reinit the tree, so we can have metadata

5 files changed, 135 insertions, 0 deletions

diff --git a/sci-biology/njplot/Manifest b/sci-biology/njplot/Manifest
new file mode 100644
index 000000000000..b90b24102bec
--- /dev/null
+++ b/sci-biology/njplot/Manifest
@@ -0,0 +1,7 @@
+AUX njplot-2.3-buildsystem.patch 1688 SHA256 2ebdf312755f1bb6915ff93959329fa20f92e2b00d681b104858d98e397f2cfb SHA512 af7f9c4e7e20f80e66e78eefb93dce0f99594987fc9ce04de0f447c03e2523b152bd5d32459ab075ca7a65da5d2fb4bb7624e7048f1d6a9ac7c3e1d4b28927b3 WHIRLPOOL 740210f26125ba444544a4394841e16e8e5c584b19ae047faedf7afcc24033caf44b615c7b21c77623efe380a6d34c42a9c46f46b25082a18acb425748478450
+AUX njplot-2.3-format-security.patch 366 SHA256 99bbf3411f8584b3cfbfbeac2c81c3b46ebda7de96279d7a1a0fc625bdec5732 SHA512 1a6a3d823eebca79da482c534f4c7e54e025900dd6f8407a9ae50e997c3585301762da1b0bdd2311f6b5698ba33d96a8fca6b8fada541323a97773146ef8e773 WHIRLPOOL a9736eb7047530d28073791924d79ef9ed65df051cc65b7e432fa9a8abd703131e2f5343266738b7727d43ffca1a918fd2341256aca5472e21a8e0a0e28be856
+DIST njplot-2.3.tar.gz 83641 SHA256 c62a8293511469ba1246c415e7f1974113d520c8a11b04c2ad4a886267c2de1f SHA512 51e7d48187f88c4afb36d55cf8de98dad3cd4cd541137262885fe84bedff9db83224cdfa3c6a14518cd8170a06139b798518afe9fbadd89162986ed788355059 WHIRLPOOL e3e9d9bd844b7d663c7724ea06027641a9948cda133baed8d311b2fb00a6ecf31553a259db67a84478ae04878716f91dd2a9f9df5e2b21254ec9e75958851eca
+EBUILD njplot-2.3-r2.ebuild 847 SHA256 737901f1562015722d18b658ca43e5de166098a0c393516e38159433c5e9e41e SHA512 8a67dfe8db133776ea7bec00d376c0b25e4044916b1d67659b1a3a8a80c68ef7a90d91005e009acb48fa3f486c7611352639f00067d514cca93a32227a243eb4 WHIRLPOOL 5880a2828b98c1585907354a3fcd50f8298cca8bd557d5ff513cd3398271567c4b20227bad12fbf74498440ae30adaf8fd06bf630cb34fdf74618f73881c433d
+MISC ChangeLog 2557 SHA256 e9561fdc8d0a5aec7df0672ed1faca36e91d11656ab7a7de8cfbc09600b42679 SHA512 e0ec62d00ab79b62802ca874215a4f78889b7f5706e135b7a27b04b034547fd001f88efbe3b986604de60848c500afa9723ebf6560b0755ee4ef48b350fe7bcc WHIRLPOOL 8f2297579749ee5079b0d6d7ddefc4af9ebdd871a564ec348fd536acd7cd11ff1cb6e0fbdd84dccde0da93e000ab61c9cc01dfd91ef9cfb7efff3d2600f2eb20
+MISC ChangeLog-2015 2256 SHA256 4958d1e7fa4caf5f2ad1ba69e7f8daf40ed151d58c0a6808956f09cb8a23c0bb SHA512 06c63bb851ce2f5bd3e6fd5aa58d0a46da8940eb81e99fd061cc9f8e3ee8093933d67b8f8c89264a54fa83d3531dcf2e18265b3894c09414f3eac8bb45884d23 WHIRLPOOL 2fd74b27c91b66c91cfa9455365a259e797470b747800d523c87de9192ab0c93794c5742e595d9258ca97f0d0f946f78ed0c67da63e641c54d2ddb3ae873500e
+MISC metadata.xml 623 SHA256 a62d170844dfa49cc9e1b16e6316f6681be21207953d7b4a3332e35b6c69a4fe SHA512 494c11097c9484cfb104a8da218202294d13e71b2a8216342c7b9b7f00a97ac19403a3f21db91de08bc38e1bbed39693bd13167b70daad40267dca5fa30e2ff1 WHIRLPOOL 7e0336a4e039f1d4d373ea044e4c46b7d893939f063c12626500d986bfe2d2e975e5e8214b8558cf87bfec1036bfcaf4cec318bbc8b2a5003b081917e94c6874
diff --git a/sci-biology/njplot/files/njplot-2.3-buildsystem.patch b/sci-biology/njplot/files/njplot-2.3-buildsystem.patch
new file mode 100644
index 000000000000..61f8b95ea160
--- /dev/null
+++ b/sci-biology/njplot/files/njplot-2.3-buildsystem.patch
@@ -0,0 +1,59 @@
+ makefile | 16 ++++++++--------
+ 1 file changed, 8 insertions(+), 8 deletions(-)
+
+diff --git a/makefile b/makefile
+index ccb7dc2..9488c2a 100644
+--- a/makefile
++++ b/makefile
+@@ -7,10 +7,10 @@ NO_PDF = -DNO_PDF
+ #PDFLIB = -L$(PDF) -lpdf
+ 
+ # c compiler and linker
+-CC = gcc
++CC ?= gcc
+ 
+ # Vibrant top directory
+-VIBRANT = /banques0/ncbiJun04
++VIBRANT = /usr/include/ncbi
