap">Use cross_match search engine as default</flag> |
76 |
+ <flag name="rmblast">Use RM-BLAST search engine as default</flag> |
77 |
+ <flag name="hmmer">Use HMMER search engine as default</flag> |
78 |
+ <flag name="wublast">Use wublast or abblast search engine as default</flag> |
79 |
+ </use> |
80 |
</pkgmetadata> |
81 |
|
82 |
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild |
83 |
deleted file mode 100644 |
84 |
index d41784eb7..000000000 |
85 |
--- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild |
86 |
+++ /dev/null |
87 |
@@ -1,111 +0,0 @@ |
88 |
-# Copyright 1999-2018 Gentoo Authors |
89 |
-# Distributed under the terms of the GNU General Public License v2 |
90 |
- |
91 |
-EAPI=6 |
92 |
- |
93 |
-inherit eutils perl-module |
94 |
- |
95 |
-MY_PV=${PV//\./-} |
96 |
- |
97 |
-DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA" |
98 |
-HOMEPAGE="http://repeatmasker.org/" |
99 |
-SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz" |
100 |
- |
101 |
-LICENSE="OSL-2.1" |
102 |
-SLOT="0" |
103 |
-KEYWORDS="~amd64 ~x86" |
104 |
-IUSE="" |
105 |
- |
106 |
-DEPEND=">=dev-lang/perl-5.8" |
107 |
-RDEPEND=" |
108 |
- dev-perl/Text-Soundex |
109 |
- sci-biology/phrap |
110 |
- <=sci-biology/repeatmasker-libraries-20160829 |
111 |
- sci-biology/rmblast |
112 |
- !sci-biology/trf |
113 |
- >=sci-biology/trf-bin-4.0.4 |
114 |
-" |
115 |
- |
116 |
-S="${WORKDIR}/RepeatMasker" |
117 |
- |
118 |
-PATCHES=( "${FILESDIR}"/"${P}"__configure.patch ) |
119 |
- |
120 |
-src_configure() { |
121 |
- sed \ |
122 |
- -e "s#/usr/bin/which#which#g" \ |
123 |
- -e "s#/usr/bin/perl#perl#g" \ |
124 |
- -i "${S}"/configure || die |
125 |
- perl_set_version |
126 |
- insinto ${VENDOR_LIB} |
127 |
- sed -e "s#/usr/perl5/lib/#${VENDOR_LIB}/#g" -i "${S}"/configure || die |
128 |
- # The below is wrong as it causes: |
129 |
- # Enter path [ /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/work/RepeatMasker ]: |
130 |
- # -- Building monolithic RM database...sh: /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/image///usr/share/repeatmasker/Libraries/RepeatMasker.lib: No such file or directory |
131 |
- # -e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|' |
132 |
- sed -i -e 's/system( "clear" );//' "${S}/configure" || die |
133 |
- mkdir -p "${ED}"/usr/share/repeatmasker/Libraries/ || die |
134 |
- # |
135 |
- # the below files is actually overwritten by buildRMLibFromEMBL.pl so the 'blah' |
136 |
- # item does not get installed |
137 |
- echo ">blah\natgc" > "${ED}"/usr/share/repeatmasker/Libraries/RepeatMasker.lib || die |
138 |
- # below try to define paths to trf, cross_match, rmblast and nhmmer as search tools |
139 |
- echo " |
140 |
-env |
141 |
-${S} |
142 |
-${EPREFIX}/opt/trf/bin |
143 |
-1 |
144 |
-${EPREFIX}/usr/bin |
145 |
-Y |
146 |
-2 |
147 |
-${EPREFIX}/usr/bin |
148 |
-Y |
149 |
-4 |
150 |
-${EPREFIX}/usr/bin |
151 |
-Y |
152 |
-5" | "${S}"/configure || die "configure failed" |
153 |
- sed -i -e "s|use lib $FindBin::RealBin;|use lib ${EPREFIX}/usr/share/${PN}/lib;|" \ |
154 |
