# The value of Makefile LIBHTS_SOVERSION. %global so_version 3 Name: htslib Version: 1.15.1 Release: 7%{?dist} Summary: C library for high-throughput sequencing data formats # The entire source code is MIT/Expat except cram/ which is Modified-BSD. # But as there is no "Expat" license in short name list, set "MIT". # Expat license is same with MIT license. # https://lists.fedoraproject.org/archives/list/legal@lists.fedoraproject.org/thread/C5AHVIW3F6LF5CYLR2PSHNANFYKP327P/ # Automatically converted from old format: MIT and BSD - review is highly recommended. License: LicenseRef-Callaway-MIT AND LicenseRef-Callaway-BSD URL: http://www.htslib.org Source0: https://github.com/samtools/%{name}/releases/download/%{version}/%{name}-%{version}.tar.bz2 # Work around a bug found using gcc-12 -O2. # https://github.com/samtools/htscodecs/commit/65bb347f6b0ea7f4a00cb768b3d8004f24ae03c3 Patch0: htslib-1.15.1-gcc12.patch BuildRequires: gcc BuildRequires: bzip2-devel BuildRequires: libcurl-devel BuildRequires: openssl-devel BuildRequires: xz-devel BuildRequires: zlib-devel # It's used in make test. BuildRequires: perl-interpreter BuildRequires: perl(Data::Dumper) BuildRequires: perl(FindBin) BuildRequires: perl(Getopt::Long) BuildRequires: perl(lib) BuildRequires: make %description HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools. %package devel Summary: Development files for %{name} Requires: %{name}%{?_isa} = %{version}-%{release} %description devel The %{name}-devel package contains libraries and header files for developing applications that use %{name}. %package tools Summary: Additional htslib-based tools Requires: %{name}%{?_isa} = %{version}-%{release} %description tools Includes the popular tabix indexer, which creates both .tbi and .csi formats, the htsfile identifier tool, and the bgzip compression utility. %prep %setup -q %patch -P0 -p1 %build %configure CFLAGS="%{optflags}" LDFLAGS="%{build_ldflags}" \ --prefix=%{_prefix} \ --libdir=%{_libdir} \ --enable-plugins \ --with-plugin-path='%{_usr}/local/libexec/htslib:$(plugindir)' \ --enable-gcs \ --enable-libcurl \ --enable-s3 %make_build # As we don't install libhts.a, the .private keywords are irrelevant. sed -i -E '/^(Libs|Requires)\.private:/d' htslib.pc.tmp %install %make_install pushd %{buildroot}/%{_libdir} chmod 755 libhts.so.%{version} popd find %{buildroot} -name '*.la' -delete rm -f %{buildroot}/%{_libdir}/libhts.a %check make test %ldconfig_scriptlets %files %license LICENSE %doc NEWS %{_libdir}/libhts.so.%{version} %{_libdir}/libhts.so.%{so_version} # The plugin so files should be in the main package, # as they are loaded when libhts.so.%%{so_version} is used. %dir %{_libexecdir}/%{name} %{_libexecdir}/%{name}/hfile_gcs.so %{_libexecdir}/%{name}/hfile_libcurl.so %{_libexecdir}/%{name}/hfile_s3.so %{_libexecdir}/%{name}/hfile_s3_write.so # The man5 pages are aimed at users. %{_mandir}/man5/faidx.5* %{_mandir}/man5/sam.5* %{_mandir}/man5/vcf.5* %{_mandir}/man7/htslib-s3-plugin.7* %files devel %dir %{_includedir}/%{name} %{_includedir}/%{name}/*.h %{_libdir}/libhts.so %{_libdir}/pkgconfig/htslib.pc %files tools %{_bindir}/bgzip %{_bindir}/htsfile %{_bindir}/tabix %{_mandir}/man1/bgzip.1* %{_mandir}/man1/htsfile.1* %{_mandir}/man1/tabix.1* %changelog * Mon Sep 02 2024 Miroslav Suchý - 1.15.1-7 - convert license to SPDX * Thu Jul 18 2024 Fedora Release Engineering - 1.15.1-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild * Wed Jan 24 2024 Fedora Release Engineering - 1.15.1-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild * Sat Jan 20 2024 Fedora Release Engineering - 1.15.1-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild * Thu Jul 20 2023 Fedora Release Engineering - 1.15.1-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild * Thu Jan 19 2023 Fedora Release Engineering - 1.15.1-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild * Mon Aug 15 2022 John Marshall - 1.15.1-1 - Update to HTSlib version 1.15.1 - Backport htscodecs GCC 12 compatibility fix * Thu Jul 21 2022 Fedora Release Engineering - 1.13-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild * Thu Jan 20 2022 Fedora Release Engineering - 1.13-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild * Tue Sep 14 2021 Sahana Prasad - 1.13-2 - Rebuilt with OpenSSL 3.0.0 * Fri Jul 23 2021 John Marshall - 1.13-1 - Update to HTSlib version 1.13 - Bump soversion to 3 (the upstream soversion changed in HTSlib 1.10) - Remove zlib-devel dependency as HTSlib headers no longer #include - Fix description: tabix creates .tbi/.csi by indexing other file formats (BAM, VCF, etc) - Add new S3 man page and additional plugin * Thu Jul 22 2021 Fedora Release Engineering - 1.9-9 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild * Tue Jan 26 2021 Fedora Release Engineering - 1.9-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild * Tue Jul 28 2020 Fedora Release Engineering - 1.9-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild * Tue Mar 17 2020 Jun Aruga - 1.9-6 - Fix the build failure adding perl(FindBin) and perl(lib) build dependencies. * Wed Jan 29 2020 Fedora Release Engineering - 1.9-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild * Sat Nov 09 2019 Jun Aruga - 1.9-4 - Align the field delimiter as 1 space. - Add check section and "make test" in it. * Tue Nov 05 2019 John Marshall - 1.9-4 - Remove unneeded pkg-config keywords for static linking, which generated unnecessary htslib-devel dependencies. - Explicitly list zlib-devel dependency, needed for htslib-1.9. * Sun Oct 27 2019 Jun Aruga - 1.9-3 - Fix a bug that %%{_libexecdir}/%%{name} directory is not removed, when uninstalling the package "rpm -e htslib". - Add %%dir to directories to verify the files in the directory. * Tue Oct 22 2019 Jun Aruga - 1.9-2 - Add configure script. - Enable separately-compiled plugins. - Enable support for Google Cloud Storage URLs. - Enable libcurl-based support for http/https/etc URLs. - Enable support for Amazon AWS S3 URLs. - Move the man5 page files to main package. * Fri Sep 06 2019 Jun Aruga - 1.9-1 - Update for htslib version 1.9 * Thu Jun 2 2016 Sam Nicholls - 1.3.1-4 - Fix changelog - Add comment RE:bzip2/lzma support * Sat May 28 2016 Sam Nicholls - 1.3.1-3 - Add LICENSE and NEWS to doc - Remove unnecessary DESTDIR from call to make_install macro - Remove explicit Provides * Thu Apr 28 2016 Sam Nicholls - 1.3.1-1 - Alter permissions of SO to permit strip * Tue Apr 26 2016 Sam Nicholls - 1.3.1-0 - Update for htslib version 1.3.1 * Tue Apr 12 2016 Sam Nicholls - 1.3.0-0 - Initial version