| 1 |
commit: 6d310e83f00757cb9568b49710d8f4eb93ee3840 |
| 2 |
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
| 3 |
AuthorDate: Sun Mar 23 15:47:27 2014 +0000 |
| 4 |
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
| 5 |
CommitDate: Sun Mar 23 15:47:27 2014 +0000 |
| 6 |
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6d310e83 |
| 7 |
|
| 8 |
sci-biology/consed: added versions 21 to 27 |
| 9 |
|
| 10 |
Package-Manager: portage-2.2.7 |
| 11 |
|
| 12 |
--- |
| 13 |
sci-biology/consed/ChangeLog | 21 ++++++++++- |
| 14 |
sci-biology/consed/consed-21.ebuild | 74 +++++++++++++++++++++++++++++++++++++ |
| 15 |
sci-biology/consed/consed-22.ebuild | 74 +++++++++++++++++++++++++++++++++++++ |
| 16 |
sci-biology/consed/consed-23.ebuild | 74 +++++++++++++++++++++++++++++++++++++ |
| 17 |
sci-biology/consed/consed-24.ebuild | 74 +++++++++++++++++++++++++++++++++++++ |
| 18 |
sci-biology/consed/consed-25.ebuild | 74 +++++++++++++++++++++++++++++++++++++ |
| 19 |
sci-biology/consed/consed-26.ebuild | 74 +++++++++++++++++++++++++++++++++++++ |
| 20 |
sci-biology/consed/consed-27.ebuild | 74 +++++++++++++++++++++++++++++++++++++ |
| 21 |
8 files changed, 537 insertions(+), 2 deletions(-) |
| 22 |
|
| 23 |
diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog |
| 24 |
index 9221d45..3ce8ee3 100644 |
| 25 |
--- a/sci-biology/consed/ChangeLog |
| 26 |
+++ b/sci-biology/consed/ChangeLog |
| 27 |
@@ -1,8 +1,25 @@ |
| 28 |
# ChangeLog for sci-biology/consed |
| 29 |
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 |
| 30 |
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 |
| 31 |
# $Header: $ |
| 32 |
|
| 33 |
+*consed-27 (23 Mar 2014) |
| 34 |
+*consed-26 (23 Mar 2014) |
| 35 |
+*consed-25 (23 Mar 2014) |
| 36 |
+*consed-24 (23 Mar 2014) |
| 37 |
+*consed-23 (23 Mar 2014) |
| 38 |
+*consed-22 (23 Mar 2014) |
| 39 |
+*consed-21 (23 Mar 2014) |
| 40 |
+ |
| 41 |
+ 23 Mar 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
| 42 |
+ consed-20-r1.ebuild, +consed-21.ebuild, +consed-22.ebuild, |
| 43 |
+ files/nLine.h.patch, files/nextPhredPipeline.cpp.patch, metadata.xml: |
| 44 |
+ Added versions 21, 22, 23, 24, 25, 26, 27. None of them need the two |
| 45 |
+ patches anymore but all of them need samtools for BAM support. |
| 46 |
+ Compiled with x86_64-pc-linux-gnu-4.3.6. |
| 47 |
+ |
| 48 |
31 Oct 2012; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
| 49 |
consed-20-r1.ebuild: |
| 50 |
- renamed dependency from openmotif to motif consed-20-r1.ebuild |
| 51 |
+ renamed dependency from openmotif to motif consed-20-r1.ebuild, |
| 52 |
+ added some extra patches files/nLine.h.patch, |
| 53 |
+ files/nextPhredPipeline.cpp.patch |
| 54 |
|
| 55 |
|
| 56 |
diff --git a/sci-biology/consed/consed-21.ebuild b/sci-biology/consed/consed-21.ebuild |
| 57 |
new file mode 100644 |
| 58 |
index 0000000..7163d60 |
| 59 |
--- /dev/null |
| 60 |
+++ b/sci-biology/consed/consed-21.ebuild |
| 61 |
@@ -0,0 +1,74 @@ |
| 62 |
+# Copyright 1999-2014 Gentoo Foundation |
| 63 |
+# Distributed under the terms of the GNU General Public License v2 |
| 64 |
+# $Header: $ |
| 65 |
+ |
| 66 |
+EAPI=3 |
| 67 |