- -e "s|.*\(taxonomy.dat\)|${EPREFIX}/usr/share/${PN}/Libraries/\1|" \ |
155 |
- -e "/$REPEATMASKER_DIR/ s|$FindBin::RealBin|${EPREFIX}/usr/share/${PN}|" \ |
156 |
- "${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die |
157 |
-} |
158 |
-# configure failed to 'cp RepeatMaskerConfig.tmpl RepeatMaskerConfig.pm' |
159 |
-# replace also /u1/local/bin/perl with proper Gentoo PATH |
160 |
- |
161 |
-src_install() { |
162 |
- exeinto /usr/share/${PN} |
163 |
- for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do |
164 |
- doexe $i |
165 |
- dosym ../share/${PN}/$i /usr/bin/$i |
166 |
- done |
167 |
- |
168 |
- perl_set_version |
169 |
- insinto "${VENDOR_LIB}" |
170 |
- doins "${S}"/*.pm "${S}"/Libraries/*.pm |
171 |
- # zap the supposedly misplaced RepeatAnnotationData.pm file |
172 |
- rm -r "${S}"/Libraries/*.pm || die |
173 |
- |
174 |
- # if sci-biology/repeatmasker-libraries is installed prevent file collision |
175 |
- # and do NOT install Libraries/RepeatMaskerLib.embl file which contains |
176 |
- # a limited version of the file: 20110419-min |
177 |
- rm -r Libraries/RepeatMaskerLib.embl || die |
178 |
- insinto /usr/share/${PN} |
179 |
- doins -r util Matrices Libraries *.help |
180 |
- keepdir /usr/share/${PN}/Libraries |
181 |
- |
182 |
- dodoc README INSTALL *.help |
183 |
-} |
184 |
- |
185 |
-pkg_postinst(){ |
186 |
- einfo "RepeatMasker provides bundled human repeats database" |
187 |
- einfo "from Dfam-1.0 database www.dfam.org" |
188 |
- einfo "You can configure which search search engine is to be used and" |
189 |
- einfo "PATHs to the search binaries are defined in" |
190 |
- einfo "${EPREFIX}/usr/share/${PN}/lib/RepeatMaskerConfig.pm" |
191 |
- einfo "Supported search engines are:" |
192 |
- optfeature "cross_match" sci-biology/phrap |
193 |
- optfeature "rmblast" sci-biology/rmblast |
194 |
- optfeature "nhmmer" \>=sci-biology/hmmer-3.1 |
195 |
- einfo "abblast/wublast from http://blast.advbiocomp.com/licensing" |
196 |
- einfo "repeatmasker-libraries-20160829 (RepBase 21.12) is the last" |
197 |
- einfo "version compatible with <repeatmasker-4.0.7" |
198 |
-} |
199 |
|
200 |
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r4.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r4.ebuild |
201 |
new file mode 100644 |
202 |
index 000000000..8216bfe7f |
203 |
--- /dev/null |
204 |
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.6-r4.ebuild |
205 |
@@ -0,0 +1,142 @@ |
206 |
+# Copyright 1999-2019 Gentoo Authors |
207 |
+# Distributed under the terms of the GNU General Public License v2 |
208 |
+ |
209 |
+EAPI=6 |
210 |
+ |
211 |
+inherit eutils perl-module |
212 |
+ |
213 |
+MY_PV=${PV//\./-} |
214 |
+ |
215 |
+DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA" |
216 |
+HOMEPAGE="http://repeatmasker.org/" |
217 |
+SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz" |
218 |
+ |
219 |
+LICENSE="OSL-2.1" |
220 |
+SLOT="0" |
221 |
+KEYWORDS="~amd64 ~x86" |
222 |
+IUSE="phrap rmblast hmmer wublast" |
223 |
+# RepeatMaskerConfig.pm says: |
224 |
+# Default search tool can be one of "hmmer", "crossmatch", "wublast", "decypher" or "ncbi". |
