CVS commit: pkgsrc/biology/hisat2

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/biology/hisat2
From: "Jason Bacon" <bacon%netbsd.org@localhost>
Date: Thu, 17 Mar 2022 16:01:12 +0000

Module Name:    pkgsrc
Committed By:   bacon
Date:           Thu Mar 17 16:01:12 UTC 2022

Modified Files:
        pkgsrc/biology/hisat2: Makefile PLIST distinfo
        pkgsrc/biology/hisat2/patches: patch-hisat2
Added Files:
        pkgsrc/biology/hisat2/patches: patch-Makefile
            patch-processor__support.h
Removed Files:
        pkgsrc/biology/hisat2/files: Makefile.pkg

Log Message:
biology/hisat2: Update to 2.2.1

pkgsrc fix: Unbreak build on Darwin

Add python3 support
Several bug fixes and enhancements
Changes: https://github.com/DaehwanKimLab/hisat2/tags


To generate a diff of this commit:
cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/hisat2/Makefile
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/hisat2/PLIST
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/hisat2/distinfo
cvs rdiff -u -r1.1 -r0 pkgsrc/biology/hisat2/files/Makefile.pkg
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/hisat2/patches/patch-Makefile \
    pkgsrc/biology/hisat2/patches/patch-processor__support.h
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/hisat2/patches/patch-hisat2

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

Modified files:

Index: pkgsrc/biology/hisat2/Makefile
diff -u pkgsrc/biology/hisat2/Makefile:1.6 pkgsrc/biology/hisat2/Makefile:1.7
--- pkgsrc/biology/hisat2/Makefile:1.6  Mon May 24 19:49:11 2021
+++ pkgsrc/biology/hisat2/Makefile      Thu Mar 17 16:01:11 2022
@@ -1,10 +1,9 @@
-# $NetBSD: Makefile,v 1.6 2021/05/24 19:49:11 wiz Exp $
+# $NetBSD: Makefile,v 1.7 2022/03/17 16:01:11 bacon Exp $
 
-DISTNAME=      hisat2-2.1.0.23
-PKGREVISION=   5
+DISTNAME=      hisat2-2.2.1
 CATEGORIES=    biology
-MASTER_SITES=  ${MASTER_SITE_GITHUB:=infphilo/}
-GITHUB_TAG=    20f333e2cfe7ff4d1362b248912893e2644683d7
+MASTER_SITES=  ${MASTER_SITE_GITHUB:=DaehwanKimLab/}
+GITHUB_TAG=    v${PKGVERSION_NOREV}
 
 MAINTAINER=    bacon%NetBSD.org@localhost
 HOMEPAGE=      https://ccb.jhu.edu/software/hisat2/index.shtml
@@ -17,13 +16,16 @@ ONLY_FOR_PLATFORM=  *-*-x86_64
 USE_LANGUAGES= c c++
 USE_TOOLS+=    bash gmake perl
 
-REPLACE_BASH=          hisatgenotype_scripts/*.sh
-REPLACE_PERL=          hisat2 scripts/*.sh scripts/*.pl
-REPLACE_PYTHON=                *.py hisat2-build hisat2-inspect
-REPLACE_PYTHON+=       hisatgenotype_modules/*.py hisatgenotype_scripts/*.py
+REPLACE_BASH=          scripts/*.sh
+REPLACE_PERL=          hisat2 scripts/*.sh scripts/*.pl scripts/*.py
+REPLACE_PYTHON=                *.py scripts/*.py hisat2-build hisat2-inspect
 
-MAKE_FILE=             ${FILESDIR}/Makefile.pkg
 PTHREAD_AUTO_VARS=     yes
+WRKSRC=                        ${WRKDIR}/hisat2-2.2.1
+
+# Unbreak #include <version> on case-insensitive file systems
+post-patch:
+       ${MV} ${WRKSRC}/VERSION ${WRKSRC}/HISAT2_VERSION
 
 .include "../../lang/python/application.mk"
 .include "../../mk/pthread.buildlink3.mk"