+ |
| 68 |
+inherit eutils toolchain-funcs |
| 69 |
+ |
| 70 |
+DESCRIPTION="A genome sequence finishing program" |
| 71 |
+HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html" |
| 72 |
+SRC_URI="${P}-sources.tar.gz |
| 73 |
+ ${P}-linux.tar.gz" |
| 74 |
+ |
| 75 |
+LICENSE="phrap" |
| 76 |
+SLOT="0" |
| 77 |
+KEYWORDS="~amd64 ~x86" |
| 78 |
+IUSE="" |
| 79 |
+ |
| 80 |
+DEPEND=">=x11-libs/motif-2.3:0" |
| 81 |
+RDEPEND="${DEPEND} |
| 82 |
+ sci-biology/samtools |
| 83 |
+ >=sci-biology/phred-000925 |
| 84 |
+ >=sci-biology/phrap-1.080721 |
| 85 |
+ dev-lang/perl" |
| 86 |
+ |
| 87 |
+S="${WORKDIR}" |
| 88 |
+ |
| 89 |
+RESTRICT="fetch" |
| 90 |
+ |
| 91 |
+pkg_nofetch() { |
| 92 |
+ einfo "Please visit ${HOMEPAGE} and obtain the file" |
| 93 |
+ einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" |
| 94 |
+ einfo "and place it in ${DISTDIR}," |
| 95 |
+ einfo "obtain the file" |
| 96 |
+ einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" |
| 97 |
+ einfo "and place it in ${DISTDIR}" |
| 98 |
+} |
| 99 |
+ |
| 100 |
+src_prepare() { |
| 101 |
+ sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die |
| 102 |
+ sed -i \ |
| 103 |
+ -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \ |
| 104 |
+ -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ |
| 105 |
+ -e 's/CFLGS=/CFLGS= ${CFLAGS} /' \ |
| 106 |
+ -e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die |
| 107 |
+ sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die |
| 108 |
+ sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die |
| 109 |
+} |
| 110 |
+ |
| 111 |
+src_compile() { |
| 112 |
+ emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152" |
| 113 |
+ emake -C misc/mktrace || die |
| 114 |
+ emake -C misc/phd2fasta || die |
| 115 |
+ (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die |
| 116 |
+} |
| 117 |
+ |
| 118 |
+src_install() { |
| 119 |
+ dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152" |
| 120 |
+ dobin scripts/* contributions/* || die |
| 121 |
+ insinto /usr/lib/screenLibs |
| 122 |
+ doins misc/*.{fa*,seq} || die |
| 123 |
+ insinto /usr/share/${PN}/examples |
| 124 |
+ doins -r standard polyphred autofinish assembly_view 454_newbler \ |
| 125 |
+ align454reads align454reads_answer solexa_example \ |
| 126 |
+ solexa_example_answer selectRegions selectRegionsAnswer || die |
| 127 |
+ echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed" |
| 128 |
+ doenvd "${S}/99consed" || die |
| 129 |
+ dodoc README.txt *_announcement.txt || die |
| 130 |
+} |
| 131 |
+ |
| 132 |
+pkg_postinst() { |
| 133 |
+ einfo "Package documentation is available at" |
| 134 |
+ einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt" |
| 135 |
+} |
| 136 |
|
| 137 |
diff --git a/sci-biology/consed/consed-22.ebuild b/sci-biology/consed/consed-22.ebuild |
| 138 |
new file mode 100644 |
| 139 |
index 0000000..7163d60 |
| 140 |
--- /dev/null |
| 141 |
+++ b/sci-biology/consed/consed-22.ebuild |
| 142 |
@@ -0,0 +1,74 @@ |
| 143 |
+# Copyright 1999-2014 Gentoo Foundation |
| 144 |
+# Distributed under the terms of the GNU General Public License v2 |
| 145 |
+# $Header: $ |
| 146 |
