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| author |   Donnie Berkholz <donnie@supernova.(none)> | 2006-04-17 22:30:24 -0700 |
|---|---|---|
| committer | Donnie Berkholz <donnie@supernova.(none)> | 2006-04-17 22:30:24 -0700 |
| commit | b084e8250f714a5d67587f1d43f40d5774d25643 (patch) | |
| tree | bc819fff34c32bd0c8c4c68df3a846f0b47316ca /sci-biology | |
| download | dberkholz-b084e8250f714a5d67587f1d43f40d5774d25643.tar.gz dberkholz-b084e8250f714a5d67587f1d43f40d5774d25643.tar.bz2 dberkholz-b084e8250f714a5d67587f1d43f40d5774d25643.zip | |
Initial commit of portage overlay.
Diffstat (limited to 'sci-biology')
63 files changed, 1258 insertions, 0 deletions
diff --git a/sci-biology/dialign-t/Manifest b/sci-biology/dialign-t/Manifest new file mode 100644 index 0000000..d5e8930 --- /dev/null +++ b/sci-biology/dialign-t/Manifest @@ -0,0 +1,30 @@ +MD5 745cc89f4cd095bf146de4ba73af1033 dialign-t-0.2.1.ebuild 1031 +RMD160 8ff474cb2eb40316fe7d7ce8da021bfaae507e1d dialign-t-0.2.1.ebuild 1031 +SHA256 20de1a581bf9d370b7dbeea53889f24a930548685607576861422dcc90fb8588 dialign-t-0.2.1.ebuild 1031 +MD5 74eaf8b13786493ed6220c0c33e09b28 files/add-libint-error-message.patch 722 +RMD160 526e57d715b65fedc763069be30f7e49e52dcbb8 files/add-libint-error-message.patch 722 +SHA256 63715cab509893817c7cfb22422c3724fd02a4d0fa5065bbb5a477d8d8a23390 files/add-libint-error-message.patch 722 +MD5 20a9e61f87048ee301d0cb690b890ede files/digest-dialign-t-0.2.1 250 +RMD160 9d920eafc14c5c82bb7f59a0589570c52ce5e292 files/digest-dialign-t-0.2.1 250 +SHA256 13b80f9063a8294da8e20803cd0ab7ac56a38eb1ba5548885f52000103db8795 files/digest-dialign-t-0.2.1 250 +MD5 2ce7fc1feec78dd7428b1bfb6dca6f48 files/digest-muscle-3.6 241 +RMD160 00cdfc0a67940e555cae9b2917a3e59e4a880f44 files/digest-muscle-3.6 241 +SHA256 ff5d1ffa1cd22ba1ee71b8af23f4f92d25ae80f8fa88bf0ed303d0d8c3799cbd files/digest-muscle-3.6 241 +MD5 09ec4c47c33e46e812d1c8a09f00a91a files/digest-probcons-1.10 241 +RMD160 2d5910f5cca5eb03d3d6e7ca83954774d4080051 files/digest-probcons-1.10 241 +SHA256 6dcaf5dcb70c5db87bebfb7d61342cc1f56758d67fc2db674ae900bc685406ef files/digest-probcons-1.10 241 +MD5 dbaa3f7804f89cfbc6b41a8fceeec0ca files/digest-psi-3.2.3 232 +RMD160 36c9c50c4c7e2ef156f0f0334b2b330435968e9b files/digest-psi-3.2.3 232 +SHA256 e9a1506870d5bf1fdfb1aee4740fc584343f0e716afe52c19411d115adf0bc4c files/digest-psi-3.2.3 232 +MD5 285e67094e0841a79a32c9301c023b39 files/dont-build-libint.patch 355 +RMD160 c3b00a7edb9af349f2321fcbbdc286168d5d6db3 files/dont-build-libint.patch 355 +SHA256 57513d9f897776055dfbe14e717761de314e79409def91ccc27563a613a66e18 files/dont-build-libint.patch 355 +MD5 9ec964134fe443be4a6d6760278bea87 files/try-more-compilers.patch 401 +RMD160 550151b01cc4362d70c3e79d250a2fb2e36af64f files/try-more-compilers.patch 401 +SHA256 cb3b404ad7725700840df7602686d651f38f3d7623857af63e3556d1317aaf08 files/try-more-compilers.patch 401 +MD5 f73030c473338710e13e3dfe3ce59463 files/try-pthread-for-blas-lapack.patch 1489 +RMD160 092e0613b7184b065bb5ffa2288ce342e84d9483 files/try-pthread-for-blas-lapack.patch 1489 +SHA256 09cf2f5bc6835697322501280de3027b932416dd939d04d0d25a9790fe02eaa5 files/try-pthread-for-blas-lapack.patch 1489 +MD5 6dc1efc685dfc6994c972eed20daf18c files/use-external-libint.patch 1359 +RMD160 560598e6d7c99d901d97dd6037480bd57c82433f files/use-external-libint.patch 1359 +SHA256 41faa20ba804e98a81cb6809c789c643fd17458b6f6bc95dbe6311dd2fb16713 files/use-external-libint.patch 1359 diff --git a/sci-biology/dialign-t/dialign-t-0.2.1.ebuild b/sci-biology/dialign-t/dialign-t-0.2.1.ebuild new file mode 100644 index 0000000..030d26c --- /dev/null +++ b/sci-biology/dialign-t/dialign-t-0.2.1.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/app-misc/colordiff/colordiff-1.0.5-r2.ebuild,v 1.7 2005/08/17 18:08:02 grobian Exp $ + +inherit multilib toolchain-funcs + +MY_P="DIALIGN-T_${PV}" +DESCRIPTION="An improved algorithm for segment-based multiple sequence alignment" +HOMEPAGE="http://dialign-t.gobics.de/" +SRC_URI="http://dialign-t.gobics.de/${MY_P}.tar.gz" +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~x86" +IUSE="" +RDEPEND="" +DEPEND="${RDEPEND}" +S="${WORKDIR}/${MY_P}" + +src_compile() { + cd ${S}/source + emake clean + emake \ + CPPFLAGS="${CFLAGS}" \ + || die "make failed" +# GPP="$(tc-getCXX)" \ +} + +src_install() { + DESTTREE="/usr" dobin ${S}/source/dialign-t + dohtml ${S}/doc/html/* + dodoc ${S}/doc/user_guide* + insinto /usr/$(get_libdir)/${PN}/conf + doins ${S}/conf/* +} + +pkg_postinst() { + ewarn "The configuration directory is" + ewarn "${ROOT}usr/$(get_libdir)/${PN}/conf" + ewarn "You will need to pass this to ${PN} on every run." +} diff --git a/sci-biology/dialign-t/files/add-libint-error-message.patch b/sci-biology/dialign-t/files/add-libint-error-message.patch new file mode 100644 index 0000000..60fb128 --- /dev/null +++ b/sci-biology/dialign-t/files/add-libint-error-message.patch @@ -0,0 +1,24 @@ +--- psi3.orig/src/lib/libint/Makefile.in 2003-11-23 11:07:51.000000000 -0800 ++++ psi3/src/lib/libint/Makefile.in 2006-02-10 22:38:37.000000000 -0800 +@@ -44,7 +44,10 @@ + $(MAKE) top_objdir=$(top_objdir_path); \ + rm -f Makefile; \ + if ! ./$(BUILD_BINARY); then \ +- cd ..; rm -fR $(TEMP_DIR); exit 1; \ ++ cd ..; \ ++ rm -fR $(TEMP_DIR); \ ++ echo "$(BUILD_BINARY) does not exist!"; \ ++ exit 1; \ + fi; \ + cp Makefile.libint Makefile; \ + ${MAKE} top_objdir=$(top_objdir_path); \ +@@ -65,7 +68,9 @@ + $(MKDIRS) $(libdir) + $(INSTALL_DATA) $< $(libdir) + $(RANLIB) $(libdir)/`basename $(TARGET)` ++ echo Finished ranlib + $(MKDIRS) $(incdir)/libint ++ echo Finished mkdirs + $(INSTALL_INCLUDE) $(TARGET_HEADERS) $(incdir)/libint + + # diff --git a/sci-biology/dialign-t/files/digest-dialign-t-0.2.1 b/sci-biology/dialign-t/files/digest-dialign-t-0.2.1 new file mode 100644 index 0000000..fd423eb --- /dev/null +++ b/sci-biology/dialign-t/files/digest-dialign-t-0.2.1 @@ -0,0 +1,3 @@ +MD5 d1d4fc381a009c68387e159b78b33801 DIALIGN-T_0.2.1.tar.gz 1635888 +RMD160 a43807668354120b873cad0120a7691b6860ca28 DIALIGN-T_0.2.1.tar.gz 1635888 +SHA256 2249bf9007588e891525b4edc085285f1390c2bf8d42ce327aa9217130d7e930 DIALIGN-T_0.2.1.tar.gz 1635888 diff --git a/sci-biology/dialign-t/files/digest-muscle-3.6 b/sci-biology/dialign-t/files/digest-muscle-3.6 new file mode 100644 index 0000000..343f62a --- /dev/null +++ b/sci-biology/dialign-t/files/digest-muscle-3.6 @@ -0,0 +1,3 @@ +MD5 e721d0859da9feec3cedeb42dcee9f59 muscle3.6_src.tar.gz 185267 +RMD160 4afda92b982ec2b05853a582479c61a7d8814f51 muscle3.6_src.tar.gz 185267 +SHA256 32b818a51f421e1d687f513dc31374a330470950151a5e7df961e64781699431 muscle3.6_src.tar.gz 185267 diff --git a/sci-biology/dialign-t/files/digest-probcons-1.10 b/sci-biology/dialign-t/files/digest-probcons-1.10 new file mode 100644 index 0000000..e49b293 --- /dev/null +++ b/sci-biology/dialign-t/files/digest-probcons-1.10 @@ -0,0 +1,3 @@ +MD5 c7938b95732a85c35225bafd4b5b174f probcons_v1_10.tar.gz 43004 +RMD160 ba7caa3cadd702c3dc00c20f01bfb22416435784 probcons_v1_10.tar.gz 43004 +SHA256 f7a775ac4ba3b3261c0bbe5d2c203c96fc2551e67448aefbac83b461c931b518 probcons_v1_10.tar.gz 43004 diff --git a/sci-biology/dialign-t/files/digest-psi-3.2.3 b/sci-biology/dialign-t/files/digest-psi-3.2.3 new file mode 100644 index 0000000..00ee001 --- /dev/null +++ b/sci-biology/dialign-t/files/digest-psi-3.2.3 @@ -0,0 +1,3 @@ +MD5 d304c9510fda1751a988b1e4f619e141 psi-3.2.3.tar.gz 2694286 +RMD160 19bc9a80380193fb3e6d6166f7aa8c98a0415222 psi-3.2.3.tar.gz 2694286 +SHA256 b966c33a82a930b90c1102ade52b7074dd50a9f70a3781d2408436fee68131be psi-3.2.3.tar.gz 2694286 diff --git a/sci-biology/dialign-t/files/dont-build-libint.patch b/sci-biology/dialign-t/files/dont-build-libint.patch new file mode 100644 index 0000000..1ad5ce7 --- /dev/null +++ b/sci-biology/dialign-t/files/dont-build-libint.patch @@ -0,0 +1,11 @@ +--- psi3.orig/src/lib/Makefile.in 