[pkgsrc/trunk]: pkgsrc/biology/bedtools biology/bedtools: import bedtools-2.29.2

[bacon <bacon%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/21a6ac67bb7d
branches:  trunk
changeset: 445398:21a6ac67bb7d
user:      bacon <bacon%pkgsrc.org@localhost>
date:      Fri Jan 22 17:07:50 2021 +0000

description:
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.

diffstat:

 biology/bedtools/DESCR                                   |  10 +++
 biology/bedtools/Makefile                                |  33 +++++++++++
 biology/bedtools/PLIST                                   |  39 +++++++++++++
 biology/bedtools/distinfo                                |   8 ++
 biology/bedtools/patches/patch-Makefile                  |  45 ++++++++++++++++
 biology/bedtools/patches/patch-src_utils_htslib_Makefile |  24 ++++++++
 6 files changed, 159 insertions(+), 0 deletions(-)

diffs (183 lines):

diff -r c36f99899033 -r 21a6ac67bb7d biology/bedtools/DESCR
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/bedtools/DESCR    Fri Jan 22 17:07:50 2021 +0000
@@ -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 -r c36f99899033 -r 21a6ac67bb7d biology/bedtools/Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/bedtools/Makefile Fri Jan 22 17:07:50 2021 +0000
@@ -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"
diff -r c36f99899033 -r 21a6ac67bb7d biology/bedtools/PLIST
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/bedtools/PLIST    Fri Jan 22 17:07:50 2021 +0000
@@ -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 -r c36f99899033 -r 21a6ac67bb7d biology/bedtools/distinfo
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/bedtools/distinfo Fri Jan 22 17:07:50 2021 +0000
@@ -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 -r c36f99899033 -r 21a6ac67bb7d biology/bedtools/patches/patch-Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/bedtools/patches/patch-Makefile   Fri Jan 22 17:07:50 2021 +0000
@@ -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 -r c36f99899033 -r 21a6ac67bb7d biology/bedtools/patches/patch-src_utils_htslib_Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/bedtools/patches/patch-src_utils_htslib_Makefile  Fri Jan 22 17:07:50 2021 +0000
@@ -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)