225 |
+# Upstream uses "hmmer" as the default. |
226 |
+ |
227 |
+DEPEND=">=dev-lang/perl-5.8" |
228 |
+RDEPEND=" |
229 |
+ <=sci-biology/repeatmasker-libraries-20160829 |
230 |
+ dev-perl/Text-Soundex |
231 |
+ phrap? ( !hmmer? ( !rmblast? ( !wublast? ( sci-biology/phrap ) ) ) ) |
232 |
+ rmblast? ( !hmmer? ( !phrap? ( !wublast? ( sci-biology/rmblast ) ) ) ) |
233 |
+ hmmer? ( !phrap? ( !wublast? ( !rmblast? ( sci-biology/hmmer ) ) ) ) |
234 |
+ !sci-biology/trf |
235 |
+ >=sci-biology/trf-bin-4.0.4 |
236 |
+" |
237 |
+# wublast? ( sci-biology/wublast || sci-biology/abblast ) |
238 |
+# ncbi? ( would that be ncbi-tools++ or ncbi-blast+ ) ??? |
239 |
+ |
240 |
+S="${WORKDIR}/RepeatMasker" |
241 |
+ |
242 |
+PATCHES=( "${FILESDIR}"/"${P}"__configure.patch ) |
243 |
+ |
244 |
+src_configure() { |
245 |
+ sed \ |
246 |
+ -e "s#/usr/bin/which#which#g" \ |
247 |
+ -e "s#/usr/bin/perl#perl#g" \ |
248 |
+ -i "${S}"/configure || die |
249 |
+ perl_set_version |
250 |
+ insinto ${VENDOR_LIB} |
251 |
+ sed -e "s#/usr/perl5/lib/#${VENDOR_LIB}/#g" -i "${S}"/configure || die |
252 |
+ # The below is wrong as it causes: |
253 |
+ # Enter path [ /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/work/RepeatMasker ]: |
254 |
+ # -- Building monolithic RM database...sh: /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/image///usr/share/repeatmasker/Libraries/RepeatMasker.lib: No such file or directory |
255 |
+ # -e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|' |
256 |
+ sed -i -e 's/system( "clear" );//' "${S}/configure" || die |
257 |
+ mkdir -p "${ED}"/usr/share/repeatmasker/Libraries/ || die |
258 |
+ # |
259 |
+ # the below files is actually overwritten by buildRMLibFromEMBL.pl so the 'blah' |
260 |
+ # item does not get installed |
261 |
+ echo ">blah\natgc" > "${ED}"/usr/share/repeatmasker/Libraries/RepeatMasker.lib || die |
262 |
+ # below try to define paths to trf, cross_match, rmblast and nhmmer as search tools |
263 |
+ # |
264 |
+ local my_crossmatch=`which cross_match 2>/dev/null` |
265 |
+ local my_rmblastn=`which rmblastn 2>/dev/null` |
266 |
+ local my_hmmer=`which nhmmscan 2>/dev/null` |
267 |
+ local my_wublast=`which xdformat 2>/dev/null` # actually configure looks for 'setdb' executable |
268 |
+ # configure is inconsistent at first, we must pass even a wrong path for cross_match, rmblastn, hmmer otherwise it enters a loop |
269 |
+ # but, for wublast we must pass in an empty string otherwise it looks for 'setdb' executable in the non-existing directory and enters a loop |
270 |
+ if [ "$my_crossmatch" != '.' ]; then local crossmatchdir=`dirname "$my_crossmatch"` else local crossmatchdir="${EPREFIX}/usr/bin"; fi |
271 |
+ if [ "$my_rmblastn" != '.' ]; then local rmblastdir=`dirname "$my_rmblastn"` else local rmblastdir="${EPREFIX}/usr/bin"; fi |
272 |
+ if [ "$my_hmmer" != '.' ]; then local hmmerdir=`dirname "$my_hmmer"` else local hmmerdir="${EPREFIX}/usr/bin"; fi |
273 |
+ if [ "$my_wublast" != '.' ]; then local wublastdir=`dirname "$my_wublast"` else local wublastdir=""; fi |