2004-01-19 09:09:53.000000000 -0800 ++++ psi3/src/lib/Makefile.in 2006-02-10 21:35:20.000000000 -0800 +@@ -2,7 +2,7 @@ + .PHONY: default all install depend clean targetclean + + subdirs = libipv1 libciomr libchkpt libqt libpsio libiwl libdpd \ +- libint libderiv libr12 libbasis ++ libbasis + + all: default + diff --git a/sci-biology/dialign-t/files/try-more-compilers.patch b/sci-biology/dialign-t/files/try-more-compilers.patch new file mode 100644 index 0000000..63d4618 --- /dev/null +++ b/sci-biology/dialign-t/files/try-more-compilers.patch @@ -0,0 +1,15 @@ +--- psi3.orig/configure.in 2005-10-29 10:15:06.000000000 -0700 ++++ psi3/configure.in 2006-02-10 20:56:59.000000000 -0800 +@@ -104,9 +104,9 @@ + ###################### + + # potential names of compilers +-FC_LIST="g77 f77 fc f2c" +-CC_LIST="gcc cc" +-CXX_LIST="g++ c++ cxx" ++FC_LIST="gfortran g77 f77 fc f2c ifc" ++CC_LIST="gcc cc icc" ++CXX_LIST="g++ c++ cxx icc" + + # set up os specific options + case $os in diff --git a/sci-biology/dialign-t/files/try-pthread-for-blas-lapack.patch b/sci-biology/dialign-t/files/try-pthread-for-blas-lapack.patch new file mode 100644 index 0000000..d9b01ed --- /dev/null +++ b/sci-biology/dialign-t/files/try-pthread-for-blas-lapack.patch @@ -0,0 +1,50 @@ +--- psi3.orig/configure.in 2005-10-29 10:15:06.000000000 -0700 ++++ psi3/configure.in 2006-02-10 20:56:59.000000000 -0800 +@@ -333,7 +333,7 @@ + AC_ARG_WITH(blas,[ --with-blas which blas library to use],[ + case $withval in + yes) +- BLAS='-lblas' ++ BLAS='-lblas -lpthread' + ;; + no) + BLAS='' +@@ -344,16 +344,16 @@ + esac + ]) + if test "X$BLAS" = X; then +- AC_CHECK_LIB(essl, DGEMM, BLAS="-lessl") ++ AC_CHECK_LIB(essl, DGEMM, BLAS="-lessl -lpthread",, [-lpthread]) + fi + if test "X$BLAS" = X; then +- AC_CHECK_LIB(scs, DGEMM, BLAS="-lscs") ++ AC_CHECK_LIB(scs, DGEMM, BLAS="-lscs -lpthread",, [-lpthread]) + fi + if test "X$BLAS" = X; then +- AC_CHECK_LIB(atlas, DGEMM, BLAS="-latlas") ++ AC_CHECK_LIB(atlas, DGEMM, BLAS="-latlas -lpthread",, [-lpthread]) + fi + if test "X$BLAS" = X; then +- AC_CHECK_LIB(blas, DGEMM, BLAS="-lblas") ++ AC_CHECK_LIB(blas, DGEMM, BLAS="-lblas -lpthread",, [-lpthread]) + fi + if test "X$BLAS" = X; then + AC_MSG_ERROR("Did not find a BLAS library") +@@ -363,7 +363,7 @@ + AC_ARG_WITH(lapack,[ --with-lapack which lapack library to use],[ + case $withval in + yes) +- LAPACK='-llapack' ++ LAPACK='-llapack -lpthread' + ;; + no) + LAPACK='' +@@ -382,7 +382,7 @@ + LIBS=$CURRENT_LIBS + fi + if test "X$LAPACK" = X; then +- AC_CHECK_LIB(lapack,DGEEV, LAPACK="-llapack",,$BLAS) ++ AC_CHECK_LIB(lapack,DGEEV, LAPACK="-llapack",,$BLAS -lpthread) + fi + if test "X$LAPACK" = X; then + AC_MSG_ERROR("Did not find a LAPACK library") diff --git a/sci-biology/dialign-t/files/use-external-libint.patch b/sci-biology/dialign-t/files/use-external-libint.patch new file mode 100644 index 0000000..1d9ce91 --- /dev/null +++ b/sci-biology/dialign-t/files/use-external-libint.patch @@ -0,0 +1,37 @@ +--- psi3.orig/src/bin/cints/Makefile.in 2003-11-14 08:15:19.000000000 -0800 ++++ psi3/src/bin/cints/Makefile.in 2006-02-10 22:42:31.000000000 -0800 +@@ -51,25 +51,25 @@ + # and form the list of the libraries. Remember that libderiv and libr12 + # depend on libint, and hence need to come first for GNU ld to work. + # +-INTLIBS := -lPSI_int ++INTLIBS := -lint + ifeq ($(findstring MP2R12,$(SUBDIRS)),MP2R12) +- ifneq ($(findstring -lPSI_r12,$(INTLIBS)),-lPSI_r12) +- INTLIBS := -lPSI_r12 $(INTLIBS) ++ ifneq ($(findstring -lr12,$(INTLIBS)),-lr12) ++ INTLIBS := -lr12 $(INTLIBS) + endif + endif + ifeq ($(findstring R12_Ints,$(SUBDIRS)),R12_Ints) +- ifneq ($(findstring -lPSI_r12,$(INTLIBS)),-lPSI_r12) +- INTLIBS := -lPSI_r12 $(INTLIBS) ++ ifneq ($(findstring -lr12,$(INTLIBS)),-lr12) ++ INTLIBS := -lr12 $(INTLIBS) + endif + endif + ifeq ($(findstring Default_Deriv1,$(SUBDIRS)),Default_Deriv1) +- ifneq ($(findstring -lPSI_deriv,$(INTLIBS)),-lPSI_deriv) +- INTLIBS := -lPSI_deriv $(INTLIBS) ++ ifneq ($(findstring -lderiv,$(INTLIBS)),-lderiv) ++ INTLIBS := -lderiv $(INTLIBS) + endif + endif + ifeq ($(findstring Default_Deriv2,$(SUBDIRS)),Default_Deriv2) +- ifneq ($(findstring -lderiv,$(INTLIBS)),-lPSI_deriv) +- INTLIBS := -lPSI_deriv $(INTLIBS) ++ ifneq ($(findstring -lderiv,$(INTLIBS)),-lderiv) ++ INTLIBS := -lderiv $(INTLIBS) + endif + endif + diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest new file mode 100644 index 0000000..714249b --- /dev/null +++ b/sci-biology/mafft/Manifest @@ -0,0 +1,6 @@ +MD5 07b166f139b73bd2ba25c8f119cfe52f files/digest-mafft-5.743 238 +RMD160 ee341224a6bba70ba4a5b9f7bde8159da6558f52 files/digest-mafft-5.743 238 +SHA256 2312e734a20b01c8518b6dff6e64c2bf92741556abf1c9f682e9ba49a8fc8aeb files/digest-mafft-5.743 238 +MD5 917c58e30c222694b9e31c76856029cb mafft-5.743.ebuild 751 +RMD160 2588c05996fcaad479831387d1a660425a174591 mafft-5.743.ebuild 751 +SHA256 fcac32dc8f7bf8b6b51ebaf4c3b7702e0241ddd04cdc0b9bed76c6ed4176d0a1 mafft-5.743.ebuild 751 diff --git a/sci-biology/mafft/files/digest-mafft-5.743 b/sci-biology/mafft/files/digest-mafft-5.743 new file mode 100644 index 0000000..e84fa31 --- /dev/null +++ b/sci-biology/mafft/files/digest-mafft-5.743 @@ -0,0 +1,3 @@ +MD5 6a4a55ad0d289c98b04c79ccf737a9f8 mafft-5.743-src.tgz 280226 +RMD160 9db53c99ba08eb52c644fcbb0e9ac56c74b98fde mafft-5.743-src.tgz 280226 +SHA256 7bf0d450fea1d44fafee27c29c74b3ae4247ad0075b41729d9dc935e2a88de66 mafft-5.743-src.tgz 280226 diff --git a/sci-biology/mafft/mafft-5.743.ebuild b/sci-biology/mafft/mafft-5.743.ebuild new file mode 100644 index 0000000..b109b60 --- /dev/null +++ b/sci-biology/mafft/mafft-5.743.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/app-misc/colordiff/colordiff-1.0.5-r2.ebuild,v 1.7 2005/08/17 18:08:02 grobian Exp $ + +inherit toolchain-funcs + +DESCRIPTION="Multiple sequence alignments using a variety of algorithms" +HOMEPAGE="http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/" +SRC_URI="http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/${P}-src.tgz" +LICENSE="free-noncomm" +SLOT="0" +KEYWORDS="~x86" +IUSE="" +RDEPEND="" +DEPEND="${RDEPEND}" + +src_compile() { + cd src + emake \ + CC="$(tc-getCC)" \ + CFLAG="${CFLAGS}" \ + || die "make failed" +} + +src_install() { + exeinto /usr/bin + doexe scripts/* binaries/* + dodoc readme +} diff --git a/sci-biology/muscle/Manifest b/sci-biology/muscle/Manifest new file mode 100644 index 0000000..172eb1a --- /dev/null +++ b/sci-biology/muscle/Manifest @@ -0,0 +1,27 @@ +MD5 74eaf8b13786493ed6220c0c33e09b28 files/add-libint-error-message.patch 722 +RMD160 526e57d715b65fedc763069be30f7e49e52dcbb8 files/add-libint-error-message.patch 722 +SHA256 63715cab509893817c7cfb22422c3724fd02a4d0fa5065bbb5a477d8d8a23390 files/add-libint-error-message.patch 722 +MD5 2ce7fc1feec78dd7428b1bfb6dca6f48 files/digest-muscle-3.6 241 +RMD160 00cdfc0a67940e555cae9b2917a3e59e4a880f44 files/digest-muscle-3.6 241 +SHA256 ff5d1ffa1cd22ba1ee71b8af23f4f92d25ae80f8fa88bf0ed303d0d8c3799cbd files/digest-muscle-3.6 241 +MD5 09ec4c47c33e46e812d1c8a09f00a91a files/digest-probcons-1.10 241 +RMD160 2d5910f5cca5eb03d3d6e7ca83954774d4080051 files/digest-probcons-1.10 241 +SHA256 6dcaf5dcb70c5db87bebfb7d61342cc1f56758d67fc2db674ae900bc685406ef files/digest-probcons-1.10 241 +MD5 dbaa3f7804f89cfbc6b41a8fceeec0ca files/digest-psi-3.2.3 232 +RMD160 36c9c50c4c7e2ef156f0f0334b2b330435968e9b files/digest-psi-3.2.3 232 +SHA256 e9a1506870d5bf1fdfb1aee4740fc584343f0e716afe52c19411d115adf0bc4c files/digest-psi-3.2.3 232 +MD5 285e67094e0841a79a32c9301c023b39 files/dont-build-libint.patch 355 +RMD160 c3b00a7edb9af349f2321fcbbdc286168d5d6db3 files/dont-build-libint.patch 355 +SHA256 57513d9f897776055dfbe14e717761de314e79409def91ccc27563a613a66e18 files/dont-build-libint.patch 355 +MD5 9ec964134fe443be4a6d6760278bea87 files/try-more-compilers.patch 401 +RMD160 550151b01cc4362d70c3e79d250a2fb2e36af64f