Index: pkgsrc/biology/hisat2/PLIST
diff -u pkgsrc/biology/hisat2/PLIST:1.1 pkgsrc/biology/hisat2/PLIST:1.2
--- pkgsrc/biology/hisat2/PLIST:1.1     Tue Jan 15 01:26:29 2019
+++ pkgsrc/biology/hisat2/PLIST Thu Mar 17 16:01:11 2022
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.1 2019/01/15 01:26:29 bacon Exp $
+@comment $NetBSD: PLIST,v 1.2 2022/03/17 16:01:11 bacon Exp $
 bin/hisat2
 bin/hisat2-align-l
 bin/hisat2-align-s
@@ -8,9 +8,8 @@ bin/hisat2-build-s
 bin/hisat2-inspect
 bin/hisat2-inspect-l
 bin/hisat2-inspect-s
-libexec/hisat2/compare_HLA_Omixon.py
+bin/hisat2-repeat
 libexec/hisat2/convert_quals.pl
-libexec/hisat2/extract_Omixon_HLA.py
 libexec/hisat2/extract_exons.py
 libexec/hisat2/extract_splice_sites.py
 libexec/hisat2/gen_2b_occ_lookup.pl
@@ -20,21 +19,8 @@ libexec/hisat2/hisat2_extract_exons.py
 libexec/hisat2/hisat2_extract_snps_haplotypes_UCSC.py
 libexec/hisat2/hisat2_extract_snps_haplotypes_VCF.py
 libexec/hisat2/hisat2_extract_splice_sites.py
+libexec/hisat2/hisat2_read_statistics.py
 libexec/hisat2/hisat2_simulate_reads.py
-libexec/hisat2/hisatgenotype.py
-libexec/hisat2/hisatgenotype_HLA_genotyping_PGs.py
-libexec/hisat2/hisatgenotype_assembly_graph.py
-libexec/hisat2/hisatgenotype_build_genome.py
-libexec/hisat2/hisatgenotype_convert_codis.py
-libexec/hisat2/hisatgenotype_extract_codis_data.py
-libexec/hisat2/hisatgenotype_extract_cyp_data.py
-libexec/hisat2/hisatgenotype_extract_reads.py
-libexec/hisat2/hisatgenotype_extract_vars.py
-libexec/hisat2/hisatgenotype_gene_typing.py
-libexec/hisat2/hisatgenotype_hla_cyp.py
-libexec/hisat2/hisatgenotype_locus.py
-libexec/hisat2/hisatgenotype_locus_samples.py
-libexec/hisat2/hisatgenotype_typing_common.py
 libexec/hisat2/infer_fraglen.pl
 libexec/hisat2/make_a_thaliana_tair.sh
 libexec/hisat2/make_b_taurus_UMD3.sh
@@ -50,7 +36,9 @@ libexec/hisat2/make_grch37_snp_tran.sh
 libexec/hisat2/make_grch37_snp_tran_ercc.sh
 libexec/hisat2/make_grch37_tran.sh
 libexec/hisat2/make_grch38.sh
+libexec/hisat2/make_grch38_rep.sh
 libexec/hisat2/make_grch38_snp.sh
+libexec/hisat2/make_grch38_snp_rep.sh
 libexec/hisat2/make_grch38_snp_tran.sh
 libexec/hisat2/make_grch38_snp_tran_ercc.sh
 libexec/hisat2/make_grch38_tran.sh
@@ -75,8 +63,5 @@ libexec/hisat2/make_sc3.sh
 libexec/hisat2/make_wbcel235.sh
 libexec/hisat2/make_wbcel235_tran.sh
 libexec/hisat2/make_zm3_snp_tran_ercc.sh
-libexec/hisat2/run_extract_CP.sh
-libexec/hisat2/run_extract_ILMN.sh
-libexec/hisat2/run_genotype_build.sh
-libexec/hisat2/run_hisat2_build.sh
-libexec/hisat2/run_type_CP.sh
+libexec/hisat2/sa.py
+libexec/hisat2/validate_repeat.py