+ |
| 147 |
+EAPI=3 |
| 148 |
+ |
| 149 |
+inherit eutils toolchain-funcs |
| 150 |
+ |
| 151 |
+DESCRIPTION="A genome sequence finishing program" |
| 152 |
+HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html" |
| 153 |
+SRC_URI="${P}-sources.tar.gz |
| 154 |
+ ${P}-linux.tar.gz" |
| 155 |
+ |
| 156 |
+LICENSE="phrap" |
| 157 |
+SLOT="0" |
| 158 |
+KEYWORDS="~amd64 ~x86" |
| 159 |
+IUSE="" |
| 160 |
+ |
| 161 |
+DEPEND=">=x11-libs/motif-2.3:0" |
| 162 |
+RDEPEND="${DEPEND} |
| 163 |
+ sci-biology/samtools |
| 164 |
+ >=sci-biology/phred-000925 |
| 165 |
+ >=sci-biology/phrap-1.080721 |
| 166 |
+ dev-lang/perl" |
| 167 |
+ |
| 168 |
+S="${WORKDIR}" |
| 169 |
+ |
| 170 |
+RESTRICT="fetch" |
| 171 |
+ |
| 172 |
+pkg_nofetch() { |
| 173 |
+ einfo "Please visit ${HOMEPAGE} and obtain the file" |
| 174 |
+ einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" |
| 175 |
+ einfo "and place it in ${DISTDIR}," |
| 176 |
+ einfo "obtain the file" |
| 177 |
+ einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" |
| 178 |
+ einfo "and place it in ${DISTDIR}" |
| 179 |
+} |
| 180 |
+ |
| 181 |
+src_prepare() { |
| 182 |
+ sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die |
| 183 |
+ sed -i \ |
| 184 |
+ -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \ |
| 185 |
+ -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ |
| 186 |
+ -e 's/CFLGS=/CFLGS= ${CFLAGS} /' \ |
| 187 |
+ -e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die |
| 188 |
+ sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die |
| 189 |
+ sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die |
| 190 |
+} |
| 191 |
+ |
| 192 |
+src_compile() { |
| 193 |
+ emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152" |
| 194 |
+ emake -C misc/mktrace || die |
| 195 |
+ emake -C misc/phd2fasta || die |
| 196 |
+ (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die |
| 197 |
+} |
| 198 |
+ |
| 199 |
+src_install() { |
| 200 |
+ dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152" |
| 201 |
+ dobin scripts/* contributions/* || die |
| 202 |
+ insinto /usr/lib/screenLibs |
| 203 |
+ doins misc/*.{fa*,seq} || die |
| 204 |
+ insinto /usr/share/${PN}/examples |
| 205 |
+ doins -r standard polyphred autofinish assembly_view 454_newbler \ |
| 206 |
+ align454reads align454reads_answer solexa_example \ |
| 207 |
+ solexa_example_answer selectRegions selectRegionsAnswer || die |
| 208 |
+ echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed" |
| 209 |
+ doenvd "${S}/99consed" || die |
| 210 |
+ dodoc README.txt *_announcement.txt || die |
| 211 |
+} |
| 212 |
+ |
| 213 |
+pkg_postinst() { |
| 214 |
+ einfo "Package documentation is available at" |
| 215 |
+ einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt" |
| 216 |
+} |
| 217 |
|
| 218 |
diff --git a/sci-biology/consed/consed-23.ebuild b/sci-biology/consed/consed-23.ebuild |
| 219 |
new file mode 100644 |
| 220 |
index 0000000..7163d60 |
| 221 |
--- /dev/null |
| 222 |
+++ b/sci-biology/consed/consed-23.ebuild |
| 223 |
@@ -0,0 +1,74 @@ |
| 224 |
+# Copyright 1999-2014 Gentoo Foundation |
| 225 |
+# Distributed under the terms of the GNU General Public License v2 |