+ 
+ 
+ # X11 include directory
+@@ -24,15 +24,15 @@ OBJECTS = njplot-vib.o
+ OBJUNROOTED = unrooted-vib.o preptree.o
+ 
+ 
+-CFLAGS  = -c -DWIN_MOTIF -Dunix -I$(VIBRANT)/include -I$(VIBRANT)/vibrant -I$(VIBRANT)/corelib \
++CFLAGS  += -c -DWIN_MOTIF -Dunix -I$(VIBRANT)/include -I$(VIBRANT)/vibrant -I$(VIBRANT)/corelib \
+ 	-I$(VIBRANT) -I$(PDF) -I$(X11INCL) -I$(MOTIFINCL) $(HELPFILENAME) $(NO_PDF) \
+-	-Wimplicit-function-declaration -g
++	-Wimplicit-function-declaration
+ 	
+ all: njplot  unrooted newicktops newicktotxt
+ 
+ 
+ njplot : $(OBJECTS)
+-	$(CC) -g -o njplot $(OBJECTS) \
++	$(CC) $(LDFLAGS) -o njplot $(OBJECTS) \
+         -L$(VIBRANT)/lib \
+         -lvibrant -lncbi \
+         $(PDFLIB)   \
+@@ -40,16 +40,16 @@ njplot : $(OBJECTS)
+         -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm
+         
+ unrooted : $(OBJUNROOTED)
+-	$(CC) -g -o unrooted $(OBJUNROOTED) \
++	$(CC) $(LDFLAGS) -o unrooted $(OBJUNROOTED) \
+         -L$(VIBRANT)/lib -lvibrant -lncbi \
+         -L$(MOTIFLIB) -lXm \
+         -L/usr/X11R6/lib -lXmu -lXt -lX11  -lm
+ 
+ newicktops: njplot-vib.c
+-	$(CC) -DNO_GUI  -DNO_PDF -o $@ njplot-vib.c -lm
++	$(CC) $(LDFLAGS) $(CFLAGS) -DNO_GUI  -DNO_PDF -o $@ njplot-vib.c -lm
+ 
+ newicktotxt: njplot-vib.c
+-	$(CC) -DTTY  -o $@ njplot-vib.c -lm
++	$(CC) -DTTY $(LDFLAGS) $(CFLAGS) -o $@ njplot-vib.c -lm
+ 
+ 
+ .c.o : 
diff --git a/sci-biology/njplot/files/njplot-2.3-format-security.patch b/sci-biology/njplot/files/njplot-2.3-format-security.patch
new file mode 100644
index 000000000000..686b8475e9ed
--- /dev/null
+++ b/sci-biology/njplot/files/njplot-2.3-format-security.patch
@@ -0,0 +1,16 @@
+ njplot-vib.c | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/njplot-vib.c b/njplot-vib.c
+index fe55609..63fd3b6 100644
+--- a/njplot-vib.c
++++ b/njplot-vib.c
+@@ -1976,7 +1976,7 @@ PDFONLY"       no window interface, just write the PDF/PostScript tree plot\n"
+ #else
+ 		fprintf(stderr,
+ #endif
+-		message);
++		"%s", message);
+ 		exit(0);
+ 		}
+ 	}
diff --git a/sci-biology/njplot/metadata.xml b/sci-biology/njplot/metadata.xml
new file mode 100644
index 000000000000..4cdb5abfd7a5
--- /dev/null
+++ b/sci-biology/njplot/metadata.xml
@@ -0,0 +1,15 @@
+<?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>
+		NJplot is a tree drawing program able to draw any phylogenetic tree
+		expressed in the Newick phylogenetic tree format (e.g., the format used
+		by the PHYLIP package). NJplot is especially convenient for rooting the
+		unrooted trees obtained from parsimony, distance or maximum likelihood
+		tree-building methods.
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/njplot/njplot-2.3-r2.ebuild b/sci-biology/njplot/njplot-2.3-r2.ebuild
new file mode 100644
index 000000000000..420861dac42b
--- /dev/null
+++ b/sci-biology/njplot/njplot-2.3-r2.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+DESCRIPTION="A phylogenetic tree drawing program which supports tree rooting"
+HOMEPAGE="http://pbil.univ-lyon1.fr/software/njplot.html"
+SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/njplot-${PV}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="
+	sci-biology/ncbi-tools[X,static-libs]
+	x11-libs/libXmu"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-format-security.patch
+	"${FILESDIR}"/${P}-buildsystem.patch
+)
+
+src_prepare() {
+	default
+	sed -i -e "s:njplot.help:${EPREFIX}/usr/share/doc/${PF}/njplot.help:" njplot-vib.c || die
+
+	tc-export CC
+}
+
+src_install() {
+	dobin newicktops newicktotxt njplot unrooted
+	doman *.1
+	dodoc README njplot.help
+}