11 files changed, 219 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
+