| 226 |
+# $Header: $ |
| 227 |
+ |
| 228 |
+EAPI=3 |
| 229 |
+ |
| 230 |
+inherit eutils toolchain-funcs |
| 231 |
+ |
| 232 |
+DESCRIPTION="A genome sequence finishing program" |
| 233 |
+HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html" |
| 234 |
+SRC_URI="${P}-sources.tar.gz |
| 235 |
+ ${P}-linux.tar.gz" |
| 236 |
+ |
| 237 |
+LICENSE="phrap" |
| 238 |
+SLOT="0" |
| 239 |
+KEYWORDS="~amd64 ~x86" |
| 240 |
+IUSE="" |
| 241 |
+ |
| 242 |
+DEPEND=">=x11-libs/motif-2.3:0" |
| 243 |
+RDEPEND="${DEPEND} |
| 244 |
+ sci-biology/samtools |
| 245 |
+ >=sci-biology/phred-000925 |
| 246 |
+ >=sci-biology/phrap-1.080721 |
| 247 |
+ dev-lang/perl" |
| 248 |
+ |
| 249 |
+S="${WORKDIR}" |
| 250 |
+ |
| 251 |
+RESTRICT="fetch" |
| 252 |
+ |
| 253 |
+pkg_nofetch() { |
| 254 |
+ einfo "Please visit ${HOMEPAGE} and obtain the file" |
| 255 |
+ einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" |
| 256 |
+ einfo "and place it in ${DISTDIR}," |
| 257 |
+ einfo "obtain the file" |
| 258 |
+ einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" |
| 259 |
+ einfo "and place it in ${DISTDIR}" |
| 260 |
+} |
| 261 |
+ |
| 262 |
+src_prepare() { |
| 263 |
+ sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die |
| 264 |
+ sed -i \ |
| 265 |
+ -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \ |
| 266 |
+ -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ |
| 267 |
+ -e 's/CFLGS=/CFLGS= ${CFLAGS} /' \ |
| 268 |
+ -e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die |
| 269 |
+ sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die |
| 270 |
+ sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die |
| 271 |
+} |
| 272 |
+ |
| 273 |
+src_compile() { |
| 274 |
+ emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152" |
| 275 |
+ emake -C misc/mktrace || die |
| 276 |
+ emake -C misc/phd2fasta || die |
| 277 |
+ (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die |
| 278 |
+} |
| 279 |
+ |
| 280 |
+src_install() { |
| 281 |
+ dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152" |
| 282 |
+ dobin scripts/* contributions/* || die |
| 283 |
+ insinto /usr/lib/screenLibs |
| 284 |
+ doins misc/*.{fa*,seq} || die |
| 285 |
+ insinto /usr/share/${PN}/examples |
| 286 |
+ doins -r standard polyphred autofinish assembly_view 454_newbler \ |
| 287 |
+ align454reads align454reads_answer solexa_example \ |
| 288 |
+ solexa_example_answer selectRegions selectRegionsAnswer || die |
| 289 |
+ echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed" |
| 290 |
+ doenvd "${S}/99consed" || die |
| 291 |
+ dodoc README.txt *_announcement.txt || die |
| 292 |
+} |
| 293 |
+ |
| 294 |
+pkg_postinst() { |
| 295 |
+ einfo "Package documentation is available at" |
| 296 |
+ einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt" |
| 297 |
+} |
| 298 |
|
| 299 |
diff --git a/sci-biology/consed/consed-24.ebuild b/sci-biology/consed/consed-24.ebuild |
| 300 |
new file mode 100644 |
| 301 |
index 0000000..7163d60 |
| 302 |
--- /dev/null |
| 303 |
+++ b/sci-biology/consed/consed-24.ebuild |
| 304 |
@@ -0,0 +1,74 @@ |
| 305 |
+# Copyright 1999-2014 Gentoo Foundation |