files/try-more-compilers.patch 401 +SHA256 cb3b404ad7725700840df7602686d651f38f3d7623857af63e3556d1317aaf08 files/try-more-compilers.patch 401 +MD5 f73030c473338710e13e3dfe3ce59463 files/try-pthread-for-blas-lapack.patch 1489 +RMD160 092e0613b7184b065bb5ffa2288ce342e84d9483 files/try-pthread-for-blas-lapack.patch 1489 +SHA256 09cf2f5bc6835697322501280de3027b932416dd939d04d0d25a9790fe02eaa5 files/try-pthread-for-blas-lapack.patch 1489 +MD5 6dc1efc685dfc6994c972eed20daf18c files/use-external-libint.patch 1359 +RMD160 560598e6d7c99d901d97dd6037480bd57c82433f files/use-external-libint.patch 1359 +SHA256 41faa20ba804e98a81cb6809c789c643fd17458b6f6bc95dbe6311dd2fb16713 files/use-external-libint.patch 1359 +MD5 5d75567eec90190cf000570cfd16c228 muscle-3.6.ebuild 813 +RMD160 7643cca1df0e58199700e15b87ac081d5b1f72b8 muscle-3.6.ebuild 813 +SHA256 8776ce3cc6abdfe998619b6be801e55f039ecfefef34f2fbe24ce6ba736812da muscle-3.6.ebuild 813 diff --git a/sci-biology/muscle/files/add-libint-error-message.patch b/sci-biology/muscle/files/add-libint-error-message.patch new file mode 100644 index 0000000..60fb128 --- /dev/null +++ b/sci-biology/muscle/files/add-libint-error-message.patch @@ -0,0 +1,24 @@ +--- psi3.orig/src/lib/libint/Makefile.in 2003-11-23 11:07:51.000000000 -0800 ++++ psi3/src/lib/libint/Makefile.in 2006-02-10 22:38:37.000000000 -0800 +@@ -44,7 +44,10 @@ + $(MAKE) top_objdir=$(top_objdir_path); \ + rm -f Makefile; \ + if ! ./$(BUILD_BINARY); then \ +- cd ..; rm -fR $(TEMP_DIR); exit 1; \ ++ cd ..; \ ++ rm -fR $(TEMP_DIR); \ ++ echo "$(BUILD_BINARY) does not exist!"; \ ++ exit 1; \ + fi; \ + cp Makefile.libint Makefile; \ + ${MAKE} top_objdir=$(top_objdir_path); \ +@@ -65,7 +68,9 @@ + $(MKDIRS) $(libdir) + $(INSTALL_DATA) $< $(libdir) + $(RANLIB) $(libdir)/`basename $(TARGET)` ++ echo Finished ranlib + $(MKDIRS) $(incdir)/libint ++ echo Finished mkdirs + $(INSTALL_INCLUDE) $(TARGET_HEADERS) $(incdir)/libint + + # diff --git a/sci-biology/muscle/files/digest-muscle-3.6 b/sci-biology/muscle/files/digest-muscle-3.6 new file mode 100644 index 0000000..343f62a --- /dev/null +++ b/sci-biology/muscle/files/digest-muscle-3.6 @@ -0,0 +1,3 @@ +MD5 e721d0859da9feec3cedeb42dcee9f59 muscle3.6_src.tar.gz 185267 +RMD160 4afda92b982ec2b05853a582479c61a7d8814f51 muscle3.6_src.tar.gz 185267 +SHA256 32b818a51f421e1d687f513dc31374a330470950151a5e7df961e64781699431 muscle3.6_src.tar.gz 185267 diff --git a/sci-biology/muscle/files/digest-probcons-1.10 b/sci-biology/muscle/files/digest-probcons-1.10 new file mode 100644 index 0000000..e49b293 --- /dev/null +++ b/sci-biology/muscle/files/digest-probcons-1.10 @@ -0,0 +1,3 @@ +MD5 c7938b95732a85c35225bafd4b5b174f probcons_v1_10.tar.gz 43004 +RMD160 ba7caa3cadd702c3dc00c20f01bfb22416435784 probcons_v1_10.tar.gz 43004 +SHA256 f7a775ac4ba3b3261c0bbe5d2c203c96fc2551e67448aefbac83b461c931b518 probcons_v1_10.tar.gz 43004 diff --git a/sci-biology/muscle/files/digest-psi-3.2.3 b/sci-biology/muscle/files/digest-psi-3.2.3 new file mode 100644 index 0000000..00ee001 --- /dev/null +++ b/sci-biology/muscle/files/digest-psi-3.2.3 @@ -0,0 +1,3 @@ +MD5 d304c9510fda1751a988b1e4f619e141 psi-3.2.3.tar.gz 2694286 +RMD160 19bc9a80380193fb3e6d6166f7aa8c98a0415222 psi-3.2.3.tar.gz 2694286 +SHA256 b966c33a82a930b90c1102ade52b7074dd50a9f70a3781d2408436fee68131be psi-3.2.3.tar.gz 2694286 diff --git a/sci-biology/muscle/files/dont-build-libint.patch b/sci-biology/muscle/files/dont-build-libint.patch new file mode 100644 index 0000000..1ad5ce7 --- /dev/null +++ b/sci-biology/muscle/files/dont-build-libint.patch @@ -0,0 +1,11 @@ +--- psi3.orig/src/lib/Makefile.in 2004-01-19 09:09:53.000000000 -0800 ++++ psi3/src/lib/Makefile.in 2006-02-10 21:35:20.000000000 -0800 +@@ -2,7 +2,7 @@ + .PHONY: default all install depend clean targetclean + + subdirs = libipv1 libciomr libchkpt libqt libpsio libiwl libdpd \ +- libint libderiv libr12 libbasis ++ libbasis + + all: default + diff --git a/sci-biology/muscle/files/try-more-compilers.patch b/sci-biology/muscle/files/try-more-compilers.patch new file mode 100644 index 0000000..63d4618 --- /dev/null +++ b/sci-biology/muscle/files/try-more-compilers.patch @@ -0,0 +1,15 @@ +--- psi3.orig/configure.in 2005-10-29 10:15:06.000000000 -0700 ++++ psi3/configure.in 2006-02-10 20:56:59.000000000 -0800 +@@ -104,9 +104,9 @@ + ###################### + + # potential names of compilers +-FC_LIST="g77 f77 fc f2c" +-CC_LIST="gcc cc" +-CXX_LIST="g++ c++ cxx" ++FC_LIST="gfortran g77 f77 fc f2c ifc" ++CC_LIST="gcc cc icc" ++CXX_LIST="g++ c++ cxx icc" + + # set up os specific options + case $os in diff --git a/sci-biology/muscle/files/try-pthread-for-blas-lapack.patch b/sci-biology/muscle/files/try-pthread-for-blas-lapack.patch new file mode 100644 index 0000000..d9b01ed --- /dev/null +++ b/sci-biology/muscle/files/try-pthread-for-blas-lapack.patch @@ -0,0 +1,50 @@ +--- psi3.orig/configure.in 2005-10-29 10:15:06.000000000 -0700 ++++ psi3/configure.in 2006-02-10 20:56:59.000000000 -0800 +@@ -333,7 +333,7 @@ + AC_ARG_WITH(blas,[ --with-blas which blas library to use],[ + case $withval in + yes) +- BLAS='-lblas' ++ BLAS='-lblas -lpthread' + ;; + no) + BLAS='' +@@ -344,16 +344,16 @@ + esac + ]) + if test "X$BLAS" = X; then +- AC_CHECK_LIB(essl, DGEMM, BLAS="-lessl") ++ AC_CHECK_LIB(essl, DGEMM, BLAS="-lessl -lpthread",, [-lpthread]) + fi + if test "X$BLAS" = X; then +- AC_CHECK_LIB(scs, DGEMM, BLAS="-lscs") ++ AC_CHECK_LIB(scs, DGEMM, BLAS="-lscs -lpthread",, [-lpthread]) + fi + if test "X$BLAS" = X; then +- AC_CHECK_LIB(atlas, DGEMM, BLAS="-latlas") ++ AC_CHECK_LIB(atlas, DGEMM, BLAS="-latlas -lpthread",, [-lpthread]) + fi + if test "X$BLAS" = X; then +- AC_CHECK_LIB(blas, DGEMM, BLAS="-lblas") ++ AC_CHECK_LIB(blas, DGEMM, BLAS="-lblas -lpthread",, [-lpthread]) + fi + if test "X$BLAS" = X; then + AC_MSG_ERROR("Did not find a BLAS library") +@@ -363,7 +363,7 @@ + AC_ARG_WITH(lapack,[ --with-lapack which lapack library to use],[ + case $withval in + yes) +- LAPACK='-llapack' ++ LAPACK='-llapack -lpthread' + ;; + no) + LAPACK='' +@@ -382,7 +382,7 @@ + LIBS=$CURRENT_LIBS + fi + if test "X$LAPACK" = X; then +- AC_CHECK_LIB(lapack,DGEEV, LAPACK="-llapack",,$BLAS) ++ AC_CHECK_LIB(lapack,DGEEV, LAPACK="-llapack",,$BLAS -lpthread) + fi + if test "X$LAPACK" = X; then + AC_MSG_ERROR("Did not find a LAPACK library") diff --git a/sci-biology/muscle/files/use-external-libint.patch b/sci-biology/muscle/files/use-external-libint.patch new file mode 100644 index 0000000..1d9ce91 --- /dev/null +++ b/sci-biology/muscle/files/use-external-libint.patch @@ -0,0 +1,37 @@ +--- psi3.orig/src/bin/cints/Makefile.in 2003-11-14 08:15:19.000000000 -0800 ++++ psi3/src/bin/cints/Makefile.in 2006-02-10 22:42:31.000000000 -0800 +@@ -51,25 +51,25 @@ + # and form the list of the libraries. Remember that libderiv and libr12 + # depend on libint, and hence need to come first for GNU ld to work. + # +-INTLIBS := -lPSI_int ++INTLIBS := -lint + ifeq ($(findstring MP2R12,$(SUBDIRS)),MP2R12) +- ifneq ($(findstring -lPSI_r12,$(INTLIBS)),-lPSI_r12) +- INTLIBS := -lPSI_r12 $(INTLIBS) ++ ifneq ($(findstring -lr12,$(INTLIBS)),-lr12) ++ INTLIBS := -lr12 $(INTLIBS) + endif + endif + ifeq ($(findstring R12_Ints,$(SUBDIRS)),R12_Ints) +- ifneq ($(findstring -lPSI_r12,$(INTLIBS)),-lPSI_r12) +- INTLIBS := -lPSI_r12 $(INTLIBS) ++ ifneq ($(findstring -lr12,$(INTLIBS)),-lr12) ++ INTLIBS := -lr12 $(INTLIBS) + endif + endif + ifeq ($(findstring Default_Deriv1,$(SUBDIRS)),Default_Deriv1) +- ifneq ($(findstring -lPSI_deriv,$(INTLIBS)),-lPSI_deriv) +- INTLIBS := -lPSI_deriv $(INTLIBS) ++ ifneq ($(findstring -lderiv,$(INTLIBS)),-lderiv) ++ INTLIBS := -lderiv $(INTLIBS) + endif + endif + ifeq ($(findstring Default_Deriv2,$(SUBDIRS)),Default_Deriv2) +- ifneq ($(findstring -lderiv,$(INTLIBS)),-lPSI_deriv) +- INTLIBS := -lPSI_deriv $(INTLIBS) ++ ifneq ($(findstring -lderiv,$(INTLIBS)),-lderiv) ++ INTLIBS := -lderiv $(INTLIBS) + endif + endif + diff --git a/sci-biology/muscle/muscle-3.6.ebuild b/sci-biology/muscle/muscle-3.6.ebuild new file mode 100644 index 0000000..23e8453 --- /dev/null +++ b/sci-biology/muscle/muscle-3.6.