diff options
author | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
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committer | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
commit | 4f2d7949f03e1c198bc888f2d05f421d35c57e21 (patch) | |
tree | ba5f07bf3f9d22d82e54a462313f5d244036c768 /sci-biology/phred |
reinit the tree, so we can have metadata
Diffstat (limited to 'sci-biology/phred')
-rw-r--r-- | sci-biology/phred/Manifest | 7 | ||||
-rw-r--r-- | sci-biology/phred/files/phred-071220-fix-build-system.patch | 82 | ||||
-rw-r--r-- | sci-biology/phred/files/phred-071220-fix-qa.patch | 36 | ||||
-rw-r--r-- | sci-biology/phred/metadata.xml | 8 | ||||
-rw-r--r-- | sci-biology/phred/phred-071220-r1.ebuild | 50 |
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 +} |