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[pkgsrc/trunk]: pkgsrc/biology/hisat2 biology/hisat2: Update to 2.2.1
details: https://anonhg.NetBSD.org/pkgsrc/rev/017059e67136
branches: trunk
changeset: 375617:017059e67136
user: bacon <bacon%pkgsrc.org@localhost>
date: Thu Mar 17 16:01:11 2022 +0000
description:
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
diffstat:
biology/hisat2/Makefile | 22 +-
biology/hisat2/PLIST | 29 +-
biology/hisat2/distinfo | 12 +-
biology/hisat2/files/Makefile.pkg | 443 ----------------------
biology/hisat2/patches/patch-Makefile | 145 +++++++
biology/hisat2/patches/patch-hisat2 | 4 +-
biology/hisat2/patches/patch-processor__support.h | 25 +
7 files changed, 198 insertions(+), 482 deletions(-)
diffs (truncated from 758 to 300 lines):
diff -r 158a2c9517dd -r 017059e67136 biology/hisat2/Makefile
--- a/biology/hisat2/Makefile Thu Mar 17 14:35:34 2022 +0000
+++ b/biology/hisat2/Makefile Thu Mar 17 16:01:11 2022 +0000
@@ -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 @@
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"
diff -r 158a2c9517dd -r 017059e67136 biology/hisat2/PLIST
--- a/biology/hisat2/PLIST Thu Mar 17 14:35:34 2022 +0000
+++ b/biology/hisat2/PLIST Thu Mar 17 16:01:11 2022 +0000
@@ -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-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_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_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_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
diff -r 158a2c9517dd -r 017059e67136 biology/hisat2/distinfo
--- a/biology/hisat2/distinfo Thu Mar 17 14:35:34 2022 +0000
+++ b/biology/hisat2/distinfo Thu Mar 17 16:01:11 2022 +0000
@@ -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
diff -r 158a2c9517dd -r 017059e67136 biology/hisat2/files/Makefile.pkg
--- a/biology/hisat2/files/Makefile.pkg Thu Mar 17 14:35:34 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,443 +0,0 @@
-#
-# Generic Makefile for package managers
-# J Bacon <bacon4000%gmail.com@localhost>
-#
-# This Makefile respects standard make variables provided by package
-# managers, such as CXX, CXXFLAGS, etc. It is intended to work on
-# any POSIX platform. Default behaviour should be similar to the
-# original Makefile.
-#
-# This file is part of HISAT2.
-#
-# HISAT 2 is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# HISAT 2 is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with HISAT. If not, see <http://www.gnu.org/licenses/>.
-#
-
-INC =
-GCC_PREFIX = $(shell dirname `which gcc`)
-GCC_SUFFIX =
-
-CC ?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
-CPP ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX)
-CXX ?= $(CPP)
-CXXFLAGS ?= -O2 -Wall
-INSTALL ?= install
-
-HEADERS = $(wildcard *.h)
-BOWTIE_MM = 1
-BOWTIE_SHARED_MEM = 0
-
-MACOS = 0
-ifneq (,$(findstring Darwin,$(shell uname)))
- MACOS = 1
-endif
-
-# EXTRA_FLAGS += -DPOPCNT_CAPABILITY
-INC += -I third_party
-
-MM_DEF =
-
-ifeq (1,$(BOWTIE_MM))
- MM_DEF = -DBOWTIE_MM
-endif
-
-SHMEM_DEF =
-
-ifeq (1,$(BOWTIE_SHARED_MEM))
- SHMEM_DEF = -DBOWTIE_SHARED_MEM