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/app-misc/colordiff/colordiff-1.0.5-r2.ebuild,v 1.7 2005/08/17 18:08:02 grobian Exp $ + +inherit toolchain-funcs + +MY_P="${PN}${PV}_src" +DESCRIPTION="Multiple sequence comparison by log-expectation" +HOMEPAGE="http://www.drive5.com/muscle/" +SRC_URI="http://www.drive5.com/muscle/downloads${PV}/${MY_P}.tar.gz" +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~x86" +IUSE="" +RDEPEND="" +DEPEND="${RDEPEND}" +S="${WORKDIR}/${MY_P}" + +src_unpack() { + unpack ${A} + sed -i \ + "s:-static::g" \ + ${S}/Makefile + sed -i \ + "/strip/d" \ + ${S}/Makefile +} + +src_compile() { + emake \ + GPP="$(tc-getCXX)" \ + CFLAGS="${CXXFLAGS}" \ + || die "make failed" +} + +src_install() { + DESTTREE="/usr" dobin muscle +} diff --git a/sci-biology/paml/Manifest b/sci-biology/paml/Manifest new file mode 100644 index 0000000..9c14bea --- /dev/null +++ b/sci-biology/paml/Manifest @@ -0,0 +1,6 @@ +MD5 f88462efabd3504f45ae6c19819dde73 files/digest-paml-3.15 229 +RMD160 37e14b567c759a51fc732980a8cc6226a5aa53fe files/digest-paml-3.15 229 +SHA256 210e7b6e10e7e973a74f6c6b5c1923395cc6e09a5745c1b5a75aafd6085c4cb0 files/digest-paml-3.15 229 +MD5 8c94550fa5a6ab7ba3ab3aaf4045cd0b paml-3.15.ebuild 825 +RMD160 c5fa480f709eb9efb2e3a01e514aab0120c6a545 paml-3.15.ebuild 825 +SHA256 e08f4aac2cbc46058eca6c0b614a2193e524882c575a820aecd7977c72177c00 paml-3.15.ebuild 825 diff --git a/sci-biology/paml/files/digest-paml-3.15 b/sci-biology/paml/files/digest-paml-3.15 new file mode 100644 index 0000000..2f071b0 --- /dev/null +++ b/sci-biology/paml/files/digest-paml-3.15 @@ -0,0 +1,3 @@ +MD5 dc4bdbf59223be97d8fae247fa9e06d1 paml3.15.tar.gz 2390607 +RMD160 98ce55500113ad3447ac0a2129c358be03e63b96 paml3.15.tar.gz 2390607 +SHA256 a0f94ac1501a29836804d0ed586533eec1fd51c3b616c758bb9e55725eb8362f paml3.15.tar.gz 2390607 diff --git a/sci-biology/paml/paml-3.15.ebuild b/sci-biology/paml/paml-3.15.ebuild new file mode 100644 index 0000000..7fee096 --- /dev/null +++ b/sci-biology/paml/paml-3.15.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/app-misc/colordiff/colordiff-1.0.5-r2.ebuild,v 1.7 2005/08/17 18:08:02 grobian Exp $ + +inherit toolchain-funcs + +MY_P="${P/-}" +DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood" +HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html" +SRC_URI="http://abacus.gene.ucl.ac.uk/software/${MY_P}.tar.gz" +LICENSE="free-noncomm" +SLOT="0" +KEYWORDS="~x86" +IUSE="" +RDEPEND="" +DEPEND="${RDEPEND}" +S="${WORKDIR}/${MY_P}" + +src_compile() { + cd src + emake \ + -f Makefile.UNIX \ + CC="$(tc-getCC)" \ + CFLAGS="${CFLAGS}" \ + || die "make failed" +} + +src_install() { + exeinto /usr/bin + pushd ${S}/src + doexe baseml codeml basemlg mcmctree pamp evolver yn00 chi2 + popd + dodoc README.txt doc/* +} diff --git a/sci-biology/paml/rst b/sci-biology/paml/rst new file mode 100644 index 0000000..e69de29 --- /dev/null +++ b/sci-biology/paml/rst diff --git a/sci-biology/paml/rst1 b/sci-biology/paml/rst1 new file mode 100644 index 0000000..e69de29 --- /dev/null +++ b/sci-biology/paml/rst1 diff --git a/sci-biology/paml/rub b/sci-biology/paml/rub new file mode 100644 index 0000000..e69de29 --- /dev/null +++ b/sci-biology/paml/rub diff --git a/sci-biology/poa/Manifest b/sci-biology/poa/Manifest new file mode 100644 index 0000000..b572670 --- /dev/null +++ b/sci-biology/poa/Manifest @@ -0,0 +1,36 @@ +MD5 74eaf8b13786493ed6220c0c33e09b28 files/add-libint-error-message.patch 722 +RMD160 526e57d715b65fedc763069be30f7e49e52dcbb8 files/add-libint-error-message.patch 722 +SHA256 63715cab509893817c7cfb22422c3724fd02a4d0fa5065bbb5a477d8d8a23390 files/add-libint-error-message.patch 722 +MD5 20a9e61f87048ee301d0cb690b890ede files/digest-dialign-t-0.2.1 250 +RMD160 9d920eafc14c5c82bb7f59a0589570c52ce5e292 files/digest-dialign-t-0.2.1 250 +SHA256 13b80f9063a8294da8e20803cd0ab7ac56a38eb1ba5548885f52000103db8795 files/digest-dialign-t-0.2.1 250 +MD5 2ce7fc1feec78dd7428b1bfb6dca6f48 files/digest-muscle-3.6 241 +RMD160 00cdfc0a67940e555cae9b2917a3e59e4a880f44 files/digest-muscle-3.6 241 +SHA256 ff5d1ffa1cd22ba1ee71b8af23f4f92d25ae80f8fa88bf0ed303d0d8c3799cbd files/digest-muscle-3.6 241 +MD5 c40b5662c1ced482b5071f596493c297 files/digest-poa-2 214 +RMD160 ca39533967c38989bfc8b08772a53dba3d09ce15 files/digest-poa-2 214 +SHA256 034b82fef594cbf7567ceca3fa49e761d5b1654df48056be2d708d63f792127a files/digest-poa-2 214 +MD5 09ec4c47c33e46e812d1c8a09f00a91a files/digest-probcons-1.10 241 +RMD160 2d5910f5cca5eb03d3d6e7ca83954774d4080051 files/digest-probcons-1.10 241 +SHA256 6dcaf5dcb70c5db87bebfb7d61342cc1f56758d67fc2db674ae900bc685406ef files/digest-probcons-1.10 241 +MD5 dbaa3f7804f89cfbc6b41a8fceeec0ca files/digest-psi-3.2.3 232 +RMD160 36c9c50c4c7e2ef156f0f0334b2b330435968e9b files/digest-psi-3.2.3 232 +SHA256 e9a1506870d5bf1fdfb1aee4740fc584343f0e716afe52c19411d115adf0bc4c files/digest-psi-3.2.3 232 +MD5 285e67094e0841a79a32c9301c023b39 files/dont-build-libint.patch 355 +RMD160 c3b00a7edb9af349f2321fcbbdc286168d5d6db3 files/dont-build-libint.patch 355 +SHA256 57513d9f897776055dfbe14e717761de314e79409def91ccc27563a613a66e18 files/dont-build-libint.patch 355 +MD5 bed0da2f6883825c195e05f8f00e5415 files/respect-cflags.patch 464 +RMD160 c5323a4944cc953336b70f924ced36aca1533301 files/respect-cflags.patch 464 +SHA256 851c738b9ecfa567b21f3b551e6819b8ae05db02a3f5a42ae4aa93d55577ed0e files/respect-cflags.patch 464 +MD5 9ec964134fe443be4a6d6760278bea87 files/try-more-compilers.patch 401 +RMD160 550151b01cc4362d70c3e79d250a2fb2e36af64f files/try-more-compilers.patch 401 +SHA256 cb3b404ad7725700840df7602686d651f38f3d7623857af63e3556d1317aaf08 files/try-more-compilers.patch 401 +MD5 f73030c473338710e13e3dfe3ce59463 files/try-pthread-for-blas-lapack.patch 1489 +RMD160 092e0613b7184b065bb5ffa2288ce342e84d9483 files/try-pthread-for-blas-lapack.patch 1489 +SHA256 09cf2f5bc6835697322501280de3027b932416dd939d04d0d25a9790fe02eaa5 files/try-pthread-for-blas-lapack.patch 1489 +MD5 6dc1efc685dfc6994c972eed20daf18c files/use-external-libint.patch 1359 +RMD160 560598e6d7c99d901d97dd6037480bd57c82433f files/use-external-libint.patch 1359 +SHA256 41faa20ba804e98a81cb6809c789c643fd17458b6f6bc95dbe6311dd2fb16713 files/use-external-libint.patch 1359 +MD5 982248cdc8920333badccd8b215b8b49 poa-2.ebuild 1039 +RMD160 d636a330a6a86fe3ea7b7e5ed47eb195fbef91c9 poa-2.ebuild 1039 +SHA256 3ba8bb3be814d4176a2d2dbb2d1dc39ec63ae4e996870c79cb9ca229ff846449 poa-2.ebuild 1039 diff --git a/sci-biology/poa/files/add-libint-error-message.patch b/sci-biology/poa/files/add-libint-error-message.patch new file mode 100644 index 0000000..60fb128 --- /dev/null +++ b/sci-biology/poa/files/add-libint-error-message.patch @@ -0,0 +1,24 @@ +--- psi3.orig/src/lib/libint/Makefile.in 2003-11-23 11:07:51.000000000 -0800 ++++ psi3/src/lib/libint/Makefile.in 2006-02-10 22:38:37.000000000 -0800 +@@ -44,7 +44,10 @@ + $(MAKE) top_objdir=$(top_objdir_path); \ + rm -f Makefile; \ + if ! ./$(BUILD_BINARY); then \ +- cd ..; rm -fR $(TEMP_DIR); exit 1; \ ++ cd ..; \ ++ rm -fR $(TEMP_DIR); \ ++ echo "$(BUILD_BINARY) does not exist!"; \ ++ exit 1; \ + fi; \ + cp Makefile.libint Makefile; \ + ${MAKE} top_objdir=$(top_objdir_path); \ +@@ -65,7 +68,9 @@ + $(MKDIRS) $(libdir) + $(INSTALL_DATA) $< $(libdir) + $(RANLIB) $(libdir)/`basename $(TARGET)` ++ echo Finished ranlib + $(MKDIRS) $(incdir)/libint ++ echo Finished mkdirs + $(INSTALL_INCLUDE) $(TARGET_HEADERS) $(incdir)/libint + + # diff --git a/sci-biology/poa/files/digest-dialign-t-0.2.1 b/sci-biology/poa/files/digest-dialign-t-0.2.1 new file mode 100644 index 0000000..fd423eb --- /dev/null +++ b/sci-biology/poa/files/digest-dialign-t-0.2.1 @@ -0,0 +1,3 @@ +MD5 d1d4fc381a009c68387e159b78b33801 DIALIGN-T_0.2.1.tar.gz 1635888 +RMD160 a43807668354120b873cad0120a7691b6860ca28 DIALIGN-T_0.2.1.tar.gz 1635888 +SHA256 2249bf9007588e891525b4edc085285f1390c2bf8d42ce327aa9217130d7e930 DIALIGN-T_0.2.1.tar.gz 1635888 diff --git a/sci-biology/poa/files/digest-muscle-3.6 b/sci-biology/poa/files/digest-muscle-3.6 new file mode 100644 index 0000000..343f62a --- /dev/null +++ b/sci-biology/poa/files/digest-muscle-3.6 @@ -0,0 +1,3 @@ +MD5 e721d0859da9feec3cedeb42dcee9f59 muscle3.6_src.tar.gz 185267 +RMD160 4afda92b982ec2b05853a582479c61a7d8814f51 muscle3.6_src.tar.gz 185267 +SHA256 32b818a51f421e1d687f513dc31374a330470950151a5e7df961e64781699431 muscle3.6_src.tar.gz 185267 diff --git a/sci-biology/poa/files/digest-poa-2 b/sci-biology/poa/files/digest-poa-2 new file mode 100644 index 0000000..acdb441 --- /dev/null +++ b/sci-biology/poa/files/digest-poa-2 @@ -0,0 +1,3 @@ +MD5 9e2eb270d4867114406f53dab1311b2b poaV2.tar.gz 62612 +RMD160 31fdc50527a826fb7fdab4256f51e4f0f03c5492 poaV2.tar.gz 62612 +SHA256 d98d8251af558f442d909a6527694825ef6f79881b7636cad4925792559092c2 poaV2.tar.gz 62612 diff --git a/sci-biology/poa/files/digest-probcons-1.10 b/sci-biology/poa/files/digest-probcons-1.10 new file mode 100644 index 0000000..e49b293 --- /dev/null +++ b/sci-biology/poa/files/digest-probcons-1.10 @@ -0,0 +1,3 @@ +MD5 c7938b95732a85c35225bafd4b5b174f probcons_v1_10.tar.gz 43004 +RMD160 ba7caa3cadd702c3dc00c20f01bfb22416435784 probcons_v1_10.tar.gz 43004 +SHA256 f7a775ac4ba3b3261c0bbe5d2c203c96fc2551e67448aefbac83b461c931b518 probcons_v1_10.tar.gz 43004 diff --git a/sci-biology/poa/files/digest-psi-3.2.3 b/sci-biology/poa/files/digest-psi-3.2.3 new file mode 100644 index 0000000..00ee001 --- /dev/null +++ b/sci-biology/poa/files/digest-psi-3.2.3 @@ -0,0 +1,3 @@ +MD5 d304c9510fda1751a988b1e4f619e141 psi-3.2.3.tar.gz 2694286 +RMD160 19bc9a80380193fb3e6d6166f7aa8c98a0415222 psi-3.2.3.tar.gz 2694286 +SHA256 b966c33a82a930b90c1102ade52b7074dd50a9f70a3781d2408436fee68131be psi-3.2.3.tar.gz 2694286 diff --git a/sci-biology/poa/files/dont-build-libint.patch b/sci-biology/poa/files/dont-build-libint.patch new file mode 100644 index 0000000..1ad5ce7 --- /dev/null +++ b/sci-biology/poa/files/dont-build-libint.patch @@ -0,0 +1,11 @@ +--- psi3.orig/src/lib/Makefile.in 2004-01-19 09:09:53.000000000 -0800 ++++ psi3/src/lib/Makefile.in 2006-02-10 21:35:20.000000000 -0800 +@@ -2,7 +2,7 @@ + .PHONY: default all install depend clean targetclean + + subdirs = libipv1 libciomr libchkpt libqt libpsio libiwl libdpd \ +- libint libderiv libr12 libbasis ++ libbasis + + all: default + diff --git a/sci-biology/poa/files/respect-cflags.patch b/sci-biology/poa/files/respect-cflags.patch new file mode 100644 index 0000000..2ae08db --- /dev/null +++ b/sci-biology/poa/files/respect-cflags.patch @@ -0,0 +1,13 @@ +diff -urN poaV2.orig/Makefile poaV2/Makefile +--- poaV2.orig/Makefile 2004-03-11 21:33:30.000000000 -0800 ++++ poaV2/Makefile 2006-03-09 20:09:27.000000000 -0800 +@@ -28,7 +28,8 @@ + + CC = gcc + #CFLAGS= -g -ansi-strict -W -Wall -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. +-CFLAGS= -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. ++OPT_CFLAGS = -g ++CFLAGS= $(OPT_CFLAGS) -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. + # -I$(HOME)/lib/include + # -DREPORT_MAX_ALLOC + diff --git a/sci-biology/poa/files/try-more-compilers.patch b/sci-biology/poa/files/try-more-compilers.patch new file mode 100644 index 0000000..63d4618 --- /dev/null +++ b/sci-biology/poa/files/try-more-compilers.patch @@ -0,0 +1,15 @@ +--- psi3.orig/configure.in 2005-10-29 10:15:06.000000000 -0700 ++++ psi3/configure.in 2006-02-10 20:56:59.000000000 -0800 +@@ -104,9 +104,9 @@ + ###################### + + # potential names of compilers +-FC_LIST="g77 f77 fc f2c" +-CC_LIST="gcc cc" +-CXX_LIST="g++ c++ cxx" ++FC_LIST="gfortran g77 f77 fc f2c ifc" ++CC_LIST="gcc cc icc" ++CXX_LIST="g++ c++ cxx icc" + + # set up os specific options + case $os in diff --git a/sci-biology/poa/files/try-pthread-for-blas-lapack.patch b/sci-biology/poa/files/try-pthread-for-blas-lapack.patch new file mode 100644 index 0000000..d9b01ed --- /dev/null +++ b/sci-biology/poa/files/try-pthread-for-blas-lapack.patch @@ -0,0 +1,50 @@ +--- psi3.orig/configure.in 2005-10-29 10:15:06.000000000 -0700 ++++ psi3/configure.in 2006-02-10 20:56:59.000000000 -0800 +@@ -333,7 +333,7 @@ + AC_ARG_WITH(blas,[ --with-blas which blas library to use],[ + case $withval in + yes) +- BLAS='-lblas' ++ BLAS='-lblas -lpthread' + ;; + no) + BLAS='' +@@ -344,16 +344,16 @@ + esac + ]) + if test "X$BLAS" = X; then +- AC_CHECK_LIB(essl, DGEMM, BLAS="-lessl") ++ AC_CHECK_LIB(essl, DGEMM, BLAS="-lessl -lpthread",, [-lpthread]) + fi + if test "X$BLAS" = X; then +- AC_CHECK_LIB(scs, DGEMM, BLAS="-lscs") ++ AC_CHECK_LIB(scs, DGEMM, BLAS="-lscs -lpthread",, [-lpthread]) + fi + if test "X$BLAS" = X; then +- AC_CHECK_LIB(atlas, DGEMM, BLAS="-latlas") ++ AC_CHECK_LIB(atlas, DGEMM, BLAS="-latlas -lpthread",, [-lpthread]) + fi + if test "X$BLAS" = X; then +- AC_CHECK_LIB(blas, DGEMM, BLAS="-lblas") ++ AC_CHECK_LIB(blas, DGEMM, BLAS="-lblas -lpthread",, [-lpthread]) + fi + if test "X$BLAS" = X; then + AC_MSG_ERROR("Did not find a BLAS library") +@@ -363,7 +363,7 @@ + AC_ARG_WITH(lapack,[ --with-lapack which lapack library to use],[ + case $withval in + yes) +- LAPACK='-llapack' ++ LAPACK='-llapack -lpthread' + ;; + no) + LAPACK='' +@@ -382,7 +382,7 @@ + LIBS=$CURRENT_LIBS + fi + if test "X$LAPACK" = X; then +- AC_CHECK_LIB(lapack,DGEEV, LAPACK="-llapack",,$BLAS) ++ AC_CHECK_LIB(lapack,DGEEV, LAPACK="-llapack",,$BLAS -lpthread) + fi + if test "X$LAPACK" = X; then + AC_MSG_ERROR("Did not find a LAPACK library") diff --git a/sci-biology/poa/files/use-external-libint.patch b/sci-biology/poa/files/use-external-libint.patch new file mode 100644 index 0000000..1d9ce91 --- /dev/null +++ b/sci-biology/poa/files/use-external-libint.patch @@ -0,0 +1,37 @@ +--- psi3.orig/src/bin/cints/Makefile.in 2003-11-14 08:15:19.000000000 -0800 ++++ psi3/src/bin/cints/Makefile.in 2006-02-10 22:42:31.000000000 -0800 +@@ -51,25 +51,25 @@ + # and form the list of the libraries. Remember that libderiv and libr12 + # depend on libint, and hence need to come first for GNU ld to work. + # +-INTLIBS := -lPSI_int ++INTLIBS := -lint + ifeq ($(findstring MP2R12,$(SUBDIRS)),MP2R12) +- ifneq ($(findstring -lPSI_r12,$(INTLIBS)),-lPSI_r12) +- INTLIBS := -lPSI_r12 $(INTLIBS) ++ ifneq ($(findstring -lr12,$(INTLIBS)),-lr12) ++ INTLIBS := -lr12 $(INTLIBS) + endif + endif + ifeq ($(findstring R12_Ints,$(SUBDIRS)),R12_Ints) +- ifneq ($(findstring -lPSI_r12,$(INTLIBS)),-lPSI_r12) +- INTLIBS := -lPSI_r12 $(INTLIBS) ++ ifneq ($(findstring -lr12,$(INTLIBS)),-lr12) ++ INTLIBS := -lr12 $(INTLIBS) + endif + endif + ifeq ($(findstring Default_Deriv1,$(SUBDIRS)),Default_Deriv1) +- ifneq ($(findstring -lPSI_deriv,$(INTLIBS)),-lPSI_deriv) +- INTLIBS := -lPSI_deriv $(INTLIBS) ++ ifneq ($(findstring -lderiv,$(INTLIBS)),-lderiv) ++ INTLIBS := -lderiv $(INTLIBS) + endif + endif + ifeq ($(findstring Default_Deriv2,$(SUBDIRS)),Default_Deriv2) +- ifneq ($(findstring -lderiv,$(INTLIBS)),-lPSI_deriv) +- INTLIBS := -lPSI_deriv $(INTLIBS) ++ ifneq ($(findstring -lderiv,$(INTLIBS)),-lderiv) ++ INTLIBS := -lderiv $(INTLIBS) + endif + endif + diff --git a/sci-biology/poa/poa-2.ebuild b/sci-biology/poa/poa-2.ebuild new file mode 100644 index 0000000..447020b --- /dev/null +++ b/sci-biology/poa/poa-2.