reinit the tree, so we can have metadata

5 files changed, 183 insertions, 0 deletions

diff --git a/sci-biology/phred/Manifest b/sci-biology/phred/Manifest
new file mode 100644
index 000000000000..d9d00191b287
--- /dev/null
+++ b/sci-biology/phred/Manifest
@@ -0,0 +1,7 @@
+AUX phred-071220-fix-build-system.patch 1981 SHA256 dcdce5aa8e23689a8d0b59f7ce0d2f336c894588e70b86a40ad2aa7de266cac0 SHA512 7647f6f6e9a1ae51cbf1aa3e39b337288e22fc26a95fdd88f92ce43fc6c0ef6ff59ec26919d14dfefff70be48e4a5604ddefef98bddf5d1d14d1e656665c878d WHIRLPOOL 7b6d72d7263d388e56c9cba872f193e0741fa1d8e55f03f53636ac2867a99b6d315bab84c70b062cca5a5fcb525878f307f336946f9fdc5dbffc9e51a24ce3ac
+AUX phred-071220-fix-qa.patch 787 SHA256 696031eca7f55242ca002e37ca8a38f27e0f05c00572fb3cdad1636c72146ea1 SHA512 27811a834358d0e1bf8281882e0420e0eb6bd9586871c8c72a4de79badc9539ea8e9258b9c3a3bf8ca1d3f6924d61abce2dcc0c0ed3b64e5fa53d4548109f5bc WHIRLPOOL cc076f36d40d60fc2eab11d5ac0007661362afdaa35c1b9f5eefcf1e08a0862952d05f1aa5c9a752a747040aeab7057b6c97b34c6d7253c16bb032535bae6477
+DIST phred-dist-071220.b-acd.tar.gz 357767 SHA256 364b0b54c29717ba4c8acc48a128eaf25ba1d7f06acab7565975f6879764a975 SHA512 0a6b0a733e6dcc0495eaab720b75f8e5815df494d0a773b8b8336d5208321c2ba475921084835a769367ec51aed156585ab97346a510100d4337e3215ec75276 WHIRLPOOL 9b14cfb1ca970a14ef613ca17efb82955c0ecec414dfad8835c883650f306b3a79846b7a410a9359cbd9ca953d890673366b6f865a2a357e81213d34b3327d3e
+EBUILD phred-071220-r1.ebuild 966 SHA256 51a4aee5de28daa085f086ef5aed2526aeede8c73be341a1a0f8c5640f0fbc92 SHA512 203ced3280f1c1bced57a1cb514533b71df1c2c9eefc94e594f61d45300da32617ff6023196d47cab7a1ca21bef61392760f5a12f25815ac5d78b9a8c58e7e91 WHIRLPOOL 73f20affc430537562a46d8f32cbe271e6c0c38854b33a1f689a9ba640583e4deee0753ef0986483fbb3a2845f46b020e30fc4fe3e67578d3b4be8c63ffdd30d
+MISC ChangeLog 2691 SHA256 35005c4acf5310f01e34dc177f0791ef5053dbd9d8d3ee0bba147c409b1cd4b2 SHA512 d494e7bfeb3cc57ff9129c7c27f3296b156fad75a59d9a12ea7edfb8f26d14228e9e1cb1e7caf19dde1253d1581754e7030f61f79470ab0a9ae7fb9dd40160b6 WHIRLPOOL e5a408d79f41596f57e53baf344512a5b2670da36ac894f8fcc28898aa8806bc1d5a42b83c5956a47645b1c5286d6748d7f0e2bd718f3821ac902bfe36dca4fd
+MISC ChangeLog-2015 716 SHA256 04a912e65a0223189d465ec11e8c64f177086b763b51f095826488cbafa5c654 SHA512 31af3a92ad7829c0e92b01c11a04acd3b6b626ea2479baafe807bb3fedc8b2bbfbcd6d16ace795c16df815a2d0ce09431d2b6fd7e7a71032db163ece4e0ae6d6 WHIRLPOOL b02865f737d32a4a74e7e73757bf6dabe464a17b080a18da8786da6bec12fd3b792b2b134da7a15400f4fc25b695b24e1d1ce65b6f0568ae70499ae77eda43b3
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
diff --git a/sci-biology/phred/files/phred-071220-fix-build-system.patch b/sci-biology/phred/files/phred-071220-fix-build-system.patch
new file mode 100644
index 000000000000..997f39941a07
--- /dev/null
+++ b/sci-biology/phred/files/phred-071220-fix-build-system.patch
@@ -0,0 +1,82 @@
+* Fix build system to honour CC, CFLAGS, CPPFLAGS and LDFLAGS
+* Specify a default target, in order to keep the ebuild slim
+
+--- a/Makefile
++++ b/Makefile
+@@ -12,9 +12,9 @@
+ 
+ # UNIX specific definitions (default)
+ #
+-CC= cc
+-CFLAGS= -O -DANSI_C $(LXFLAGS)
+-CLIB= -lm
++CC ?= cc
++CPPFLAGS += -DANSI_C $(LXFLAGS)
++LIBS += -lm
+ 
+ # Windows 'nmake' specific definitions
+ #
+@@ -133,9 +133,6 @@
+   $(objdir)writeSDF.o \
+   $(objdir)writeSeq.o
+ 
+-SRCS = $(OBJS:.o=.c)
+-WOBJ = $(OBJS:.o=.obj)
+-
+ INCS = \
+   $(incdir)chromatData.h \
+   $(incdir)freeChromatData.h \
+@@ -179,48 +176,18 @@
+ # UNIX make specific phred target
+ # note: a horizontal tab character must precede `$(CC)'
+ #
+-phred: $(OBJS)
+-	$(CC) $(CFLAGS) -o phred $(OBJS) $(CLIB)
+ 
+ 