274 |
+ echo "crossmatchdir=${crossmatchdir} rmblastdir=${rmblastdir} wublastdir=${wublastdir} hmmerdir=${hmmerdir}" |
275 |
+ # pick the preferred-one |
276 |
+ local CONF=( x env ${S} "${EPREFIX}"/opt/bin ) |
277 |
+ if use phrap; then |
278 |
+ CONF+=( 1 "${crossmatchdir}" Y ) |
279 |
+ else |
280 |
+ CONF+=( 1 "${crossmatchdir}" N ) |
281 |
+ fi |
282 |
+ if use rmblast; then |
283 |
+ CONF+=( 2 "${rmblastdir}" Y ) |
284 |
+ else |
285 |
+ CONF+=( 2 "${rmblastdir}" N ) |
286 |
+ fi |
287 |
+ if use wublast; then |
288 |
+ # no ebuild available but pick anything from PATH |
289 |
+ CONF+=( 3 "${wublastdir}" Y ) |
290 |
+ else |
291 |
+ CONF+=( 3 "${wublastdir}" N ) |
292 |
+ fi |
293 |
+ if use hmmer; then |
294 |
+ CONF+=( 4 "${hmmerdir}" Y ) |
295 |
+ else |
296 |
+ CONF+=( 4 "${hmmerdir}" N ) |
297 |
+ fi |
298 |
+ CONF+=( 5 ) |
299 |
+ echo "Will feed configure with: ${CONF[@]}" |
300 |
+ printf '%s\n' "${CONF[@]}" | "${S}/configure" || die "configure failed" |
301 |
+ |
302 |
+ sed -i -e "/use lib/s|\"\$FindBin::RealBin|\"${EPREFIX}/usr/share/${PN}/lib|" \ |
303 |
+ -e "/use lib/s|\$FindBin::RealBin|\"${EPREFIX}/usr/share/${PN}/lib\"|" \ |
304 |
+ -e "/\$REPEATMASKER_DIR/ s|\$FindBin::RealBin|${EPREFIX}/usr/share/${PN}|" \ |
305 |
+ "${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die |
306 |
+} |
307 |
+ |
308 |
+src_install() { |
309 |
+ exeinto /usr/share/${PN} |
310 |
+ for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do |
311 |
+ doexe $i |
312 |
+ dosym ../share/${PN}/$i /usr/bin/$i |
313 |
+ done |
314 |
+ |
315 |
+ perl_set_version |
316 |
+ insinto "${VENDOR_LIB}" |
317 |
+ doins "${S}"/*.pm "${S}"/Libraries/*.pm |
318 |
+ # zap the supposedly misplaced RepeatAnnotationData.pm file |
319 |
+ rm -r "${S}"/Libraries/*.pm || die |
320 |
+ |
321 |
+ # if sci-biology/repeatmasker-libraries is installed prevent file collision |
322 |
+ # and do NOT install Libraries/RepeatMaskerLib.embl file which contains |
323 |
+ # a limited version of the file: 20110419-min |
324 |
+ rm -r Libraries/RepeatMaskerLib.embl || die |
325 |
+ insinto /usr/share/${PN} |
326 |
+ doins -r util Matrices Libraries *.help |
327 |
+ keepdir /usr/share/${PN}/Libraries |
328 |
+ |
329 |
+ dodoc README INSTALL *.help |
330 |
+} |
331 |
+ |
332 |
+pkg_postinst(){ |
333 |
+ cd "${S}" || die |
334 |
+ einfo "RepeatMasker provides bundled human repeats database from" |
335 |
+ einfo " Dfam-1.0 database www.dfam.org" |
336 |
+ einfo "You can configure which search search engine is to be used and" |
337 |
+ einfo "Current default search engine defined in" |
338 |
+ einfo " ${EPREFIX}${VENDOR_LIB}/RepeatMaskerConfig.pm is:" |
339 |
+ einfo `grep 'DEFAULT_SEARCH_ENGINE =' RepeatMaskerConfig.pm` |
340 |
+ einfo "\nSupported search engines are:" |
341 |
+ optfeature "cross_match" sci-biology/phrap |
342 |
+ optfeature "rmblast" sci-biology/rmblast |
343 |
+ optfeature "nhmmer" \>=sci-biology/hmmer-3.1 |
344 |
+ einfo "abblast/wublast from http://blast.advbiocomp.com/licensing" |
345 |