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/app-misc/colordiff/colordiff-1.0.5-r2.ebuild,v 1.7 2005/08/17 18:08:02 grobian Exp $ + +inherit eutils + +MY_P="${PN}V${PV}" +DESCRIPTION="Fast multiple sequence alignments using partial-order graphs" +HOMEPAGE="http://www.bioinformatics.ucla.edu/poa/" +SRC_URI="http://www.bioinformatics.ucla.edu/poa/${MY_P}.tar.gz" +LICENSE="as-is" +SLOT="0" +KEYWORDS="~x86" +IUSE="" +RDEPEND="" +DEPEND="${RDEPEND}" +S="${WORKDIR}/${MY_P}" + +src_unpack() { + unpack ${A} + epatch ${FILESDIR}/respect-cflags.patch +} + +src_compile() { + emake \ + OPT_CFLAGS="${CFLAGS}" \ + poa \ + || die "make failed" +} + +src_install() { + exeinto /usr/bin + doexe ${S}/poa ${S}/make_pscores.pl + dolib.a ${S}/liblpo.a + dodoc ${S}/README ${S}/multidom.* + insinto /usr/share/poa + doins ${S}/*.mat +} + +pkg_postinst() { + einfo "poa requires a score matrix as the first argument." + einfo "This package installs two examples to ${ROOT}usr/share/poa/." +} diff --git a/sci-biology/probcons/Manifest b/sci-biology/probcons/Manifest new file mode 100644 index 0000000..8f4dd74 --- /dev/null +++ b/sci-biology/probcons/Manifest @@ -0,0 +1,27 @@ +MD5 bcc20b9c5e249f07fb535f0744f816e2 files/1.10-fix-cxxflags.patch 845 +RMD160 1e04c84b35c245623619c6d5a7128a8ab1c880af files/1.10-fix-cxxflags.patch 845 +SHA256 73a298114996b5d879b9ec3253d104464cb456d19382668cdf75bfe9f93f11de files/1.10-fix-cxxflags.patch 845 +MD5 74eaf8b13786493ed6220c0c33e09b28 files/add-libint-error-message.patch 722 +RMD160 526e57d715b65fedc763069be30f7e49e52dcbb8 files/add-libint-error-message.patch 722 +SHA256 63715cab509893817c7cfb22422c3724fd02a4d0fa5065bbb5a477d8d8a23390 files/add-libint-error-message.patch 722 +MD5 09ec4c47c33e46e812d1c8a09f00a91a files/digest-probcons-1.10 241 +RMD160 2d5910f5cca5eb03d3d6e7ca83954774d4080051 files/digest-probcons-1.10 241 +SHA256 6dcaf5dcb70c5db87bebfb7d61342cc1f56758d67fc2db674ae900bc685406ef files/digest-probcons-1.10 241 +MD5 dbaa3f7804f89cfbc6b41a8fceeec0ca files/digest-psi-3.2.3 232 +RMD160 36c9c50c4c7e2ef156f0f0334b2b330435968e9b files/digest-psi-3.2.3 232 +SHA256 e9a1506870d5bf1fdfb1aee4740fc584343f0e716afe52c19411d115adf0bc4c files/digest-psi-3.2.3 232 +MD5 285e67094e0841a79a32c9301c023b39 files/dont-build-libint.patch 355 +RMD160 c3b00a7edb9af349f2321fcbbdc286168d5d6db3 files/dont-build-libint.patch 355 +SHA256 57513d9f897776055dfbe14e717761de314e79409def91ccc27563a613a66e18 files/dont-build-libint.patch 355 +MD5 9ec964134fe443be4a6d6760278bea87 files/try-more-compilers.patch 401 +RMD160 550151b01cc4362d70c3e79d250a2fb2e36af64f files/try-more-compilers.patch 401 +SHA256 cb3b404ad7725700840df7602686d651f38f3d7623857af63e3556d1317aaf08 files/try-more-compilers.patch 401 +MD5 f73030c473338710e13e3dfe3ce59463 files/try-pthread-for-blas-lapack.patch 1489 +RMD160 092e0613b7184b065bb5ffa2288ce342e84d9483 files/try-pthread-for-blas-lapack.patch 1489 +SHA256 09cf2f5bc6835697322501280de3027b932416dd939d04d0d25a9790fe02eaa5 files/try-pthread-for-blas-lapack.patch 1489 +MD5 6dc1efc685dfc6994c972eed20daf18c files/use-external-libint.patch 1359 +RMD160 560598e6d7c99d901d97dd6037480bd57c82433f files/use-external-libint.patch 1359 +SHA256 41faa20ba804e98a81cb6809c789c643fd17458b6f6bc95dbe6311dd2fb16713 files/use-external-libint.patch 1359 +MD5 dfce50503ba4abc4c4d4845cef79faef probcons-1.10.ebuild 1238 +RMD160 6fe62998a1b18aa4700deb574d9edc2c99dd8025 probcons-1.10.ebuild 1238 +SHA256 abb10a9fea1636935526bb6cdaa195a4c17b3ba38e7554c460a746afff68b657 probcons-1.10.ebuild 1238 diff --git a/sci-biology/probcons/files/1.10-fix-cxxflags.patch b/sci-biology/probcons/files/1.10-fix-cxxflags.patch new file mode 100644 index 0000000..bf76e77 --- /dev/null +++ b/sci-biology/probcons/files/1.10-fix-cxxflags.patch @@ -0,0 +1,21 @@ +diff -urN probcons.orig/Makefile probcons/Makefile +--- probcons.orig/Makefile 2006-02-21 12:14:37.000000000 -0800 ++++ probcons/Makefile 2006-02-21 12:15:15.000000000 -0800 +@@ -15,6 +15,8 @@ + # c) RELEASE mode + ################################################################################ + ++OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops ++ + OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.10" + + # debug mode +@@ -25,7 +27,7 @@ + + # release mode + #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer +-CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops ++CXXFLAGS = $(OPT_CXXFLAGS) -DNDEBUG $(OTHERFLAGS) + + ################################################################################ + # 3) Dependencies diff --git a/sci-biology/probcons/files/add-libint-error-message.patch b/sci-biology/probcons/files/add-libint-error-message.patch new file mode 100644 index 0000000..60fb128 --- /dev/null +++ b/sci-biology/probcons/files/add-libint-error-message.patch @@ -0,0 +1,24 @@ +--- psi3.orig/src/lib/libint/Makefile.in 2003-11-23 11:07:51.000000000 -0800 ++++ psi3/src/lib/libint/Makefile.in 2006-02-10 22:38:37.000000000 -0800 +@@ -44,7 +44,10 @@ + $(MAKE) top_objdir=$(top_objdir_path); \ + rm -f Makefile; \ + if ! ./$(BUILD_BINARY); then \ +- cd ..; rm -fR $(TEMP_DIR); exit 1; \ ++ cd ..; \ ++ rm -fR $(TEMP_DIR); \ ++ echo "$(BUILD_BINARY) does not exist!"; \ ++ exit 1; \ + fi; \ + cp Makefile.libint Makefile; \ + ${MAKE} top_objdir=$(top_objdir_path); \ +@@ -65,7 +68,9 @@ + $(MKDIRS) $(libdir) + $(INSTALL_DATA) $< $(libdir) + $(RANLIB) $(libdir)/`basename $(TARGET)` ++ echo Finished ranlib + $(MKDIRS) $(incdir)/libint ++ echo Finished mkdirs + $(INSTALL_INCLUDE) $(TARGET_HEADERS) $(incdir)/libint + + # diff --git a/sci-biology/probcons/files/digest-probcons-1.10 b/sci-biology/probcons/files/digest-probcons-1.10 new file mode 100644 index 0000000..e49b293 --- /dev/null +++ b/sci-biology/probcons/files/digest-probcons-1.10 @@ -0,0 +1,3 @@ +MD5 c7938b95732a85c35225bafd4b5b174f probcons_v1_10.tar.gz 43004 +RMD160 ba7caa3cadd702c3dc00c20f01bfb22416435784 probcons_v1_10.tar.gz 43004 +SHA256 f7a775ac4ba3b3261c0bbe5d2c203c96fc2551e67448aefbac83b461c931b518 probcons_v1_10.tar.gz 43004 diff --git a/sci-biology/probcons/files/digest-psi-3.2.3 b/sci-biology/probcons/files/digest-psi-3.2.3 new file mode 100644 index 0000000..00ee001 --- /dev/null +++ b/sci-biology/probcons/files/digest-psi-3.2.3 @@ -0,0 +1,3 @@ +MD5 d304c9510fda1751a988b1e4f619e141 psi-3.2.3.tar.gz 2694286 +RMD160 19bc9a80380193fb3e6d6166f7aa8c98a0415222 psi-3.2.3.tar.gz 2694286 +SHA256 b966c33a82a930b90c1102ade52b7074dd50a9f70a3781d2408436fee68131be psi-3.2.3.tar.gz 2694286 diff --git a/sci-biology/probcons/files/dont-build-libint.patch b/sci-biology/probcons/files/dont-build-libint.patch new file mode 100644 index 0000000..1ad5ce7 --- /dev/null +++ b/sci-biology/probcons/files/dont-build-libint.patch @@ -0,0 +1,11 @@ +--- psi3.orig/src/lib/Makefile.in 2004-01-19 09:09:53.000000000 -0800 ++++ psi3/src/lib/Makefile.in 2006-02-10 21:35:20.000000000 -0800 +@@ -2,7 +2,7 @@ + .PHONY: default all install depend clean targetclean + + subdirs = libipv1 libciomr libchkpt libqt libpsio libiwl libdpd \ +- libint libderiv libr12 libbasis ++ libbasis + + all: default + diff --git a/sci-biology/probcons/files/try-more-compilers.patch b/sci-biology/probcons/files/try-more-compilers.patch new file mode 100644 index 0000000..63d4618 --- /dev/null +++ b/sci-biology/probcons/files/try-more-compilers.patch @@ -0,0 +1,15 @@ +--- psi3.orig/configure.in 2005-10-29 10:15:06.000000000 -0700 ++++ psi3/configure.in 2006-02-10 20:56:59.000000000 -0800 +@@ -104,9 +104,9 @@ + ###################### + + # potential names of compilers +-FC_LIST="g77 f77 fc f2c" +-CC_LIST="gcc cc" +-CXX_LIST="g++ c++ cxx" ++FC_LIST="gfortran g77 f77 fc f2c ifc" ++CC_LIST="gcc cc icc" ++CXX_LIST="g++ c++ cxx icc" + + # set up os specific options + case $os in diff --git a/sci-biology/probcons/files/try-pthread-for-blas-lapack.patch b/sci-biology/probcons/files/try-pthread-for-blas-lapack.patch new file mode 100644 index 0000000..d9b01ed --- /dev/null +++ b/sci-biology/probcons/files/try-pthread-for-blas-lapack.patch @@ -0,0 +1,50 @@ +--- psi3.orig/configure.in 2005-10-29 10:15:06.000000000 -0700 ++++ psi3/configure.in 2006-02-10 20:56:59.000000000 -0800 +@@ -333,7 +333,7 @@ + AC_ARG_WITH(blas,[ --with-blas which blas library to use],[ + case $withval