CVS commit: pkgsrc/biology/bedtools

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Fri Jan 22 17:07:50 UTC 2021

Added Files:
        pkgsrc/biology/bedtools: DESCR Makefile PLIST distinfo
        pkgsrc/biology/bedtools/patches: patch-Makefile
            patch-src_utils_htslib_Makefile

Log Message:
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.


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/bedtools/DESCR \
    pkgsrc/biology/bedtools/Makefile pkgsrc/biology/bedtools/PLIST \
    pkgsrc/biology/bedtools/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/bedtools/patches/patch-Makefile \
    pkgsrc/biology/bedtools/patches/patch-src_utils_htslib_Makefile

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Added files:

Index: pkgsrc/biology/bedtools/DESCR
diff -u /dev/null pkgsrc/biology/bedtools/DESCR:1.1
--- /dev/null   Fri Jan 22 17:07:50 2021
+++ pkgsrc/biology/bedtools/DESCR       Fri Jan 22 17:07:50 2021
@@ -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.
Index: pkgsrc/biology/bedtools/Makefile
diff -u /dev/null pkgsrc/biology/bedtools/Makefile:1.1
--- /dev/null   Fri Jan 22 17:07:50 2021
+++ pkgsrc/biology/bedtools/Makefile    Fri Jan 22 17:07:50 2021
@@ -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@localhost
+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 <version> 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"
Index: pkgsrc/biology/bedtools/PLIST
diff -u /dev/null pkgsrc/biology/bedtools/PLIST:1.1
--- /dev/null   Fri Jan 22 17:07:50 2021
+++ pkgsrc/biology/bedtools/PLIST       Fri Jan 22 17:07:50 2021
@@ -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
Index: pkgsrc/biology/bedtools/distinfo
diff -u /dev/null pkgsrc/biology/bedtools/distinfo:1.1
--- /dev/null   Fri Jan 22 17:07:50 2021
+++ pkgsrc/biology/bedtools/distinfo    Fri Jan 22 17:07:50 2021
@@ -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

Index: pkgsrc/biology/bedtools/patches/patch-Makefile
diff -u /dev/null pkgsrc/biology/bedtools/patches/patch-Makefile:1.1
--- /dev/null   Fri Jan 22 17:07:50 2021
+++ pkgsrc/biology/bedtools/patches/patch-Makefile      Fri Jan 22 17:07:50 2021
@@ -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:
Index: pkgsrc/biology/bedtools/patches/patch-src_utils_htslib_Makefile
diff -u /dev/null pkgsrc/biology/bedtools/patches/patch-src_utils_htslib_Makefile:1.1
--- /dev/null   Fri Jan 22 17:07:50 2021
+++ pkgsrc/biology/bedtools/patches/patch-src_utils_htslib_Makefile     Fri Jan 22 17:07:50 2021
@@ -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)