| 306 |
+# Distributed under the terms of the GNU General Public License v2 |
| 307 |
+# $Header: $ |
| 308 |
+ |
| 309 |
+EAPI=3 |
| 310 |
+ |
| 311 |
+inherit eutils toolchain-funcs |
| 312 |
+ |
| 313 |
+DESCRIPTION="A genome sequence finishing program" |
| 314 |
+HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html" |
| 315 |
+SRC_URI="${P}-sources.tar.gz |
| 316 |
+ ${P}-linux.tar.gz" |
| 317 |
+ |
| 318 |
+LICENSE="phrap" |
| 319 |
+SLOT="0" |
| 320 |
+KEYWORDS="~amd64 ~x86" |
| 321 |
+IUSE="" |
| 322 |
+ |
| 323 |
+DEPEND=">=x11-libs/motif-2.3:0" |
| 324 |
+RDEPEND="${DEPEND} |
| 325 |
+ sci-biology/samtools |
| 326 |
+ >=sci-biology/phred-000925 |
| 327 |
+ >=sci-biology/phrap-1.080721 |
| 328 |
+ dev-lang/perl" |
| 329 |
+ |
| 330 |
+S="${WORKDIR}" |
| 331 |
+ |
| 332 |
+RESTRICT="fetch" |
| 333 |
+ |
| 334 |
+pkg_nofetch() { |
| 335 |
+ einfo "Please visit ${HOMEPAGE} and obtain the file" |
| 336 |
+ einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" |
| 337 |
+ einfo "and place it in ${DISTDIR}," |
| 338 |
+ einfo "obtain the file" |
| 339 |
+ einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" |
| 340 |
+ einfo "and place it in ${DISTDIR}" |
| 341 |
+} |
| 342 |
+ |
| 343 |
+src_prepare() { |
| 344 |
+ sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die |
| 345 |
+ sed -i \ |
| 346 |
+ -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \ |
| 347 |
+ -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ |
| 348 |
+ -e 's/CFLGS=/CFLGS= ${CFLAGS} /' \ |
| 349 |
+ -e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die |
| 350 |
+ sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die |
| 351 |
+ sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die |
| 352 |
+} |
| 353 |
+ |
| 354 |
+src_compile() { |
| 355 |
+ emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152" |
| 356 |
+ emake -C misc/mktrace || die |
| 357 |
+ emake -C misc/phd2fasta || die |
| 358 |
+ (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die |
| 359 |
+} |
| 360 |
+ |
| 361 |
+src_install() { |
| 362 |
+ dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152" |
| 363 |
+ dobin scripts/* contributions/* || die |
| 364 |
+ insinto /usr/lib/screenLibs |
| 365 |
+ doins misc/*.{fa*,seq} || die |
| 366 |
+ insinto /usr/share/${PN}/examples |
| 367 |
+ doins -r standard polyphred autofinish assembly_view 454_newbler \ |
| 368 |
+ align454reads align454reads_answer solexa_example \ |
| 369 |
+ solexa_example_answer selectRegions selectRegionsAnswer || die |
| 370 |
+ echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed" |
| 371 |
+ doenvd "${S}/99consed" || die |
| 372 |
+ dodoc README.txt *_announcement.txt || die |
| 373 |
+} |
| 374 |
+ |
| 375 |
+pkg_postinst() { |
| 376 |
+ einfo "Package documentation is available at" |
| 377 |
+ einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt" |
| 378 |
+} |
| 379 |
|
| 380 |
diff --git a/sci-biology/consed/consed-25.ebuild b/sci-biology/consed/consed-25.ebuild |
| 381 |
new file mode 100644 |
| 382 |
index 0000000..7163d60 |
| 383 |
--- /dev/null |
| 384 |
+++ b/sci-biology/consed/consed-25.ebuild |