in + yes) +- BLAS='-lblas' ++ BLAS='-lblas -lpthread' + ;; + no) + BLAS='' +@@ -344,16 +344,16 @@ + esac + ]) + if test "X$BLAS" = X; then +- AC_CHECK_LIB(essl, DGEMM, BLAS="-lessl") ++ AC_CHECK_LIB(essl, DGEMM, BLAS="-lessl -lpthread",, [-lpthread]) + fi + if test "X$BLAS" = X; then +- AC_CHECK_LIB(scs, DGEMM, BLAS="-lscs") ++ AC_CHECK_LIB(scs, DGEMM, BLAS="-lscs -lpthread",, [-lpthread]) + fi + if test "X$BLAS" = X; then +- AC_CHECK_LIB(atlas, DGEMM, BLAS="-latlas") ++ AC_CHECK_LIB(atlas, DGEMM, BLAS="-latlas -lpthread",, [-lpthread]) + fi + if test "X$BLAS" = X; then +- AC_CHECK_LIB(blas, DGEMM, BLAS="-lblas") ++ AC_CHECK_LIB(blas, DGEMM, BLAS="-lblas -lpthread",, [-lpthread]) + fi + if test "X$BLAS" = X; then + AC_MSG_ERROR("Did not find a BLAS library") +@@ -363,7 +363,7 @@ + AC_ARG_WITH(lapack,[ --with-lapack which lapack library to use],[ + case $withval in + yes) +- LAPACK='-llapack' ++ LAPACK='-llapack -lpthread' + ;; + no) + LAPACK='' +@@ -382,7 +382,7 @@ + LIBS=$CURRENT_LIBS + fi + if test "X$LAPACK" = X; then +- AC_CHECK_LIB(lapack,DGEEV, LAPACK="-llapack",,$BLAS) ++ AC_CHECK_LIB(lapack,DGEEV, LAPACK="-llapack",,$BLAS -lpthread) + fi + if test "X$LAPACK" = X; then + AC_MSG_ERROR("Did not find a LAPACK library") diff --git a/sci-biology/probcons/files/use-external-libint.patch b/sci-biology/probcons/files/use-external-libint.patch new file mode 100644 index 0000000..1d9ce91 --- /dev/null +++ b/sci-biology/probcons/files/use-external-libint.patch @@ -0,0 +1,37 @@ +--- psi3.orig/src/bin/cints/Makefile.in 2003-11-14 08:15:19.000000000 -0800 ++++ psi3/src/bin/cints/Makefile.in 2006-02-10 22:42:31.000000000 -0800 +@@ -51,25 +51,25 @@ + # and form the list of the libraries. Remember that libderiv and libr12 + # depend on libint, and hence need to come first for GNU ld to work. + # +-INTLIBS := -lPSI_int ++INTLIBS := -lint + ifeq ($(findstring MP2R12,$(SUBDIRS)),MP2R12) +- ifneq ($(findstring -lPSI_r12,$(INTLIBS)),-lPSI_r12) +- INTLIBS := -lPSI_r12 $(INTLIBS) ++ ifneq ($(findstring -lr12,$(INTLIBS)),-lr12) ++ INTLIBS := -lr12 $(INTLIBS) + endif + endif + ifeq ($(findstring R12_Ints,$(SUBDIRS)),R12_Ints) +- ifneq ($(findstring -lPSI_r12,$(INTLIBS)),-lPSI_r12) +- INTLIBS := -lPSI_r12 $(INTLIBS) ++ ifneq ($(findstring -lr12,$(INTLIBS)),-lr12) ++ INTLIBS := -lr12 $(INTLIBS) + endif + endif + ifeq ($(findstring Default_Deriv1,$(SUBDIRS)),Default_Deriv1) +- ifneq ($(findstring -lPSI_deriv,$(INTLIBS)),-lPSI_deriv) +- INTLIBS := -lPSI_deriv $(INTLIBS) ++ ifneq ($(findstring -lderiv,$(INTLIBS)),-lderiv) ++ INTLIBS := -lderiv $(INTLIBS) + endif + endif + ifeq ($(findstring Default_Deriv2,$(SUBDIRS)),Default_Deriv2) +- ifneq ($(findstring -lderiv,$(INTLIBS)),-lPSI_deriv) +- INTLIBS := -lPSI_deriv $(INTLIBS) ++ ifneq ($(findstring -lderiv,$(INTLIBS)),-lderiv) ++ INTLIBS := -lderiv $(INTLIBS) + endif + endif + diff --git a/sci-biology/probcons/probcons-1.10.ebuild b/sci-biology/probcons/probcons-1.10.ebuild new file mode 100644 index 0000000..937372d --- /dev/null +++ b/sci-biology/probcons/probcons-1.10.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/app-misc/colordiff/colordiff-1.0.5-r2.ebuild,v 1.7 2005/08/17 18:08:02 grobian Exp $ + +inherit eutils toolchain-funcs + +MY_P="${PN}_v${PV/./_}" +DESCRIPTION="Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences" +HOMEPAGE="http://probcons.stanford.edu/" +SRC_URI="http://probcons.stanford.edu/${MY_P}.tar.gz" +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~x86" +IUSE="" +# Gnuplot is explicitly runtime-only, it's run using system() +RDEPEND="sci-visualization/gnuplot" +DEPEND="" +S="${WORKDIR}/${PN}" + +src_unpack() { + unpack ${A} + epatch ${FILESDIR}/${PV}-fix-cxxflags.patch +} + +src_compile() { + emake \ + CXX="$(tc-getCXX)" \ + OPT_CXXFLAGS="${CXXFLAGS}" \ + || die "make failed" +} + +src_install() { + DESTTREE="/usr" dobin probcons project makegnuplot + # Overlap with imagemagick + DESTTREE="/usr" newbin compare compare-probcons + dodoc README +} + +pkg_postinst() { + ewarn "The 'compare' binary is installed as 'compare-probcons'" + ewarn "to avoid overlap with other packages." + einfo "You may also want to download the user manual" + einfo "from http://probcons.stanford.edu/manual.pdf" +} diff --git a/sci-biology/seaview/ChangeLog b/sci-biology/seaview/ChangeLog new file mode 100644 index 0000000..14bd747 --- /dev/null +++ b/sci-biology/seaview/ChangeLog @@ -0,0 +1,55 @@ +# ChangeLog for sci-biology/seaview +# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/seaview/ChangeLog,v 1.6 2005/08/07 14:41:58 ribosome Exp $ + +*seaview-20050713 (07 Aug 2005) + + 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> + +seaview-20050713.ebuild: + New version. + + 24 Apr 2005; Michael Hanselmann <hansmi@gentoo.org> + seaview-20041220.ebuild: + Stable on ppc. + + 30 Jan 2005; Olivier Fisette <ribosome@gentoo.org> + seaview-20041220.ebuild: + Ebuild cleanup. + +*seaview-20041220 (09 Jan 2005) + + 09 Jan 2005; Olivier Fisette <ribosome@gentoo.org> -files/29seaview, + -seaview-1-r1.ebuild, +seaview-20041220.ebuild: + Changed versioning scheme. (Upstream does not use version numbers.) + +*seaview-1-r1 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +files/29seaview, +seaview-1-r1.ebuild: + Moved from app-sci/seaview to sci-biology/seaview. + + 22 Nov 2004; Karol Wojtaszek <sekretarz@gentoo.org> seaview-1-r1.ebuild: + Added to ~amd64, bug #72078 + + 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> seaview-1-r1.ebuild: + Added to x86. + +*seaview-1 (24 Jun 2004) + + 24 Jun 2004; Olivier Fisette <ribosome@gentoo.org> + seaview-1-r1.ebuild, metedata.xml: + Added app-sci/clustalw as a mandatory dependency. + Set maintainer (ribosome). + +*seaview-1 (24 Jun 2004) + + 24 Jun 2004; David Holm <dholm@gentoo.org> seaview-1.ebuild: + Added to ~ppc. + +*seaview-1 (23 Jun 2004) + + 23 Jun 2004; Olivier Fisette <ribosome@gentoo.org> + seaview-1.ebuild, metadata.xml, files/29seaview : + Initial import. Ebuild submitted by Olivier Fisette <ribosome@gentoo.org>. + Reference: Gentoo Bugzilla, bug #54055 + diff --git a/sci-biology/seaview/Manifest b/sci-biology/seaview/Manifest new file mode 100644 index 0000000..eae9f87 --- /dev/null +++ b/sci-biology/seaview/Manifest @@ -0,0 +1,12 @@ +MD5 55363db428f3719eb3bcfd88b01297b5 ChangeLog 1712 +RMD160 72ff94bdfd6843492fece6f469677725cd16b62a ChangeLog 1712 +SHA256 aa9017a97936c042d50bbe41fdd40692009e6d4c68807d5e9542648eb5bca2ff ChangeLog 1712 +MD5 12f7be8bda68958f3fd458149b5cdb6a files/digest-seaview-20060213 253 +RMD160 2c5874f5e8f1e778044c4f1c462ae158c9aaaf25 files/digest-seaview-20060213 253 +SHA256 b91aecb8cac59c15a14b1e5f925c8b065f3a929f636adbea74e5331fbe4153e5 files/digest-seaview-20060213 253 +MD5 7b87a6c33de5295e356b67218bd4fba9 metadata.xml 614 +RMD160 2d85f3408f8dc02063c111c5e41a149f637ef6b0 metadata.xml 614 +SHA256 ad0460ad24070f0337367a8dd91c16959e8f8ad3b739121c9772a25ef78ea4bf metadata.xml 614 +MD5 ad474bbfb4b096697e33e22e150fd489 seaview-20060213.ebuild 911 +RMD160 c4a662fb8b4f13bd7e9bccfa0bd65e56792a5bdc seaview-20060213.ebuild 911 +SHA256 696f69974a42e99a1f60080bbac4d19f80d94034fc29b47a026c4f77c8b1a521 seaview-20060213.ebuild 911 diff --git a/sci-biology/seaview/files/digest-seaview-20060213 b/sci-biology/seaview/files/digest-seaview-20060213 new file mode 100644 index 0000000..331a45c --- /dev/null +++ b/sci-biology/seaview/files/digest-seaview-20060213 @@ -0,0 +1,3 @@ +MD5 f44a1ea1ef0922e97fb26cbfeb80ca9d seaview-20060213.tar.bz2 114995 +RMD160 c3409b5e06f15e983db4912812381ee5d5894ea9 seaview-20060213.tar.bz2 114995 +SHA256 be058f53f07cec46978f10ddad8794bbe79762cf089d18b5cbe7cb6ed15c54fc seaview-20060213.tar.bz2 114995 diff --git a/sci-biology/seaview/metadata.xml b/sci-biology/seaview/metadata.xml new file mode 100644 index 0000000..29c4ec7 --- /dev/null +++ b/sci-biology/seaview/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci</herd> + <maintainer> + <email>ribosome@gentoo.org</email> + <name>Olivier Fisette</name> + </maintainer> + <longdescription> + SeaView is a graphical multiple sequence alignment editor developped by + Manolo Gouy. SeaView is able to read and write various alignment + formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to + manually edit the alignment, and also to run DOT-PLOT or CLUSTALW + programs to locally improve the alignment. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/seaview/seaview-20060213.ebuild b/sci-biology/seaview/seaview-20060213.ebuild new file mode 100644 index 0000000..0372f44 --- /dev/null +++ b/sci-biology/seaview/seaview-20060213.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/seaview/seaview-20050713.ebuild,v 1.1 2005/08/07 14:41:58 ribosome Exp $ + +DESCRIPTION="A graphical multiple sequence alignment editor" +HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html" +SRC_URI="mirror://gentoo/${P}.tar.bz2" +LICENSE="public-domain" + +SLOT="0" +KEYWORDS="~x86 ~ppc ~amd64" +IUSE="" + +DEPEND="x11-libs/fltk + =media-libs/pdflib-6.0* + sci-biology/clustalw" + +src_compile() { + # Corrects location of libfltk. + CFLAGS="${CFLAGS} -c -I/usr/include/fltk-1.1" + sed -i -e "s%\"seaview.help\", %\"/usr/share/${PN}/seaview.help\", %" seaview.cxx || die + sed -i -e 's:-L$(FLTK)/lib:-L/usr/lib/fltk-1.1:' Makefile || die + + emake -e || die +} + +src_install() { + dobin seaview seaview_align.sh + insinto /usr/share/${PN} + doins protein.mase seaview.help +} diff --git a/sci-biology/t-coffee/ChangeLog b/sci-biology/t-coffee/ChangeLog new file mode 100644 index 0000000..ca1dfe8 --- /dev/null +++ b/sci-biology/t-coffee/ChangeLog @@ -0,0 +1,61 @@ +# ChangeLog for sci-biology/t-coffee +# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.12 2005/12/08 19:52:39 ribosome Exp $ + + 08 Dec 2005; Olivier Fisette <ribosome@gentoo.org> -t-coffee-3.18.ebuild: + Pruning old version. + + 08 Dec 2005; Olivier Fisette <ribosome@gentoo.org> t-coffee-3.27.ebuild: + Added a warning regarding an internal compiler error (see bug #114745). + +*t-coffee-3.27 (08 Dec 2005) + + 08 Dec 2005; Olivier Fisette <ribosome@gentoo.org> +t-coffee-3.27.ebuild: + New version. + +*t-coffee-3.18 (19 Oct 2005) + + 19 Oct 2005; Olivier Fisette <ribosome@gentoo.org> +t-coffee-3.18.ebuild: + New version. + + 17 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -t-coffee-2.50.ebuild: + Pruning old version. + + 17 Oct 2005; Joseph Jezak <josejx@gentoo.org> t-coffee-2.66.ebuild: + Marked ppc stable for bug #108340. + + 13 Oct 2005; Mark Loeser <halcy0n@gentoo.org> t-coffee-2.66.ebuild: + Stable on x86 + + 08 Aug 2005; David Holm <dholm@gentoo.org> t-coffee-2.66.ebuild: + Added to ~ppc. + +*t-coffee-2.66 (07 Aug 2005) + + 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> -t-coffee-2.26.ebuild, + t-coffee-2.50.ebuild, +t-coffee-2.66.ebuild: + New version. Added 2.50 to x86. Removed old version. + +*t-coffee-2.50 (12 May 2005) + + 12 May 2005; Olivier Fisette <ribosome@gentoo.org> -t-coffee-2.03.ebuild, + t-coffee-2.26.ebuild, +t-coffee-2.50.ebuild: + Removed obsolete version. + +*t-coffee-2.50 (12 May 2005) + + 12 May 2005; Olivier Fisette <ribosome@gentoo.org> t-coffee-2.26.ebuild, + +t-coffee-2.50.ebuild: + New version: 2.50. Added 2.26 to x86. + +*t-coffee-2.26 (30 Mar 2005) + + 30 Mar 2005; Olivier Fisette <ribosome@gentoo.org> +t-coffee-2.26.ebuild: + New version. + +*t-coffee-2.03 (03 Mar 2005) + + 03 Mar 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +t-coffee-2.03.ebuild: + Initial import. + diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest new file mode 100644 index 0000000..e05407a --- /dev/null +++ b/sci-biology/t-coffee/Manifest @@ -0,0 +1,12 @@ +MD5 a8e10e03e808c4708b17b4568bd52f10 ChangeLog 1916 +RMD160 77dbcc0def9cb3ee57c8adc6b079598917e1b8a5 ChangeLog 1916 +SHA256 70dbf24743e39f2003370c7683b5d9d5b2ed47c283c130ceea3995f5aa26c78a ChangeLog 1916 +MD5 8663d9c02294b9417b3c82f0e9d3a570 files/digest-t-coffee-3.84 307 +RMD160 e234918666e5de1a15e6a0ccb831d7597608a08a files/digest-t-coffee-3.84 307 +SHA256 6717825503db3a5cc4d64a2506dc81d25498dcc2625f37eb64c8df50c25462f9 files/digest-t-coffee-3.84 307 +MD5 0bbfd32ca9864625c55ab6460dbbd963 metadata.xml 755 +RMD160 ef787b368ef20594ac1af412ab7ded9bd853c90d metadata.xml 755 +SHA256 c8669c3b6b58e9abbb36358b6577c76d595fab96fed1410c41694cff7cbe780a metadata.xml 755 +MD5 14f801a8843f6bd12714937cd1b623b2 t-coffee-3.84.ebuild 1735 +RMD160 c1e6a17b069edfb77ceac44cc1740d7083c799e2 t-coffee-3.84.ebuild 1735 +SHA256 97324873d7ce74b289af6bce8f9e7c289a7667a768a7b7329adda475b1161ce9 t-coffee-3.84.ebuild 1735 diff --git a/sci-biology/t-coffee/files/digest-t-coffee-3.84 b/sci-biology/t-coffee/files/digest-t-coffee-3.84 new file mode 100644 index 0000000..bc927af --- /dev/null +++ b/sci-biology/t-coffee/files/digest-t-coffee-3.84 @@ -0,0 +1,3 @@ +MD5 f8f74db4132573b0ec8790e64c4cda4c T-COFFEE_distribution_Version_3.84.tar.gz 1625217 +RMD160 cda295fd0c2c432c8f802739a3748fcb01f40389 T-COFFEE_distribution_Version_3.84.tar.gz 1625217 +SHA256 1c062fe67b1817570fdce8f57999ce637863cc91b4feb91053ef805cc3f48eab T-COFFEE_distribution_Version_3.84.tar.gz 1625217 diff --git a/sci-biology/t-coffee/metadata.xml b/sci-biology/t-coffee/metadata.xml new file mode 100644 index 0000000..a6dacf3 --- /dev/null +++ b/sci-biology/t-coffee/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer> + <email>ribosome@gentoo.org</email> + <name>Olivier Fisette</name> + </maintainer> + <herd>sci</herd> + <longdescription> + T-Coffee is a multiple sequence alignment package. Given a set of + sequences (Proteins or DNA), T-Coffee generates a multiple sequence + alignment. Version 2.00 and higher can mix sequences and structures. + T-Coffee allows the combination of a collection of multiple/pairwise, + global or local alignments into a single model. It also allows to + estimate the level of consistency of each position within the new + alignment with the rest of the alignments. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/t-coffee/t-coffee-3.84.ebuild b/sci-biology/t-coffee/t-coffee-3.84.ebuild new file mode 100644 index 0000000..867b7c9 --- /dev/null +++ b/sci-biology/t-coffee/t-coffee-3.84.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/t-coffee-3.27.ebuild,v 1.2 2005/12/08 19:48:52 ribosome Exp $ + +inherit toolchain-funcs + +DESCRIPTION="A multiple sequence alignment package" +LICENSE="t-coffee" +HOMEPAGE="http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html" +SRC_URI="http://igs-server.cnrs-mrs.fr/~cnotred/Packages/T-COFFEE_distribution_Version_${PV}.tar.gz" + +SLOT="0" +IUSE="" +KEYWORDS="~ppc ~x86" + +RESTRICT="nomirror" + +DEPEND="sci-biology/clustalw" + +TCDIR="${WORKDIR}/T-COFFEE_distribution_Version_${PV}" +S="${TCDIR}/t_coffee_source" + +src_unpack() { + unpack ${A} + cd "${S}" + sed -e "s/CC = cc/CC = $(tc-getCC) ${CFLAGS}/" -i makefile || die \ + "Failed to patch makefile." +} + +die_compile() { + echo + eerror "If you experience an internal compiler error (consult the above" + eerror "messages), try compiling t-coffee using very modest compiler flags." + eerror "See bug #114745 on the Gentoo Bugzilla for more details." + die "Compilation failed" +} + +src_compile() { + make all || die_compile +} + +src_install() { + cd "${TCDIR}"/bin + dobin t_coffee || die "Failed to install program." + insinto /usr/share/${PN}/lib/html + doins ${TCDIR}/html/* || die "Failed to install HTML documentation," + + dodoc ${TCDIR}/doc/README4T-COFFEE || die \ + "Failed to install basic documentation." + insinto /usr/share/doc/${PF} + doins ${TCDIR}/doc/t_coffee{_doc.{doc,pdf},.pdf} || die \ + "Failed to install manuals and articles." + doins ${TCDIR}/doc/*.txt || die "Failed to install documentation." + + insinto /usr/share/${PN}/example + doins ${TCDIR}/example/* || die "Failed to install example files." +} |