+ einfo "\nThe repeatmasker-libraries-20160829 (RepBase 21.12) was the last" |
346 |
+ einfo "version compatible with <repeatmasker-4.0.7" |
347 |
+} |
348 |
|
349 |
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.8-r1.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.8-r1.ebuild |
350 |
deleted file mode 100644 |
351 |
index 9b4af2312..000000000 |
352 |
--- a/sci-biology/repeatmasker/repeatmasker-4.0.8-r1.ebuild |
353 |
+++ /dev/null |
354 |
@@ -1,111 +0,0 @@ |
355 |
-# Copyright 1999-2018 Gentoo Authors |
356 |
-# Distributed under the terms of the GNU General Public License v2 |
357 |
- |
358 |
-EAPI=6 |
359 |
- |
360 |
-inherit eutils perl-module |
361 |
- |
362 |
-MY_PV=${PV//\./-} |
363 |
- |
364 |
-DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA" |
365 |
-HOMEPAGE="http://repeatmasker.org/" |
366 |
-SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz" |
367 |
- |
368 |
-LICENSE="OSL-2.1" |
369 |
-SLOT="0" |
370 |
-KEYWORDS="~amd64 ~x86" |
371 |
-IUSE="" |
372 |
- |
373 |
-DEPEND=">=dev-lang/perl-5.8" |
374 |
-RDEPEND=" |
375 |
- dev-perl/Text-Soundex |
376 |
- sci-biology/phrap |
377 |
- >sci-biology/repeatmasker-libraries-20160829 |
378 |
- sci-biology/rmblast |
379 |
- !sci-biology/trf |
380 |
- >=sci-biology/trf-bin-4.0.4 |
381 |
-" |
382 |
- |
383 |
-S="${WORKDIR}/RepeatMasker" |
384 |
- |
385 |
-PATCHES=( "${FILESDIR}"/"${P}"__configure.patch ) |
386 |
- |
387 |
-src_configure() { |
388 |
- sed \ |
389 |
- -e "s#/usr/bin/which#which#g" \ |
390 |
- -e "s#/usr/bin/perl#perl#g" \ |
391 |
- -i "${S}"/configure || die |
392 |
- perl_set_version |
393 |
- insinto ${VENDOR_LIB} |
394 |
- sed -e "s#/usr/perl5/lib/#${VENDOR_LIB}/#g" -i "${S}"/configure || die |
395 |
- # The below is wrong as it causes: |
396 |
- # Enter path [ /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/work/RepeatMasker ]: |
397 |
- # -- Building monolithic RM database...sh: /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/image///usr/share/repeatmasker/Libraries/RepeatMasker.lib: No such file or directory |
398 |
- # -e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|' |
399 |
- sed -i -e 's/system( "clear" );//' "${S}/configure" || die |
400 |
- mkdir -p "${ED}"/usr/share/repeatmasker/Libraries/ || die |
401 |
- # |
402 |
- # the below files is actually overwritten by buildRMLibFromEMBL.pl so the 'blah' |
403 |
- # item does not get installed |
404 |
- echo ">blah\natgc" > "${ED}"/usr/share/repeatmasker/Libraries/RepeatMasker.lib || die |
405 |
- # below try to define paths to trf, cross_match, rmblast and nhmmer as search tools |
406 |
- echo " |
407 |
-env |
408 |
-${S} |
409 |
-${EPREFIX}/opt/trf/bin |
410 |
-1 |
411 |
-${EPREFIX}/usr/bin |
412 |
-Y |
413 |
-2 |
414 |
-${EPREFIX}/usr/bin |
415 |
-Y |
416 |
-4 |
417 |
-${EPREFIX}/usr/bin |
418 |
-Y |
419 |
-5" | "${S}"/configure || die "configure failed" |
420 |
- sed -i -e "s|use lib $FindBin::RealBin;|use lib ${EPREFIX}/usr/share/${PN}/lib;|" \ |
421 |
- -e "s|.*\(taxonomy.dat\)|${EPREFIX}/usr/share/${PN}/Libraries/\1|" \ |
422 |
- -e "/$REPEATMASKER_DIR/ s|$FindBin::RealBin|${EPREFIX}/usr/share/${PN}|" \ |
