Initial import

5 files changed, 89 insertions, 1 deletions

diff --git a/app-sci/hmmer/ChangeLog b/app-sci/hmmer/ChangeLog
new file mode 100644
index 000000000000..09de799cc615
--- /dev/null
+++ b/app-sci/hmmer/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for app-sci/hmmer
+# Copyright 2000-2003 Gentoo Technologies, Inc.; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/app-sci/hmmer/ChangeLog,v 1.1 2003/05/07 18:47:31 avenj Exp $
+
+*hmmer-2.2g (07 May 2003)
+
+  07 May 2003; Jon Portnoy <avenj@gentoo.org> hmmer-2.2g.ebuild :
+  Initial import. Ebuild submitted by Steve Diener and Gontran Zepeda
+  in bug #20449.
diff --git a/app-sci/hmmer/Manifest b/app-sci/hmmer/Manifest
index a7b569269737..ef4da39ca6ac 100644
--- a/app-sci/hmmer/Manifest
+++ b/app-sci/hmmer/Manifest
@@ -1,3 +1,4 @@
-MD5 6eb341b123204ac248e065d923b5e4a7 hmmer-2.2g.ebuild 808
+MD5 a676c9096480978d032ed2b58efceabf hmmer-2.2g.ebuild 903
+MD5 89b013567d8503b76ba599f0e19707ba ChangeLog 387
 MD5 bd33e448c26a59469256420a3b920600 files/digest-hmmer-2.2g 62
 MD5 9fbc129db1a886510ff026fd89e131f1 files/Makefile-hmmer-2.2g.patch 1040
diff --git a/app-sci/hmmer/files/Makefile-hmmer-2.2g.patch b/app-sci/hmmer/files/Makefile-hmmer-2.2g.patch
new file mode 100644
index 000000000000..fe9c8fdbcbfa
--- /dev/null
+++ b/app-sci/hmmer/files/Makefile-hmmer-2.2g.patch
@@ -0,0 +1,33 @@
+--- Makefile.in.orig	2003-05-05 15:21:41.000000000 +0100
++++ Makefile.in	2003-05-05 15:22:11.000000000 +0100
+@@ -84,6 +84,12 @@
+ 	sindex\
+ 	shuffle\
+ 	sreformat
++SQUIDMANS = afetch\
++	alistat\
++	seqstat\
++	sfetch\
++	shuffle\
++	sreformat
+ 
+ # all: Compile everything (except the testsuite),
+ #      and stick the supported programs in binaries/
+@@ -146,13 +152,14 @@
+ 	for file in $(PROGS) $(SQUIDPROGS) $(PVMPROGS); do\
+ 	   cp binaries/$$file $(BINDIR)/;\
+ 	done
+-	for file in hmmer $(PROGS) $(SQUIDPROGS); do\
++	for file in hmmer $(PROGS); do\
+ 	   $(INSTMAN) documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
++	   chmod 0644 $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
+ 	done
+-	for file in $(SQUIDPROGS); do\
++	for file in $(SQUIDMANS); do\
+ 	   $(INSTMAN) squid/Man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
++	   chmod 0644 $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
+ 	done
+-
+ # "make clean" removes almost everything except configuration files
+ #              and binaries.
+ clean:
diff --git a/app-sci/hmmer/files/digest-hmmer-2.2g b/app-sci/hmmer/files/digest-hmmer-2.2g
new file mode 100644
index 000000000000..78a5f3430c3f
--- /dev/null
+++ b/app-sci/hmmer/files/digest-hmmer-2.2g
@@ -0,0 +1 @@
+MD5 d7def2007a0aaf2eafb9a96a07986b8c hmmer-2.2g.tar.gz 931569
diff --git a/app-sci/hmmer/hmmer-2.2g.ebuild b/app-sci/hmmer/hmmer-2.2g.ebuild
new file mode 100644
index 000000000000..56ee3d5c2ae9
--- /dev/null
+++ b/app-sci/hmmer/hmmer-2.2g.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2003 Gentoo Technologies, Inc.
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/app-sci/hmmer/hmmer-2.2g.ebuild,v 1.1 2003/05/07 18:47:31 avenj Exp $
+
+DESCRIPTION="HMMER - Biological sequence analysis with profile HMMs"
+HOMEPAGE="http://hmmer.wustl.edu/"
+SRC_URI="ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/CURRENT/${P}.tar.gz"
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+DEPEND=""
+
+S=${WORKDIR}/${P}
+
+src_unpack(){
+	unpack ${A}
+	cd ${S}
+	epatch ${FILESDIR}/Makefile-${P}.patch
+}
+
+src_compile() {
+
+	./configure \
+		--host=${CHOST} \
+		--prefix=${D}/usr \
+		--mandir=${D}/usr/share/man || die "./configure failed"
+
+	emake || die
+}
+
+src_install() {
+
+	dodir usr/bin
+	dodir usr/share/man/man1
+	
+	einstall || die
+	
+	dodoc 00README COPYRIGHT INSTALL LICENSE NOTES Userguide.pdf
+
+	# include the squid docs
+	dodoc squid/Docs/*.tex
+
+}