From 9b23dec46f27a62b42f1569a8a7b98eefbc32a25 Mon Sep 17 00:00:00 2001 From: bacon Date: Fri, 22 Jan 2021 17:07:50 +0000 Subject: biology/bedtools: import bedtools-2.29.2 The bedtools utilities are a suite of tools for performing a wide range of genomics analysis tasks. The most widely-used of these tools enable genome arithmetic, i.e., set theory on the genome. For example, with bedtools one can intersect, merge, count, complement, and shuffle genomic intervals from multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF. Although each individual utility is designed to do a relatively simple task, e.g., intersect two interval files, more sophisticated analyses can be conducted by stringing together multiple bedtools operations on the command line or in shell scripts. --- biology/bedtools/DESCR | 10 +++++ biology/bedtools/Makefile | 33 ++++++++++++++++ biology/bedtools/PLIST | 39 +++++++++++++++++++ biology/bedtools/distinfo | 8 ++++ biology/bedtools/patches/patch-Makefile | 45 ++++++++++++++++++++++ .../patches/patch-src_utils_htslib_Makefile | 24 ++++++++++++ 6 files changed, 159 insertions(+) create mode 100644 biology/bedtools/DESCR create mode 100644 biology/bedtools/Makefile create mode 100644 biology/bedtools/PLIST create mode 100644 biology/bedtools/distinfo create mode 100644 biology/bedtools/patches/patch-Makefile create mode 100644 biology/bedtools/patches/patch-src_utils_htslib_Makefile (limited to 'biology') diff --git a/biology/bedtools/DESCR b/biology/bedtools/DESCR new file mode 100644 index 00000000000..bf60338ab77 --- /dev/null +++ b/biology/bedtools/DESCR @@ -0,0 +1,10 @@ +The bedtools utilities are a suite of tools for performing a wide range of +genomics analysis tasks. The most widely-used of these tools enable genome +arithmetic, i.e., set theory on the genome. For example, with bedtools one +can intersect, merge, count, complement, and shuffle genomic intervals from +multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF. + +Although each individual utility is designed to do a relatively simple task, +e.g., intersect two interval files, more sophisticated analyses can be +conducted by stringing together multiple bedtools operations on the command +line or in shell scripts. diff --git a/biology/bedtools/Makefile b/biology/bedtools/Makefile new file mode 100644 index 00000000000..b8c917dc20d --- /dev/null +++ b/biology/bedtools/Makefile @@ -0,0 +1,33 @@ +# $NetBSD: Makefile,v 1.1 2021/01/22 17:07:50 bacon Exp $ + +DISTNAME= bedtools-2.29.2 +CATEGORIES= biology +MASTER_SITES= ${MASTER_SITE_GITHUB:=arq5x/} +GITHUB_PROJECT= bedtools2 +GITHUB_TAG= v${PKGVERSION_NOREV} + +MAINTAINER= bacon@NetBSD.org +HOMEPAGE= https://bedtools.readthedocs.io/en/latest/ +COMMENT= Swiss army knife for genome arithmetic +LICENSE= mit + +USE_LANGUAGES= c c++ +USE_TOOLS+= gmake +REPLACE_SH+= scripts/vcfsort.sh +REPLACE_PYTHON= scripts/makeBashScripts.py + +SUBST_CLASSES+= pybin +SUBST_STAGE.pybin= pre-configure +SUBST_SED.pybin= -e 's|python|${PYTHONBIN}|g' +SUBST_FILES.pybin= Makefile + +# Avoid conflict with C++20 by adding .txt suffix +post-extract: + ${MV} ${WRKSRC}/src/utils/gzstream/version \ + ${WRKSRC}/src/utils/gzstream/version.txt + +.include "../../devel/zlib/buildlink3.mk" +.include "../../archivers/bzip2/buildlink3.mk" +.include "../../archivers/xz/buildlink3.mk" +.include "../../lang/python/application.mk" +.include "../../mk/bsd.pkg.mk" diff --git a/biology/bedtools/PLIST b/biology/bedtools/PLIST new file mode 100644 index 00000000000..c7fd8967b11 --- /dev/null +++ b/biology/bedtools/PLIST @@ -0,0 +1,39 @@ +@comment $NetBSD: PLIST,v 1.1 2021/01/22 17:07:50 