423 |
- "${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die |
424 |
-} |
425 |
-# configure failed to 'cp RepeatMaskerConfig.tmpl RepeatMaskerConfig.pm' |
426 |
-# replace also /u1/local/bin/perl with proper Gentoo PATH |
427 |
- |
428 |
-src_install() { |
429 |
- exeinto /usr/share/${PN} |
430 |
- for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do |
431 |
- doexe $i |
432 |
- dosym ../share/${PN}/$i /usr/bin/$i |
433 |
- done |
434 |
- |
435 |
- perl_set_version |
436 |
- insinto "${VENDOR_LIB}" |
437 |
- doins "${S}"/*.pm "${S}"/Libraries/*.pm |
438 |
- # zap the supposedly misplaced RepeatAnnotationData.pm file |
439 |
- rm -r "${S}"/Libraries/*.pm || die |
440 |
- |
441 |
- # if sci-biology/repeatmasker-libraries is installed prevent file collision |
442 |
- # and do NOT install Libraries/RepeatMaskerLib.embl file which contains |
443 |
- # a limited version of the file: 20110419-min |
444 |
- rm -r Libraries/RepeatMaskerLib.embl || die |
445 |
- insinto /usr/share/${PN} |
446 |
- doins -r util Matrices Libraries *.help |
447 |
- keepdir /usr/share/${PN}/Libraries |
448 |
- |
449 |
- dodoc README.md INSTALL *.help |
450 |
-} |
451 |
- |
452 |
-pkg_postinst(){ |
453 |
- einfo "RepeatMasker provides bundled human repeats database" |
454 |
- einfo "from Dfam-1.0 database www.dfam.org" |
455 |
- einfo "You can configure which search search engine is to be used and" |
456 |
- einfo "PATHs to the search binaries are defined in" |
457 |
- einfo "${EPREFIX}/usr/share/${PN}/lib/RepeatMaskerConfig.pm" |
458 |
- einfo "Supported search engines are:" |
459 |
- optfeature "cross_match" sci-biology/phrap |
460 |
- optfeature "rmblast" sci-biology/rmblast |
461 |
- optfeature "nhmmer" \>=sci-biology/hmmer-3.1 |
462 |
- einfo "abblast/wublast from http://blast.advbiocomp.com/licensing" |
463 |
- einfo "repeatmasker-libraries-20160829 (RepBase 21.12) was the last" |
464 |
- einfo "version compatible with <repeatmasker-4.0.7" |
465 |
-} |
466 |
|
467 |
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.8-r2.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.8-r2.ebuild |
468 |
new file mode 100644 |
469 |
index 000000000..02700ba2b |
470 |
--- /dev/null |
471 |
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.8-r2.ebuild |
472 |
@@ -0,0 +1,142 @@ |
473 |
+# Copyright 1999-2019 Gentoo Authors |
474 |
+# Distributed under the terms of the GNU General Public License v2 |
475 |
+ |
476 |
+EAPI=6 |
477 |
+ |
478 |
+inherit eutils perl-module |
479 |
+ |
480 |
+MY_PV=${PV//\./-} |
481 |
+ |
482 |
+DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA" |
483 |
+HOMEPAGE="http://repeatmasker.org/" |
484 |
+SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz" |
485 |
+ |
486 |
+LICENSE="OSL-2.1" |
487 |
+SLOT="0" |
488 |
+KEYWORDS="~amd64 ~x86" |
489 |
+IUSE="phrap rmblast hmmer wublast" |
490 |
+# RepeatMaskerConfig.pm says: |
491 |
+# Default search tool can be one of "hmmer", "crossmatch", "wublast", "decypher" or "ncbi". |
492 |
+# Upstream uses "hmmer" as the default. |
493 |
+ |
494 |
