reinit the tree, so we can have metadata

5 files changed, 157 insertions, 0 deletions

diff --git a/sci-biology/rnaview/Manifest b/sci-biology/rnaview/Manifest
new file mode 100644
index 000000000000..c891931aaa3e
--- /dev/null
+++ b/sci-biology/rnaview/Manifest
@@ -0,0 +1,7 @@
+AUX rnaview-20040713-implicit.patch 347 SHA256 129554c5ae9ed20c2cd24759b1007669c5f5ad19ddb76698c2b9157fcf79fb97 SHA512 698369b7640a36c26970649a8e0fd240c3177b3a3f7d9b8059fb6c294c39ad61389ba8a6eb3d465c3a999981fff47e2aa175ea52b38068145e2941c5934c4a0b WHIRLPOOL 5dcec3fe99bfd1efa66ecdfc55f6c553700421b0de833361fc7af3fa2654b3dd78e180d215ef1f880c1c059cad402a5ea478db23f6ee550f599ae32f5f008f43
+AUX rnaview-20040713-makefile.patch 2131 SHA256 dc2324a361132df317683a3a9d835364a7e3cff73f953920a97ca53bfc951c1a SHA512 9cde6186c0865405546bbee68ec64bd11cdfe91747b90739b237368b2724763ac4dd9206defec7f00a918449fc2a8451c3a5e447cfddfb7ca5c5fed00bb29de6 WHIRLPOOL 5f0d15d5df23d759448b763ec9c204a86658a852040c6b9e60f3dc07b37d45073c82e8ab83d0da7e2abc6bdf483b6d1258401ff0d730d24809941072aa5eba17
+DIST rnaview-20040713.tar.bz2 433916 SHA256 0961779c83e247a4b04c02d90d3850e8c4c889b630194ea1516cbeb6c6dbad17 SHA512 c63bb728bad0f358ab36f4ca18f4f9ef046811f21d3b8f3c6fdd3e6e6fcb367a9a52710476c5daea001f8f3262f72b64f0c0546f0c1423f463f2e0d288809e8e WHIRLPOOL 7ae8953a8028da0eb525a6b33964267b15721dbe148f5077cf2c7e47c7cc2e3a47616bcc944e7f8180c0696c27ac16c53bd3847d02db5a575df3cebba29dd169
+EBUILD rnaview-20040713-r4.ebuild 657 SHA256 0fd743ab75e230858ec718a38fc78ee0546ab9efee8c4777763f78cbdc1c865f SHA512 20ed56130c1a2cdd18cfc0717cdaca75030bdc2315343b390d0f01aa7ee9fc760734c9ec692bbe13c0930007dd47bfefea13b0d0c205bf1ee6850221e8df96c8 WHIRLPOOL fec4dc68525793ff6e6e4e23e5f488d72b42e0d628ead54acfbf6c525c46e9dba7185f222b488ddebc5ff9f0205948699019cd5b84f228f35e9210e334ffd5ba
+MISC ChangeLog 2650 SHA256 70228c3d62c3eaa2af2bf408e233ec0e400da428c470cd3a596063289799dd19 SHA512 364ec65547eb21057e712b6a5eaa65ab6f1c43d6f74dd828ce4ed1306b2359302aaf2e757970865dd64944f3db941786d2cd30fbc8987ab33be71126a985af47 WHIRLPOOL 7257821dd89f1dc2f4cdbc0b4c3e3dd4b48e870ad3d086089d9be88477f026fe95a2758b32996525a9f28451c863dc757150f715999474660ff9c77031b03cbe
+MISC ChangeLog-2015 2098 SHA256 2357f106dbfddb6705444747a5f16ae3dc5209853222057da45aa8312b70a99e SHA512 5ad5c09bf14cfefa9281b88db3ea8b23365c36bc4574ef309f3745b7ca560302e8b3f98ab201ed940c123fbd1968507208b8d6655d85c4fa937518aab1404d06 WHIRLPOOL 8f795a1decab226ce65affc5234c79852bc979580dddbdc116e41182f59a8aba0231c7bea737b3d089f4db5b6eb2aa6e87128bda6daabe97df711540b9044f06
+MISC metadata.xml 666 SHA256 1449cb6570fdd20b89395441b6f7b9482202827474ba53a2a602378ac9c58a99 SHA512 70614f391a69e8f2b21d1b3a277d7693436fb8d2089e390b61a1d71ecacdadf2818f7d255a083dcb4c585df90817c5e9d129e38f365635197d74e81e84c33786 WHIRLPOOL aba4dc0921474d53184fa09237bf1ba240b50a60c65324254f112ef264b8032e939f39d1d2f849b25f6c88a1449571b171aecf20c245ea55fcd08409a3a3a7ad
diff --git a/sci-biology/rnaview/files/rnaview-20040713-implicit.patch b/sci-biology/rnaview/files/rnaview-20040713-implicit.patch
new file mode 100644
index 000000000000..90ea72ab6f8c
--- /dev/null
+++ b/sci-biology/rnaview/files/rnaview-20040713-implicit.patch
@@ -0,0 +1,13 @@
+Fix implicit function declaration
+
+--- a/src/xml2ps.c
++++ b/src/xml2ps.c
+@@ -36,7 +36,7 @@
+ void read_sugar_syn(char *inpfile, long **sugar_syn);
+ void get_sugar_syn(FILE *inp, char *value_ch);
+ void get_chain_broken(long nres, double **a, double **b, long *chain_broken);
+-
++extern void get_BDIR(char *BDIR, char *filename);
+ 
+ 
+ FILE  *psfile; 
diff --git a/sci-biology/rnaview/files/rnaview-20040713-makefile.patch b/sci-biology/rnaview/files/rnaview-20040713-makefile.patch
new file mode 100644
index 000000000000..1af72f581fbf