bacon Exp $ +bin/annotateBed +bin/bamToBed +bin/bamToFastq +bin/bed12ToBed6 +bin/bedToBam +bin/bedToIgv +bin/bedpeToBam +bin/bedtools +bin/closestBed +bin/clusterBed +bin/complementBed +bin/coverageBed +bin/expandCols +bin/fastaFromBed +bin/flankBed +bin/genomeCoverageBed +bin/getOverlap +bin/groupBy +bin/intersectBed +bin/linksBed +bin/mapBed +bin/maskFastaFromBed +bin/mergeBed +bin/multiBamCov +bin/multiIntersectBed +bin/nucBed +bin/pairToBed +bin/pairToPair +bin/randomBed +bin/shiftBed +bin/shuffleBed +bin/slopBed +bin/sortBed +bin/subtractBed +bin/tagBam +bin/unionBedGraphs +bin/windowBed +bin/windowMaker diff --git a/biology/bedtools/distinfo b/biology/bedtools/distinfo new file mode 100644 index 00000000000..de0e24bd048 --- /dev/null +++ b/biology/bedtools/distinfo @@ -0,0 +1,8 @@ +$NetBSD: distinfo,v 1.1 2021/01/22 17:07:50 bacon Exp $ + +SHA1 (bedtools-2.29.2.tar.gz) = 51f03e1cac60f99c062d9babb6385800c89c78f6 +RMD160 (bedtools-2.29.2.tar.gz) = 08ea14501ddfc85f2d4a5a756a10512a61ec93f2 +SHA512 (bedtools-2.29.2.tar.gz) = 06b0016674acb08fd85b80fe1a8ff1ebce5c54c0a30ff7f4e52e63fe5b3f3841413f49df3c51088454d79048ca267fde8c23d9ed51f309ee6916d9b49610be41 +Size (bedtools-2.29.2.tar.gz) = 20638840 bytes +SHA1 (patch-Makefile) = d6a76cb23e623842d6d5c60d67eff928b45b091c +SHA1 (patch-src_utils_htslib_Makefile) = ba513efa59eed05321c176185fb576f4892ea7a5 diff --git a/biology/bedtools/patches/patch-Makefile b/biology/bedtools/patches/patch-Makefile new file mode 100644 index 00000000000..635ff4b1c2e --- /dev/null +++ b/biology/bedtools/patches/patch-Makefile @@ -0,0 +1,45 @@ +$NetBSD: patch-Makefile,v 1.1 2021/01/22 17:07:50 bacon Exp $ + +# Respect pkgsrc env, drop bash dep + +--- Makefile.orig 2019-12-17 20:12:15.000000000 +0000 ++++ Makefile +@@ -4,7 +4,7 @@ + # (c) 2009 Aaron Quinlan + # ========================== + +-SHELL := /bin/bash -e ++SHELL := /bin/sh -e + + VERSION_FILE=./src/utils/version/version_git.h + RELEASED_VERSION_FILE=./src/utils/version/version_release.txt +@@ -21,7 +21,7 @@ OBJ_DIR = obj + BIN_DIR = bin + SRC_DIR = src + +-CXX = g++ ++CXX ?= g++ + + ifeq ($(DEBUG),1) + BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES) +@@ -41,7 +41,7 @@ endif + BT_LDFLAGS = + BT_LIBS = -lz -lm -lbz2 -llzma -lpthread + +-prefix ?= /usr/local ++PREFIX ?= /usr/local + + SUBDIRS = $(SRC_DIR)/annotateBed \ + $(SRC_DIR)/bamToBed \ +@@ -191,9 +191,9 @@ $(BIN_DIR)/intersectBed: | $(BIN_DIR) + .PHONY: all + + install: all +- mkdir -p $(DESTDIR)$(prefix)/bin ++ mkdir -p $(DESTDIR)$(PREFIX)/bin + for file in bin/* ; do \ +- cp -f $$file $(DESTDIR)$(prefix)/bin; \ ++ cp -f $$file $(DESTDIR)$(PREFIX)/bin; \ + done + + print_banner: diff --git a/biology/bedtools/patches/patch-src_utils_htslib_Makefile b/biology/bedtools/patches/patch-src_utils_htslib_Makefile new file mode 100644 index 00000000000..82e9b790b08 --- /dev/null +++ b/biology/bedtools/patches/patch-src_utils_htslib_Makefile @@ -0,0 +1,24 @@ +$NetBSD: patch-src_utils_htslib_Makefile,v 1.1 2021/01/22 17:07:50 bacon Exp $ + +# Respect pkgsrc env + +--- src/utils/htslib/Makefile.orig 2021-01-21 22:49:18.823750624 +0000 ++++ src/utils/htslib/Makefile +@@ -22,7 +22,7 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc ++CC ?= gcc + AR = ar + RANLIB = ranlib + +@@ -33,7 +33,7 @@ CPPFLAGS = + # TODO: probably update cram code to make it compile cleanly with -Wc++-compat + # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600 + #CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__ +-CFLAGS = -g -Wall -O2 ++CFLAGS ?= -g -Wall -O2 + EXTRA_CFLAGS_PIC = -fpic + LDFLAGS = + LIBS = $(htslib_default_libs) -- cgit v1.2.3