+DEPEND=">=dev-lang/perl-5.8" |
495 |
+RDEPEND=" |
496 |
+ >sci-biology/repeatmasker-libraries-20160829 |
497 |
+ dev-perl/Text-Soundex |
498 |
+ phrap? ( !hmmer? ( !rmblast? ( !wublast? ( sci-biology/phrap ) ) ) ) |
499 |
+ rmblast? ( !hmmer? ( !phrap? ( !wublast? ( sci-biology/rmblast ) ) ) ) |
500 |
+ hmmer? ( !phrap? ( !wublast? ( !rmblast? ( sci-biology/hmmer ) ) ) ) |
501 |
+ !sci-biology/trf |
502 |
+ >=sci-biology/trf-bin-4.0.4 |
503 |
+" |
504 |
+# wublast? ( sci-biology/wublast || sci-biology/abblast ) |
505 |
+# ncbi? ( would that be ncbi-tools++ or ncbi-blast+ ) ??? |
506 |
+ |
507 |
+S="${WORKDIR}/RepeatMasker" |
508 |
+ |
509 |
+PATCHES=( "${FILESDIR}"/"${P}"__configure.patch ) |
510 |
+ |
511 |
+src_configure() { |
512 |
+ sed \ |
513 |
+ -e "s#/usr/bin/which#which#g" \ |
514 |
+ -e "s#/usr/bin/perl#perl#g" \ |
515 |
+ -i "${S}"/configure || die |
516 |
+ perl_set_version |
517 |
+ insinto ${VENDOR_LIB} |
518 |
+ sed -e "s#/usr/perl5/lib/#${VENDOR_LIB}/#g" -i "${S}"/configure || die |
519 |
+ # The below is wrong as it causes: |
520 |
+ # Enter path [ /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/work/RepeatMasker ]: |
521 |
+ # -- Building monolithic RM database...sh: /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/image///usr/share/repeatmasker/Libraries/RepeatMasker.lib: No such file or directory |
522 |
+ # -e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|' |
523 |
+ sed -i -e 's/system( "clear" );//' "${S}/configure" || die |
524 |
+ mkdir -p "${ED}"/usr/share/repeatmasker/Libraries/ || die |
525 |
+ # |
526 |
+ # the below files is actually overwritten by buildRMLibFromEMBL.pl so the 'blah' |
527 |
+ # item does not get installed |
528 |
+ echo ">blah\natgc" > "${ED}"/usr/share/repeatmasker/Libraries/RepeatMasker.lib || die |
529 |
+ # below try to define paths to trf, cross_match, rmblast and nhmmer as search tools |
530 |
+ # |
531 |
+ local my_crossmatch=`which cross_match 2>/dev/null` |
532 |
+ local my_rmblastn=`which rmblastn 2>/dev/null` |
533 |
+ local my_hmmer=`which nhmmscan 2>/dev/null` |
534 |
+ local my_wublast=`which xdformat 2>/dev/null` # actually configure looks for 'setdb' executable |
535 |
+ # configure is inconsistent at first, we must pass even a wrong path for cross_match, rmblastn, hmmer otherwise it enters a loop |
536 |
+ # but, for wublast we must pass in an empty string otherwise it looks for 'setdb' executable in the non-existing directory and enters a loop |
537 |
+ if [ "$my_crossmatch" != '.' ]; then local crossmatchdir=`dirname "$my_crossmatch"` else local crossmatchdir="${EPREFIX}/usr/bin"; fi |
538 |
+ if [ "$my_rmblastn" != '.' ]; then local rmblastdir=`dirname "$my_rmblastn"` else local rmblastdir="${EPREFIX}/usr/bin"; fi |
539 |
+ if [ "$my_hmmer" != '.' ]; then local hmmerdir=`dirname "$my_hmmer"` else local hmmerdir="${EPREFIX}/usr/bin"; fi |
540 |
+ if [ "$my_wublast" != '.' ]; then local wublastdir=`dirname "$my_wublast"` else local wublastdir=""; fi |
541 |
+ echo "crossmatchdir=${crossmatchdir} rmblastdir=${rmblastdir} wublastdir=${wublastdir} hmmerdir=${hmmerdir}" |