| 385 |
@@ -0,0 +1,74 @@ |
| 386 |
+# Copyright 1999-2014 Gentoo Foundation |
| 387 |
+# Distributed under the terms of the GNU General Public License v2 |
| 388 |
+# $Header: $ |
| 389 |
+ |
| 390 |
+EAPI=3 |
| 391 |
+ |
| 392 |
+inherit eutils toolchain-funcs |
| 393 |
+ |
| 394 |
+DESCRIPTION="A genome sequence finishing program" |
| 395 |
+HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html" |
| 396 |
+SRC_URI="${P}-sources.tar.gz |
| 397 |
+ ${P}-linux.tar.gz" |
| 398 |
+ |
| 399 |
+LICENSE="phrap" |
| 400 |
+SLOT="0" |
| 401 |
+KEYWORDS="~amd64 ~x86" |
| 402 |
+IUSE="" |
| 403 |
+ |
| 404 |
+DEPEND=">=x11-libs/motif-2.3:0" |
| 405 |
+RDEPEND="${DEPEND} |
| 406 |
+ sci-biology/samtools |
| 407 |
+ >=sci-biology/phred-000925 |
| 408 |
+ >=sci-biology/phrap-1.080721 |
| 409 |
+ dev-lang/perl" |
| 410 |
+ |
| 411 |
+S="${WORKDIR}" |
| 412 |
+ |
| 413 |
+RESTRICT="fetch" |
| 414 |
+ |
| 415 |
+pkg_nofetch() { |
| 416 |
+ einfo "Please visit ${HOMEPAGE} and obtain the file" |
| 417 |
+ einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" |
| 418 |
+ einfo "and place it in ${DISTDIR}," |
| 419 |
+ einfo "obtain the file" |
| 420 |
+ einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" |
| 421 |
+ einfo "and place it in ${DISTDIR}" |
| 422 |
+} |
| 423 |
+ |
| 424 |
+src_prepare() { |
| 425 |
+ sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die |
| 426 |
+ sed -i \ |
| 427 |
+ -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \ |
| 428 |
+ -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ |
| 429 |
+ -e 's/CFLGS=/CFLGS= ${CFLAGS} /' \ |
| 430 |
+ -e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die |
| 431 |
+ sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die |
| 432 |
+ sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die |
| 433 |
+} |
| 434 |
+ |
| 435 |
+src_compile() { |
| 436 |
+ emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152" |
| 437 |
+ emake -C misc/mktrace || die |
| 438 |
+ emake -C misc/phd2fasta || die |
| 439 |
+ (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die |
| 440 |
+} |
| 441 |
+ |
| 442 |
+src_install() { |
| 443 |
+ dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152" |
| 444 |
+ dobin scripts/* contributions/* || die |
| 445 |
+ insinto /usr/lib/screenLibs |
| 446 |
+ doins misc/*.{fa*,seq} || die |
| 447 |
+ insinto /usr/share/${PN}/examples |
| 448 |
+ doins -r standard polyphred autofinish assembly_view 454_newbler \ |
| 449 |
+ align454reads align454reads_answer solexa_example \ |
| 450 |
+ solexa_example_answer selectRegions selectRegionsAnswer || die |
| 451 |
+ echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed" |
| 452 |
+ doenvd "${S}/99consed" || die |
| 453 |
+ dodoc README.txt *_announcement.txt || die |
| 454 |
+} |
| 455 |
+ |
| 456 |
+pkg_postinst() { |
| 457 |
+ einfo "Package documentation is available at" |
| 458 |
+ einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt" |
| 459 |
+} |
| 460 |
|
| 461 |
diff --git a/sci-biology/consed/consed-26.ebuild b/sci-biology/consed/consed-26.ebuild |
| 462 |
new file mode 100644 |
| 463 |
index 0000000..7163d60 |
| 464 |