--- /dev/null
+++ b/sci-biology/rnaview/files/rnaview-20040713-makefile.patch
@@ -0,0 +1,87 @@
+ Makefile          |   20 +++++++++++++++++---
+ rnaml2ps/Makefile |   19 ++++++++++++-------
+ 2 files changed, 29 insertions(+), 10 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 452e6c4..00d35f0 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,4 +1,4 @@
+-CC        = cc
++CC        ?= cc
+ 
+ 
+ 
+@@ -56,12 +56,17 @@ OBJ_FILE = $(OBJ)/rnaview.o \
+            $(OBJ)/multiple.o \
+            $(OBJ)/statistics.o
+ 
++.PHONY: clean all install
++
++SUBDIRS = rnaml2ps
++
+ all: $(RNAVIEW)
++	for dir in ${SUBDIRS} ; do ( cd $$dir ; ${MAKE} all ) ; done
+ 
+-CFLAGS  =  $(LINCLUDES) 
++CFLAGS  +=  $(LINCLUDES)
+ 
+ $(RNAVIEW) : $(HFILES) $(OBJ_FILE) 
+-	$(CC) $(CFLAGS) -o $@ $(OBJ_FILE) $(LDFLAGS) -lm $(MALLOCLIB)
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OBJ_FILE) -lm $(MALLOCLIB)
+ 
+ 
+ 
+@@ -111,6 +116,15 @@ $(OBJ)/statistics.o :  $(SRC)/statistics.c
+ clean:
+ 	@rm -f $(OBJ)/*.o
+ 	@rm -f $(ALLTARGETS)
++	for dir in ${SUBDIRS} ; do ( cd $$dir ; ${MAKE} clean ) ; done
++
++install:
++	install -D -m 0755 bin/rnaview $(DESTDIR)/usr/bin/rnaview
++	mkdir -p $(DESTDIR)/usr/share/rnaview/BASEPARS
++	install -m 0644 BASEPARS/* $(DESTDIR)/usr/share/rnaview/BASEPARS
++	mkdir -p $(DESTDIR)/usr/share/rnaview/test
++	install -m 0644 test/* $(DESTDIR)/usr/share/rnaview/test
++	for dir in ${SUBDIRS} ; do ( cd $$dir ; ${MAKE} install ) ; done
+ 
+ export:
+ 	mkdir -p $(EXPORT_DIR)
+diff --git a/rnaml2ps/Makefile b/rnaml2ps/Makefile
+index d207655..2278ccc 100644
+--- a/rnaml2ps/Makefile
++++ b/rnaml2ps/Makefile
+@@ -1,20 +1,25 @@
+-CFLAGS        = -O
+-CC            = cc
++CFLAGS        ?= -O
++CC            ?= cc
+ 
+ # ++++++++++++++++++++++++++++ Program RNADRAW
+ RNADRAW = rnaml2ps
+ OBJS_RNADRAW = rnaml2ps.o nrutil.o 
+ 
++all: $(RNADRAW)
++
+ $(RNADRAW):   $(OBJS_RNADRAW)
+-	$(CC) -o $(RNADRAW) $(OBJS_RNADRAW) -lm
++	$(CC) $(LDFLAGS) -o $(RNADRAW) $(OBJS_RNADRAW) -lm
+ 
+ nrutil.o : nrutil.c 
+-	cc -c  nrutil.c
++	$(CC) $(CFLAGS) -c  nrutil.c
+ 
+ rnaml2ps.o :  rnaml2ps.c
+-	cc -c  rnaml2ps.c
++	$(CC) $(CFLAGS) -c  rnaml2ps.c
+ 
+ 
+-.PHONY : clean
++.PHONY : clean all install
+ clean:
+-	rm *.o
++	rm -f *.o
++
++install:
++	install -D -m 0755 $(RNADRAW) $(DESTDIR)/usr/bin/$(RNADRAW)
diff --git a/sci-biology/rnaview/metadata.xml b/sci-biology/rnaview/metadata.xml
new file mode 100644
index 000000000000..cfffc1223753
--- /dev/null
+++ b/sci-biology/rnaview/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<longdescription>
+		The RNAView program generates 2-dimensional displays of RNA/DNA
+		secondary structures with tertiary interactions. RNAView
+		automatically identifies and classifies the types of base pairs that
+		are formed in nucleic acid structures, fully implementing Leontis and
+		Westhof's (RNA (2001) 7, 499-512), convention for edge-to-edge
+		hydrogen bonding interactions.
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/rnaview/rnaview-20040713-r4.ebuild b/sci-biology/rnaview/rnaview-20040713-r4.ebuild
new file mode 100644
index 000000000000..729095be063c
--- /dev/null
+++ b/sci-biology/rnaview/rnaview-20040713-r4.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+DESCRIPTION="Generates 2D displays of RNA/DNA secondary structures with tertiary interactions"
+HOMEPAGE="http://ndbserver.rutgers.edu/services/download/index.html"
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+PATCHES=(
+	"${FILESDIR}"/${P}-makefile.patch
+	"${FILESDIR}"/${P}-implicit.patch
+)
+
+src_prepare() {
+	default
+	tc-export CC
+}
+
+src_install() {
+	default
+
+	cat > 22rnaview <<- EOF || die
+		RNAVIEW="${EPREFIX}/usr/share/${PN}"
+	EOF
+	doenvd 22rnaview
+}