Index: pkgsrc/biology/hisat2/distinfo
diff -u pkgsrc/biology/hisat2/distinfo:1.3 pkgsrc/biology/hisat2/distinfo:1.4
--- pkgsrc/biology/hisat2/distinfo:1.3  Tue Oct 26 10:03:40 2021
+++ pkgsrc/biology/hisat2/distinfo      Thu Mar 17 16:01:11 2022
@@ -1,6 +1,8 @@
-$NetBSD: distinfo,v 1.3 2021/10/26 10:03:40 nia Exp $
+$NetBSD: distinfo,v 1.4 2022/03/17 16:01:11 bacon Exp $
 
-BLAKE2s (hisat2-2.1.0.23-20f333e2cfe7ff4d1362b248912893e2644683d7.tar.gz) = 6b114a873cfb9fa79a3e5e8d72495893d4d3fbadebc924e5826e5de2176e1397
-SHA512 (hisat2-2.1.0.23-20f333e2cfe7ff4d1362b248912893e2644683d7.tar.gz) = 
5514f7462a6738e5fed5ef3bd2eb782e867178cd68eb36324407628b446a151d096326d859b2986877a26206ad182281ecac29f2abd01991c0640c5e4c5e5e0b
-Size (hisat2-2.1.0.23-20f333e2cfe7ff4d1362b248912893e2644683d7.tar.gz) = 3975385 bytes
-SHA1 (patch-hisat2) = ea55c8a99dcd2fd3651e832fbb402b94d0ea3fed
+BLAKE2s (hisat2-2.2.1.tar.gz) = 1cc424a10f1fcf25c70294bef3b21e67b07cebcb7b73e36c0176a2dfdec51bdb
+SHA512 (hisat2-2.2.1.tar.gz) = a5a688ad0ccfaf326b3ec6dc97206995306aa6f5b6e58223c2113adbca2745f1e8205b436fdf8e01f42da7a38718f9f3bf214b951fb5360d53247d99a0bdbf46
+Size (hisat2-2.2.1.tar.gz) = 6761242 bytes
+SHA1 (patch-Makefile) = 067b766ecebacd840db4a287bba25d2d2264b339
+SHA1 (patch-hisat2) = 6010f5fcc1e7dfcb383a4defc4e3d9f06322370d
+SHA1 (patch-processor__support.h) = 56d9cd4ba18e37879acba521a0f431fe2b4290af

Index: pkgsrc/biology/hisat2/patches/patch-hisat2
diff -u pkgsrc/biology/hisat2/patches/patch-hisat2:1.1 pkgsrc/biology/hisat2/patches/patch-hisat2:1.2
--- pkgsrc/biology/hisat2/patches/patch-hisat2:1.1      Tue Jan 15 01:26:29 2019
+++ pkgsrc/biology/hisat2/patches/patch-hisat2  Thu Mar 17 16:01:12 2022
@@ -1,6 +1,6 @@
-$NetBSD: patch-hisat2,v 1.1 2019/01/15 01:26:29 bacon Exp $
+$NetBSD: patch-hisat2,v 1.2 2022/03/17 16:01:12 bacon Exp $
 
-# Limit Windows-specific patches to Windows
+# Support BSD, etc.
 
 --- hisat2.orig        2018-11-07 21:43:32 UTC
 +++ hisat2

Added files:

Index: pkgsrc/biology/hisat2/patches/patch-Makefile
diff -u /dev/null pkgsrc/biology/hisat2/patches/patch-Makefile:1.1
--- /dev/null   Thu Mar 17 16:01:12 2022
+++ pkgsrc/biology/hisat2/patches/patch-Makefile        Thu Mar 17 16:01:12 2022
@@ -0,0 +1,145 @@
+$NetBSD: patch-Makefile,v 1.1 2022/03/17 16:01:12 bacon Exp $
+
+# Respect env
+
+--- Makefile.orig      2020-07-24 20:07:54.000000000 +0000
++++ Makefile
+@@ -23,9 +23,11 @@
+ INC =
+ GCC_PREFIX = $(shell dirname `which gcc`)
+ GCC_SUFFIX =
+-CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
+-CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
+-CXX = $(CPP)
++CC    ?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
++CPP   ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX)
++CXX   ?= $(CPP)
++INSTALL       ?= install
++
+ HEADERS = $(wildcard *.h)
+ BOWTIE_MM = 1
+ BOWTIE_SHARED_MEM = 0
+@@ -55,7 +57,7 @@ ifneq (,$(findstring Darwin,$(shell unam
+       MACOS = 1
+ endif
+ 
+-EXTRA_FLAGS += -DPOPCNT_CAPABILITY -std=c++11
++EXTRA_FLAGS += -std=c++11
+ INC += -I. -I third_party 
+ 
+ MM_DEF = 
+@@ -150,33 +152,11 @@ HISAT2_BUILD_CPPS_MAIN = $(BUILD_CPPS) h
+ HISAT2_REPEAT_CPPS_MAIN = $(REPEAT_CPPS) $(BUILD_CPPS) hisat2_repeat_main.cpp
+ 
+ SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
+-VERSION = $(shell cat VERSION)
+-
+-# Convert BITS=?? to a -m flag
+-BITS=32
+-ifeq (x86_64,$(shell uname -m))
+-BITS=64
+-endif
+-# msys will always be 32 bit so look at the cpu arch instead.
+-ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
+-      ifeq (1,$(MINGW))
+-              BITS=64
+-      endif
+-endif
+-BITS_FLAG =
+-
+-ifeq (32,$(BITS))
+-      BITS_FLAG = -m32
+-endif
+-
+-ifeq (64,$(BITS))
+-      BITS_FLAG = -m64
+-endif
+-SSE_FLAG=-msse2
++HISAT2_VERSION = $(shell cat HISAT2_VERSION)
+ 
+ DEBUG_FLAGS    = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG)
+ DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
+-RELEASE_FLAGS  = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3
++RELEASE_FLAGS  = $(CXXFLAGS)
+ RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
+ NOASSERT_FLAGS = -DNDEBUG
+ FILE_FLAGS     = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
+@@ -251,7 +231,7 @@ GENERAL_LIST = $(wildcard scripts/*.sh) 
+       MANUAL \
+       MANUAL.markdown \
+       TUTORIAL \
+-      VERSION
++      HISAT2_VERSION
+ 
+ ifeq (1,$(WINDOWS))
+       HISAT2_BIN_LIST := $(HISAT2_BIN_LIST) hisat2.bat hisat2-build.bat hisat2-inspect.bat 
+@@ -287,7 +267,7 @@ repeat: hisat2-repeat
+ repeat-debug: hisat2-repeat-debug
+ 
+ DEFS=-fno-strict-aliasing \
+-     -DHISAT2_VERSION="\"`cat VERSION`\"" \
++     -DHISAT2_VERSION="\"`cat HISAT2_VERSION`\"" \
+      -DBUILD_HOST="\"`hostname`\"" \
+      -DBUILD_TIME="\"`date`\"" \
+      -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
+@@ -517,12 +497,12 @@ hisat2-inspect.bat:
+ hisat2-src: $(SRC_PKG_LIST)
+       chmod a+x scripts/*.sh scripts/*.pl
+       mkdir .src.tmp
+-      mkdir .src.tmp/hisat2-$(VERSION)
++      mkdir .src.tmp/hisat2-$(HISAT2_VERSION)
+       zip tmp.zip $(SRC_PKG_LIST)
+-      mv tmp.zip .src.tmp/hisat2-$(VERSION)
+-      cd .src.tmp/hisat2-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
+-      cd .src.tmp ; zip -r hisat2-$(VERSION)-source.zip hisat2-$(VERSION)
+-      cp .src.tmp/hisat2-$(VERSION)-source.zip .