--- /dev/null |
| 465 |
+++ b/sci-biology/consed/consed-26.ebuild |
| 466 |
@@ -0,0 +1,74 @@ |
| 467 |
+# Copyright 1999-2014 Gentoo Foundation |
| 468 |
+# Distributed under the terms of the GNU General Public License v2 |
| 469 |
+# $Header: $ |
| 470 |
+ |
| 471 |
+EAPI=3 |
| 472 |
+ |
| 473 |
+inherit eutils toolchain-funcs |
| 474 |
+ |
| 475 |
+DESCRIPTION="A genome sequence finishing program" |
| 476 |
+HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html" |
| 477 |
+SRC_URI="${P}-sources.tar.gz |
| 478 |
+ ${P}-linux.tar.gz" |
| 479 |
+ |
| 480 |
+LICENSE="phrap" |
| 481 |
+SLOT="0" |
| 482 |
+KEYWORDS="~amd64 ~x86" |
| 483 |
+IUSE="" |
| 484 |
+ |
| 485 |
+DEPEND=">=x11-libs/motif-2.3:0" |
| 486 |
+RDEPEND="${DEPEND} |
| 487 |
+ sci-biology/samtools |
| 488 |
+ >=sci-biology/phred-000925 |
| 489 |
+ >=sci-biology/phrap-1.080721 |
| 490 |
+ dev-lang/perl" |
| 491 |
+ |
| 492 |
+S="${WORKDIR}" |
| 493 |
+ |
| 494 |
+RESTRICT="fetch" |
| 495 |
+ |
| 496 |
+pkg_nofetch() { |
| 497 |
+ einfo "Please visit ${HOMEPAGE} and obtain the file" |
| 498 |
+ einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" |
| 499 |
+ einfo "and place it in ${DISTDIR}," |
| 500 |
+ einfo "obtain the file" |
| 501 |
+ einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" |
| 502 |
+ einfo "and place it in ${DISTDIR}" |
| 503 |
+} |
| 504 |
+ |
| 505 |
+src_prepare() { |
| 506 |
+ sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die |
| 507 |
+ sed -i \ |
| 508 |
+ -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \ |
| 509 |
+ -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ |
| 510 |
+ -e 's/CFLGS=/CFLGS= ${CFLAGS} /' \ |
| 511 |
+ -e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die |
| 512 |
+ sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die |
| 513 |
+ sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die |
| 514 |
+} |
| 515 |
+ |
| 516 |
+src_compile() { |
| 517 |
+ emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152" |
| 518 |
+ emake -C misc/mktrace || die |
| 519 |
+ emake -C misc/phd2fasta || die |
| 520 |
+ (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die |
| 521 |
+} |
| 522 |
+ |
| 523 |
+src_install() { |
| 524 |
+ dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152" |
| 525 |
+ dobin scripts/* contributions/* || die |
| 526 |
+ insinto /usr/lib/screenLibs |
| 527 |
+ doins misc/*.{fa*,seq} || die |
| 528 |
+ insinto /usr/share/${PN}/examples |
| 529 |
+ doins -r standard polyphred autofinish assembly_view 454_newbler \ |
| 530 |
+ align454reads align454reads_answer solexa_example \ |
| 531 |
+ solexa_example_answer selectRegions selectRegionsAnswer || die |
| 532 |
+ echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed" |
| 533 |
+ doenvd "${S}/99consed" || die |
| 534 |
+ dodoc README.txt *_announcement.txt || die |
| 535 |
+} |
| 536 |
+ |
| 537 |
+pkg_postinst() { |
| 538 |
+ einfo "Package documentation is available at" |
| 539 |
+ einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt" |
| 540 |
+} |
| 541 |
|
| 542 |
diff --git a/sci-biology/consed/consed-27.ebuild b/sci-biology/consed/consed-27.ebuild |
| 543 |