542 |
+ # pick the preferred-one |
543 |
+ local CONF=( x env ${S} "${EPREFIX}"/opt/bin ) |
544 |
+ if use phrap; then |
545 |
+ CONF+=( 1 "${crossmatchdir}" Y ) |
546 |
+ else |
547 |
+ CONF+=( 1 "${crossmatchdir}" N ) |
548 |
+ fi |
549 |
+ if use rmblast; then |
550 |
+ CONF+=( 2 "${rmblastdir}" Y ) |
551 |
+ else |
552 |
+ CONF+=( 2 "${rmblastdir}" N ) |
553 |
+ fi |
554 |
+ if use wublast; then |
555 |
+ # no ebuild available but pick anything from PATH |
556 |
+ CONF+=( 3 "${wublastdir}" Y ) |
557 |
+ else |
558 |
+ CONF+=( 3 "${wublastdir}" N ) |
559 |
+ fi |
560 |
+ if use hmmer; then |
561 |
+ CONF+=( 4 "${hmmerdir}" Y ) |
562 |
+ else |
563 |
+ CONF+=( 4 "${hmmerdir}" N ) |
564 |
+ fi |
565 |
+ CONF+=( 5 ) |
566 |
+ echo "Will feed configure with: ${CONF[@]}" |
567 |
+ printf '%s\n' "${CONF[@]}" | "${S}/configure" || die "configure failed" |
568 |
+ |
569 |
+ sed -i -e "/use lib/s|\"\$FindBin::RealBin|\"${EPREFIX}/usr/share/${PN}/lib|" \ |
570 |
+ -e "/use lib/s|\$FindBin::RealBin|\"${EPREFIX}/usr/share/${PN}/lib\"|" \ |
571 |
+ -e "/\$REPEATMASKER_DIR/ s|\$FindBin::RealBin|${EPREFIX}/usr/share/${PN}|" \ |
572 |
+ "${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die |
573 |
+} |
574 |
+ |
575 |
+src_install() { |
576 |
+ exeinto /usr/share/${PN} |
577 |
+ for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do |
578 |
+ doexe $i |
579 |
+ dosym ../share/${PN}/$i /usr/bin/$i |
580 |
+ done |
581 |
+ |
582 |
+ perl_set_version |
583 |
+ insinto "${VENDOR_LIB}" |
584 |
+ doins "${S}"/*.pm "${S}"/Libraries/*.pm |
585 |
+ # zap the supposedly misplaced RepeatAnnotationData.pm file |
586 |
+ rm -r "${S}"/Libraries/*.pm || die |
587 |
+ |
588 |
+ # if sci-biology/repeatmasker-libraries is installed prevent file collision |
589 |
+ # and do NOT install Libraries/RepeatMaskerLib.embl file which contains |
590 |
+ # a limited version of the file: 20110419-min |
591 |
+ rm -r Libraries/RepeatMaskerLib.embl || die |
592 |
+ insinto /usr/share/${PN} |
593 |
+ doins -r util Matrices Libraries *.help |
594 |
+ keepdir /usr/share/${PN}/Libraries |
595 |
+ |
596 |
+ dodoc README.md INSTALL *.help |
597 |
+} |
598 |
+ |
599 |
+pkg_postinst(){ |
600 |
+ cd "${S}" || die |
601 |
+ einfo "RepeatMasker provides bundled human repeats database from" |
602 |
+ einfo " Dfam-1.0 database www.dfam.org" |
603 |
+ einfo "You can configure which search search engine is to be used and" |
604 |
+ einfo "Current default search engine defined in" |
605 |
+ einfo " ${EPREFIX}${VENDOR_LIB}/RepeatMaskerConfig.pm is:" |
606 |
+ einfo `grep 'DEFAULT_SEARCH_ENGINE =' RepeatMaskerConfig.pm` |
607 |
+ einfo "\nSupported search engines are:" |
608 |
+ optfeature "cross_match" sci-biology/phrap |
609 |
+ optfeature "rmblast" sci-biology/rmblast |
610 |
+ optfeature "nhmmer" \>=sci-biology/hmmer-3.1 |
611 |
+ einfo "abblast/wublast from http://blast.advbiocomp.com/licensing" |
612 |
+ einfo "\nThe repeatmasker-libraries-20160829 (RepBase 21.12) was the last" |
613 |
+ einfo "version compatible with <repeatmasker-4.0.7" |
614 |
+} |