-endif
-
-SEARCH_LIBS =
-BUILD_LIBS =
-INSPECT_LIBS =
-
-USE_SRA = 0
-SRA_DEF =
-SRA_LIB =
-SERACH_INC =
-ifeq (1,$(USE_SRA))
- SRA_DEF = -DUSE_SRA
- SRA_LIB = -lncbi-ngs-c++-static -lngs-c++-static -lncbi-vdb-static -ldl
- SEARCH_INC += -I$(NCBI_NGS_DIR)/include -I$(NCBI_VDB_DIR)/include
- SEARCH_LIBS += -L$(NCBI_NGS_DIR)/lib64 -L$(NCBI_VDB_DIR)/lib64
-endif
-
-LIBS = $(LDFLAGS)
-
-SHARED_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \
- edit.cpp gfm.cpp \
- reference.cpp ds.cpp multikey_qsort.cpp limit.cpp \
- random_source.cpp tinythread.cpp
-SEARCH_CPPS = qual.cpp pat.cpp \
- read_qseq.cpp aligner_seed_policy.cpp \
- aligner_seed.cpp \
- aligner_seed2.cpp \
- aligner_sw.cpp \
- aligner_sw_driver.cpp aligner_cache.cpp \
- aligner_result.cpp ref_coord.cpp mask.cpp \
- pe.cpp aln_sink.cpp dp_framer.cpp \
- scoring.cpp presets.cpp unique.cpp \
- simple_func.cpp \
- random_util.cpp \
- aligner_bt.cpp sse_util.cpp \
- aligner_swsse.cpp outq.cpp \
- aligner_swsse_loc_i16.cpp \
- aligner_swsse_ee_i16.cpp \
- aligner_swsse_loc_u8.cpp \
- aligner_swsse_ee_u8.cpp \
- aligner_driver.cpp \
- splice_site.cpp
-
-SEARCH_OBJS = qual.o pat.o \
- read_qseq.o aligner_seed_policy.o \
- aligner_seed.o \
- aligner_seed2.o \
- aligner_sw.o \
- aligner_sw_driver.o aligner_cache.o \
- aligner_result.o ref_coord.o mask.o \
- pe.o aln_sink.o dp_framer.o \
- scoring.o presets.o unique.o \
- simple_func.o \
- random_util.o \
- aligner_bt.o sse_util.o \
- aligner_swsse.o outq.o \
- aligner_swsse_loc_i16.o \
- aligner_swsse_ee_i16.o \
- aligner_swsse_loc_u8.o \
- aligner_swsse_ee_u8.o \
- aligner_driver.o \
- splice_site.o
-
-BUILD_CPPS = diff_sample.cpp
-
-HISAT2_CPPS_MAIN = $(SEARCH_CPPS) hisat2_main.cpp
-HISAT2_BUILD_CPPS_MAIN = $(BUILD_CPPS) hisat2_build_main.cpp
-
-SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
-VERSION = $(shell cat VERSION)
-
-DEBUG_FLAGS = $(CXXFLAGS) -O0 -g3
-DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
-RELEASE_FLAGS = $(CXXFLAGS)
-RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
-NOASSERT_FLAGS = -DNDEBUG
-FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
-
-ifeq (1,$(USE_SRA))
- ifeq (1, $(MACOS))
- DEBUG_FLAGS += -mmacosx-version-min=10.6
- RELEASE_FLAGS += -mmacosx-version-min=10.6
- endif
-endif
-
-
-HISAT2_BIN_LIST = hisat2-build-s \
- hisat2-build-l \
- hisat2-align-s \
- hisat2-align-l \
- hisat2-inspect-s \
- hisat2-inspect-l
-HISAT2_BIN_LIST_AUX = hisat2-build-s-debug \
- hisat2-build-l-debug \
- hisat2-align-s-debug \
- hisat2-align-l-debug \
- hisat2-inspect-s-debug \
- hisat2-inspect-l-debug
-
-GENERAL_LIST = $(wildcard scripts/*.sh) \
- $(wildcard scripts/*.pl) \
- $(wildcard *.py) \
- $(wildcard hisatgenotype_modules/*.py) \
- $(wildcard hisatgenotype_scripts/*.py) \
- doc/manual.inc.html \
- doc/README \
- doc/style.css \
- $(wildcard example/index/*.ht2) \
- $(wildcard example/reads/*.fa) \
- example/reference/22_20-21M.fa \
- example/reference/22_20-21M.snp \
- $(PTHREAD_PKG) \
- hisat2 \
- hisat2-build \
- hisat2-inspect \
- AUTHORS \
- LICENSE \
- NEWS \
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