diff options
author | Jason W. Bacon <jwb@FreeBSD.org> | 2018-04-16 14:50:46 +0000 |
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committer | Jason W. Bacon <jwb@FreeBSD.org> | 2018-04-16 14:50:46 +0000 |
commit | 1cef8da47043faaf7f7fb7965138e1b35b948eec (patch) | |
tree | 6579eb951d28a05550235101c4e42f27ebfa0014 | |
parent | 625428c73ab7a6de24115b9efed1ff2b2d155176 (diff) | |
download | ports-1cef8da47043faaf7f7fb7965138e1b35b948eec.tar.gz ports-1cef8da47043faaf7f7fb7965138e1b35b948eec.zip |
Notes
-rw-r--r-- | biology/Makefile | 1 | ||||
-rw-r--r-- | biology/fastahack/Makefile | 19 | ||||
-rw-r--r-- | biology/fastahack/distinfo | 3 | ||||
-rw-r--r-- | biology/fastahack/files/Makefile | 62 | ||||
-rw-r--r-- | biology/fastahack/pkg-descr | 7 | ||||
-rw-r--r-- | biology/fastahack/pkg-plist | 7 |
6 files changed, 99 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 7508cc78b981..88e9aa1a1e54 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -26,6 +26,7 @@ SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 + SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastqc diff --git a/biology/fastahack/Makefile b/biology/fastahack/Makefile new file mode 100644 index 000000000000..1fe12a33dabb --- /dev/null +++ b/biology/fastahack/Makefile @@ -0,0 +1,19 @@ +# $FreeBSD$ + +PORTNAME= fastahack +DISTVERSION= g20160702 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Utility for indexing and sequence extraction from FASTA files + +LICENSE= GPLv2 + +USE_GITHUB= yes +GH_ACCOUNT= ekg +GH_TAGNAME= bbc645f2f7966cb7b44446200c02627c3168b399 + +MAKEFILE= ${FILESDIR}/Makefile +INSTALL_TARGET= install-strip + +.include <bsd.port.mk> diff --git a/biology/fastahack/distinfo b/biology/fastahack/distinfo new file mode 100644 index 000000000000..0de12c1b521a --- /dev/null +++ b/biology/fastahack/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1523600462 +SHA256 (ekg-fastahack-g20160702-bbc645f2f7966cb7b44446200c02627c3168b399_GH0.tar.gz) = dc8ef61765b7720fd2d163143696f1c82251bfd906ac5261642e7230d81d5da6 +SIZE (ekg-fastahack-g20160702-bbc645f2f7966cb7b44446200c02627c3168b399_GH0.tar.gz) = 18200 diff --git a/biology/fastahack/files/Makefile b/biology/fastahack/files/Makefile new file mode 100644 index 000000000000..3d878de6e14c --- /dev/null +++ b/biology/fastahack/files/Makefile @@ -0,0 +1,62 @@ + +# Use ?= to allow overriding from the env or command-line, e.g. +# +# make CXXFLAGS="-O3 -fPIC" install +# +# Package managers will override many of these variables automatically, so +# this is aimed at making it easy to create packages (Debian packages, +# FreeBSD ports, MacPorts, pkgsrc, etc.) + +CXX ?= c++ +CXXFLAGS ?= -O3 +DESTDIR ?= stage +PREFIX ?= /usr/local +STRIP ?= strip +INSTALL ?= install -c +MKDIR ?= mkdir -p +AR ?= ar + +# Required flags that we shouldn't override +# Must be compiler-independent +CXXFLAGS += -D_FILE_OFFSET_BITS=64 + +BIN = fastahack +LIB = libfastahack.a +OBJS = Fasta.o split.o disorder.o +MAIN = FastaHack.o + +all: $(BIN) $(LIB) + +$(BIN): $(OBJS) $(MAIN) + $(CXX) $(CXXFLAGS) $(OBJS) $(MAIN) -o $(BIN) + +$(LIB): $(OBJS) + ${AR} -rs $(LIB) $(OBJS) + +FastaHack.o: Fasta.h FastaHack.cpp + $(CXX) $(CXXFLAGS) -c FastaHack.cpp + +Fasta.o: Fasta.h Fasta.cpp + $(CXX) $(CXXFLAGS) -c Fasta.cpp + +split.o: split.h split.cpp + $(CXX) $(CXXFLAGS) -c split.cpp + +disorder.o: disorder.c disorder.h + $(CXX) $(CXXFLAGS) -c disorder.c + +install: all + $(MKDIR) $(DESTDIR)$(PREFIX)/bin + $(MKDIR) $(DESTDIR)$(PREFIX)/include/fastahack + $(MKDIR) $(DESTDIR)$(PREFIX)/lib + $(INSTALL) $(BIN) $(DESTDIR)$(PREFIX)/bin + $(INSTALL) *.h $(DESTDIR)$(PREFIX)/include/fastahack + $(INSTALL) $(LIB) $(DESTDIR)$(PREFIX)/lib + +install-strip: install + $(STRIP) $(DESTDIR)$(PREFIX)/bin/$(BIN) + +clean: + rm -rf $(BIN) $(LIB) $(OBJS) $(DESTDIR) + +.PHONY: clean diff --git a/biology/fastahack/pkg-descr b/biology/fastahack/pkg-descr new file mode 100644 index 000000000000..c1ca6d3c68cf --- /dev/null +++ b/biology/fastahack/pkg-descr @@ -0,0 +1,7 @@ +Fastahack is a small application for indexing and extracting sequences and +subsequences from FASTA files. The included Fasta.cpp library provides a FASTA +reader and indexer that can be embedded into applications which would benefit +from directly reading subsequences from FASTA files. The library automatically +handles index file generation and use. + +WWW: https://github.com/ekg/fastahack diff --git a/biology/fastahack/pkg-plist b/biology/fastahack/pkg-plist new file mode 100644 index 000000000000..99f591c84b84 --- /dev/null +++ b/biology/fastahack/pkg-plist @@ -0,0 +1,7 @@ +bin/fastahack +include/fastahack/Fasta.h +include/fastahack/LargeFileSupport.h +include/fastahack/Region.h +include/fastahack/disorder.h +include/fastahack/split.h +lib/libfastahack.a |