+-# Windows nmake specific phred target
+-#
+-forwindows: $(WOBJ)
+-	$(CC) $(CFLAGS) /Fephred $(WOBJ)
+-#	$(CC) $(CFLAGS) /Fedaev daev.c
++.PHONY: all
++all: phred daev
+ 
+ 
+-# test CC: refuse to compile if
+-#
+-#   o  SunOS
+-#
+-#   AND
+-#
+-#   o  using /usr/ucb/cc compiler
+-#
+-#   NOTE: this compiler causes problems: see PHRED.DOC
+-#
+-test_cc:
+-	@if [ `uname` = SunOS ] ; \
+-        then \
+-          if [ `which $(CC)` = "/usr/ucb/cc" ] ; \
+-          then \
+-            echo ""; \
+- echo "============================================================"; \
+- echo "|                                                          |"; \
+- echo "|   This SUN C compiler produces a bad phred executable.   |"; \
+- echo "|                                                          |"; \
+- echo "|   Please see the PHRED.DOC file for more information.    |"; \
+- echo "|                                                          |"; \
+- echo "============================================================"; \
+-            echo ""; \
+-             exit 1; \
+-          fi \
+-        fi
++phred: $(OBJS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o phred $^ $(LIBS)
+ 
+ 
+ daev: daev.o
+-	$(CC) $(CFLAGS) -o daev daev.o -lm
++	$(CC) $(LDFLAGS) $(CFLAGS) -o daev $^ $(LIBS)
+ 
+ 
+ clean:
diff --git a/sci-biology/phred/files/phred-071220-fix-qa.patch b/sci-biology/phred/files/phred-071220-fix-qa.patch
new file mode 100644
index 000000000000..ab4d2ea023f6
--- /dev/null
+++ b/sci-biology/phred/files/phred-071220-fix-qa.patch
@@ -0,0 +1,36 @@
+Fix implicit declarations:
+* daev.c: In function ‘processParameters’:
+* daev.c:849:14: warning: implicit declaration of function ‘isdigit’ [-Wimplicit-function-declaration]
+*          if( !isdigit( argv[iarg][0] ) )
+
+--- a/autoPhred.c
++++ b/autoPhred.c
+@@ -57,6 +57,7 @@
+ static int xstrcmp();
+ #endif
+ 
++int freeMBRData( MBRData *mbrData );
+ #ifdef ANSI_C
+ int autoPhred( Option *option )
+ #else
+--- a/daev.c
++++ b/daev.c
+@@ -58,6 +58,7 @@
+ #include <sys/stat.h>
+ #include <time.h>
+ #include <math.h>
++#include <ctype.h>
+ 
+ #ifndef _WIN32
+ #include <dirent.h>
+--- a/mergedBaseRead.c
++++ b/mergedBaseRead.c
+@@ -63,7 +63,7 @@
+   Peak *peak;
+   Observed_peak *obs_peak;
+ 
+-  static initFlag = 0;
++  static int initFlag = 0;
+   static char mchar[256][256];
+ 
+   if( initFlag == 0 )
diff --git a/sci-biology/phred/metadata.xml b/sci-biology/phred/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/phred/metadata.xml
@@ -0,0 +1,8 @@
+<?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>
+</pkgmetadata>
diff --git a/sci-biology/phred/phred-071220-r1.ebuild b/sci-biology/phred/phred-071220-r1.ebuild
new file mode 100644
index 000000000000..e09c456b27d9
--- /dev/null
+++ b/sci-biology/phred/phred-071220-r1.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+DESCRIPTION="A base caller for Sanger DNA sequencing"
+HOMEPAGE="http://phrap.org/phredphrapconsed.html"
+SRC_URI="phred-dist-071220.b-acd.tar.gz"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}"
+
+RESTRICT="fetch"
+PATCHES=(
+	"${FILESDIR}/${PN}-071220-fix-build-system.patch"
+	"${FILESDIR}/${PN}-071220-fix-qa.patch"
+)
+
+pkg_nofetch() {
+	einfo "Please visit ${HOMEPAGE} and obtain the file"
+	einfo "${SRC_URI}, then place it in ${DISTDIR}"
+}
+
+src_compile() {
+	emake CC="$(tc-getCC)" \
+		CFLAGS="${CFLAGS}" \
+		LDFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+	dobin phred daev
+
+	insinto /usr/share/${PN}
+	doins phredpar.dat
+
+	echo "PHRED_PARAMETER_FILE=${EPREFIX}/usr/share/${PN}/phredpar.dat" > 99phred || die
+	doenvd 99phred
+
+	newdoc DAEV.DOC DAEV.DOC.txt
+	newdoc PHRED.DOC PHRED.DOC.txt
+}