new file mode 100644 |
| 544 |
index 0000000..7163d60 |
| 545 |
--- /dev/null |
| 546 |
+++ b/sci-biology/consed/consed-27.ebuild |
| 547 |
@@ -0,0 +1,74 @@ |
| 548 |
+# Copyright 1999-2014 Gentoo Foundation |
| 549 |
+# Distributed under the terms of the GNU General Public License v2 |
| 550 |
+# $Header: $ |
| 551 |
+ |
| 552 |
+EAPI=3 |
| 553 |
+ |
| 554 |
+inherit eutils toolchain-funcs |
| 555 |
+ |
| 556 |
+DESCRIPTION="A genome sequence finishing program" |
| 557 |
+HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html" |
| 558 |
+SRC_URI="${P}-sources.tar.gz |
| 559 |
+ ${P}-linux.tar.gz" |
| 560 |
+ |
| 561 |
+LICENSE="phrap" |
| 562 |
+SLOT="0" |
| 563 |
+KEYWORDS="~amd64 ~x86" |
| 564 |
+IUSE="" |
| 565 |
+ |
| 566 |
+DEPEND=">=x11-libs/motif-2.3:0" |
| 567 |
+RDEPEND="${DEPEND} |
| 568 |
+ sci-biology/samtools |
| 569 |
+ >=sci-biology/phred-000925 |
| 570 |
+ >=sci-biology/phrap-1.080721 |
| 571 |
+ dev-lang/perl" |
| 572 |
+ |
| 573 |
+S="${WORKDIR}" |
| 574 |
+ |
| 575 |
+RESTRICT="fetch" |
| 576 |
+ |
| 577 |
+pkg_nofetch() { |
| 578 |
+ einfo "Please visit ${HOMEPAGE} and obtain the file" |
| 579 |
+ einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" |
| 580 |
+ einfo "and place it in ${DISTDIR}," |
| 581 |
+ einfo "obtain the file" |
| 582 |
+ einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" |
| 583 |
+ einfo "and place it in ${DISTDIR}" |
| 584 |
+} |
| 585 |
+ |
| 586 |
+src_prepare() { |
| 587 |
+ sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die |
| 588 |
+ sed -i \ |
| 589 |
+ -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \ |
| 590 |
+ -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ |
| 591 |
+ -e 's/CFLGS=/CFLGS= ${CFLAGS} /' \ |
| 592 |
+ -e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die |
| 593 |
+ sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die |
| 594 |
+ sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die |
| 595 |
+} |
| 596 |
+ |
| 597 |
+src_compile() { |
| 598 |
+ emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152" |
| 599 |
+ emake -C misc/mktrace || die |
| 600 |
+ emake -C misc/phd2fasta || die |
| 601 |
+ (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die |
| 602 |
+} |
| 603 |
+ |
| 604 |
+src_install() { |
| 605 |
+ dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152" |
| 606 |
+ dobin scripts/* contributions/* || die |
| 607 |
+ insinto /usr/lib/screenLibs |
| 608 |
+ doins misc/*.{fa*,seq} || die |
| 609 |
+ insinto /usr/share/${PN}/examples |
| 610 |
+ doins -r standard polyphred autofinish assembly_view 454_newbler \ |
| 611 |
+ align454reads align454reads_answer solexa_example \ |
| 612 |
+ solexa_example_answer selectRegions selectRegionsAnswer || die |
| 613 |
+ echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed" |
| 614 |
+ doenvd "${S}/99consed" || die |
| 615 |
+ dodoc README.txt *_announcement.txt || die |
| 616 |
+} |
| 617 |
+ |
| 618 |
+pkg_postinst() { |
| 619 |
+ einfo "Package documentation is available at" |
| 620 |
+ einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt" |
| 621 |
+} |
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