Import from Science overlay

Package-Manager: portage-2.2_rc20/cvs/Linux 2.6.26-gentoo-r4 x86_64

5 files changed, 112 insertions, 0 deletions

diff --git a/sci-biology/mpiblast/ChangeLog b/sci-biology/mpiblast/ChangeLog
new file mode 100644
index 000000000000..4e540a73b469
--- /dev/null
+++ b/sci-biology/mpiblast/ChangeLog
@@ -0,0 +1,15 @@
+# ChangeLog for sci-biology/mpiblast
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mpiblast/ChangeLog,v 1.1 2009/04/13 00:58:49 weaver Exp $
+
+*mpiblast-1.5.0 (12 Apr 2009)
+
+  12 Apr 2009; Andrey Kislyuk <weaver@gentoo.org>
+  +files/mpiblast-1.5.0-fix-build.patch, +metadata.xml,
+  +mpiblast-1.5.0.ebuild:
+  Import from Science overlay. Thanks to Justin Bronder for build patch.
+
+  02 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
+  New package sci-biology/mpiblast (previously bundled with
+  sci-biology/ncbi-tools), ebuild written by me
+
diff --git a/sci-biology/mpiblast/Manifest b/sci-biology/mpiblast/Manifest
new file mode 100644
index 000000000000..9652b85bbed4
--- /dev/null
+++ b/sci-biology/mpiblast/Manifest
@@ -0,0 +1,5 @@
+AUX mpiblast-1.5.0-fix-build.patch 1985 RMD160 afbca2b7a67ffba5f8149c7a3548d958ea553188 SHA1 62416f4b5019048214e3dfbd3c8a3549bd806db9 SHA256 d22b9a446da5222a3895b8053e86a6fa170dcea7a011482c711b604a1a7a8e3c
+DIST mpiBLAST-1.5.0-pio.tgz 16386783 RMD160 d2690b5d4f18c2288f95ef329cee131ea7275cad SHA1 9688db5984761b5aaf25c4d1dcd9e38529ca069f SHA256 af0b2e9b0a93f1d4bc13df02dcae4dc91f8030707f954d7c25684604a9aebdc8
+EBUILD mpiblast-1.5.0.ebuild 718 RMD160 95ce72cd2c6318d179144d19d74bebbff7b297f5 SHA1 9da9439b18139dd9f97b15280cfb01f3fede53cb SHA256 fb5fe25a9fcdd8c2946b24ef68acad08dd90539989826cbdb37aeb7003847976
+MISC ChangeLog 620 RMD160 df1726f260778ddda81f7bd8cb8336a8725598cd SHA1 91872b00d740766889546e79ba2152377b10442f SHA256 01d2e3db89c0f9fba974dfd48cdff3808e8a9aeb535df9aa51fcb576ffe95d36
+MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
diff --git a/sci-biology/mpiblast/files/mpiblast-1.5.0-fix-build.patch b/sci-biology/mpiblast/files/mpiblast-1.5.0-fix-build.patch
new file mode 100644
index 000000000000..93aa68309777
--- /dev/null
+++ b/sci-biology/mpiblast/files/mpiblast-1.5.0-fix-build.patch
@@ -0,0 +1,48 @@
+diff -u mpiblast-1.5.0-pio{_c,}/ncbi/make/makedis.csh 
+--- mpiblast-1.5.0-pio_c/ncbi/make/makedis.csh	2006-09-14 11:37:03.000000000 -0400
++++ mpiblast-1.5.0-pio/ncbi/make/makedis.csh	2009-04-02 17:01:08.411742006 -0400
+@@ -419,9 +419,11 @@
+    CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE $PNG_INCLUDE\" \
+    LDFLAGS1=\"$NCBI_LDFLAGS1\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
+    SHELL=\"$NCBI_MAKE_SHELL\" LCL=\"$NCBI_DEFAULT_LCL\" \
+-   RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" $ALL_VIB all'
+-eval echo $CMD
+-eval echo $CMD | sh 
++   RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" $ALL_VIB '
++eval echo $CMD copy
++eval echo $CMD copy | sh 
++eval echo $CMD all
++eval echo $CMD all | sh 
+ 
+ set make_stat = $status
+ 
+@@ -473,14 +475,28 @@
+ 		THREAD_OBJ=$NCBI_THREAD_OBJ \
+ 		THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \
+ 		NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB'
++    set CPY='make $MFLG -f makenet.unx \
++		CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \
++		LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
++		AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
++		THREAD_OBJ=$NCBI_THREAD_OBJ \
++		THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \
++		NETENTREZVERSION=\"$NETENTREZVERSION\" copy'
+ else
+ 	set CMD='make $MFLG -f makenet.unx \
+ 		CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \
+ 		LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
+ 		AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
+ 		NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB'
++    set CPY='make $MFLG -f makenet.unx \
++		CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \
++		LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
++		AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
++		NETENTREZVERSION=\"$NETENTREZVERSION\" copy'
+ endif
+-eval echo $CMD
++eval echo $CPY
++eval echo $CPY | sh
++eval echo $CMD 
+ eval echo $CMD | sh 
+ 
+ set net_stat = $status
diff --git a/sci-biology/mpiblast/metadata.xml b/sci-biology/mpiblast/metadata.xml
new file mode 100644
index 000000000000..3302123e5718
--- /dev/null
+++ b/sci-biology/mpiblast/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer>
+		<email>weaver@gentoo.org</email>
+		<name>Andrey Kislyuk</name>
+	</maintainer>
+	<herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/mpiblast/mpiblast-1.5.0.ebuild b/sci-biology/mpiblast/mpiblast-1.5.0.ebuild
new file mode 100644
index 000000000000..dab9edf50038
--- /dev/null
+++ b/sci-biology/mpiblast/mpiblast-1.5.0.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mpiblast/mpiblast-1.5.0.ebuild,v 1.1 2009/04/13 00:58:49 weaver Exp $
+
+EAPI="2"
+
+inherit eutils
+
+DESCRIPTION="An MPI implementation of NCBI BLAST"
+HOMEPAGE="http://www.mpiblast.org/"
+SRC_URI="http://www.mpiblast.org/downloads/files/mpiBLAST-${PV}-pio.tgz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="virtual/mpi
+	app-shells/tcsh"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${P}-pio"
+
+src_configure() {
+	epatch "${FILESDIR}"/${P}-*.patch
+}
+
+src_compile() {
+	# configure also runs build
+	econf
+}
+
+src_install() {
+	emake DESTDIR="${D}" install || die
+}