++      mv tmp.zip .src.tmp/hisat2-$(HISAT2_VERSION)
++      cd .src.tmp/hisat2-$(HISAT2_VERSION) ; unzip tmp.zip ; rm -f tmp.zip
++      cd .src.tmp ; zip -r hisat2-$(HISAT2_VERSION)-source.zip hisat2-$(HISAT2_VERSION)
++      cp .src.tmp/hisat2-$(HISAT2_VERSION)-source.zip .
+       rm -rf .src.tmp
+ 
+ .PHONY: hisat2-bin
+@@ -530,16 +510,16 @@ hisat2-bin: $(BIN_PKG_LIST) $(HISAT2_BIN
+       chmod a+x scripts/*.sh scripts/*.pl
+       rm -rf .bin.tmp
+       mkdir .bin.tmp
+-      mkdir .bin.tmp/hisat2-$(VERSION)
++      mkdir .bin.tmp/hisat2-$(HISAT2_VERSION)
+       if [ -f hisat2.exe ] ; then \
+               zip tmp.zip $(BIN_PKG_LIST) $(addsuffix .exe,$(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX)) ; \
+       else \
+               zip tmp.zip $(BIN_PKG_LIST) $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX) ; \
+       fi
+-      mv tmp.zip .bin.tmp/hisat2-$(VERSION)
+-      cd .bin.tmp/hisat2-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
+-      cd .bin.tmp ; zip -r hisat2-$(VERSION)-$(BITS).zip hisat2-$(VERSION)
+-      cp .bin.tmp/hisat2-$(VERSION)-$(BITS).zip .
++      mv tmp.zip .bin.tmp/hisat2-$(HISAT2_VERSION)
++      cd .bin.tmp/hisat2-$(HISAT2_VERSION) ; unzip tmp.zip ; rm -f tmp.zip
++      cd .bin.tmp ; zip -r hisat2-$(HISAT2_VERSION)-$(BITS).zip hisat2-$(HISAT2_VERSION)
++      cp .bin.tmp/hisat2-$(HISAT2_VERSION)-$(BITS).zip .
+       rm -rf .bin.tmp
+ 
+ .PHONY: doc
+@@ -554,6 +534,20 @@ doc/manual.inc.html: MANUAL.markdown
+ MANUAL: MANUAL.markdown
+       perl doc/strip_markdown.pl < $^ > $@
+ 
++# Install per filesystem hierarchy standard:
++# https://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard
++
++.PHONY: install
++install:
++      mkdir -p ${DESTDIR}${PREFIX}/bin
++      ${INSTALL} -c -s ${HISAT2_BIN_LIST} ${DESTDIR}${PREFIX}/bin
++      ${INSTALL} -c hisat2 hisat2-build hisat2-inspect \
++              ${DESTDIR}${PREFIX}/bin
++
++      mkdir -p ${DESTDIR}${PREFIX}/libexec/hisat2
++      ${INSTALL} -c scripts/*.sh scripts/*.pl scripts/*.py *.py \
++              ${DESTDIR}${PREFIX}/libexec/hisat2
++
+ .PHONY: clean
+ clean:
+       rm -f $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX) \
Index: pkgsrc/biology/hisat2/patches/patch-processor__support.h
diff -u /dev/null pkgsrc/biology/hisat2/patches/patch-processor__support.h:1.1
--- /dev/null   Thu Mar 17 16:01:12 2022
+++ pkgsrc/biology/hisat2/patches/patch-processor__support.h    Thu Mar 17 16:01:12 2022
@@ -0,0 +1,25 @@
+$NetBSD: patch-processor__support.h,v 1.1 2022/03/17 16:01:12 bacon Exp $
+
+# Support non-x86
+
+--- processor_support.h.orig   2020-07-24 20:07:54 UTC
++++ processor_support.h
+@@ -12,7 +12,7 @@
+ 
+ #if defined(__INTEL_COMPILER)
+ #   define USING_INTEL_COMPILER
+-#elif defined(__GNUC__)
++#elif defined(__GNUC__) && (defined(__amd64__) || defined(__i386__))
+ #   define USING_GCC_COMPILER
+ #   include <cpuid.h>
+ #elif defined(_MSC_VER)
+@@ -52,8 +52,7 @@ class ProcessorSupport { (public)
+ #elif defined(USING_GCC_COMPILER)
+         __get_cpuid(0x1, &regs.EAX, &regs.EBX, &regs.ECX, &regs.EDX);
+ #else
+-        std::cerr << "ERROR: please define __cpuid() for this build.\n"; 
+-        assert(0);
++      return false;
+ #endif
+         if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false;
+     }

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