Merge pull request #21769 from jpecar/20241030133828_new_pr_BCFtools121

{bio}[GCC/13.3.0] BCFtools v1.21, HTSlib v1.21, SAMtools v1.21

easybuild/easyconfigs/b/BCFtools/BCFtools-1.21-GCC-13.3.0.eb

@@ -0,0 +1,40 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Author: Jonas Demeulemeester
+# The Francis Crick Insitute, London, UK
+# Updated to 1.21 jpecar / EMBL
+
+easyblock = 'ConfigureMake'
+
+name = 'BCFtools'
+version = '1.21'
+
+homepage = 'https://www.htslib.org/'
+description = """Samtools is a suite of programs for interacting with high-throughput sequencing data.
+ BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence
+ variants"""
+
+toolchain = {'name': 'GCC', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
+sources = [SOURCELOWER_TAR_BZ2]
+checksums = ['528a4cc1d3555368db75a700b22a3c95da893fd1827f6d304716dfd45ea4e282']
+
+dependencies = [
+    ('zlib', '1.3.1'),
+    ('HTSlib', '1.21'),
+    ('bzip2', '1.0.8'),
+    ('XZ', '5.4.5'),
+    ('GSL', '2.8'),
+]
+
+configopts = "--with-htslib=$EBROOTHTSLIB --enable-libgsl"
+
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s', 'bin/plot-vcfstats', 'bin/vcfutils.pl'],
+    'dirs': ['libexec/%(namelower)s'],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/h/HTSlib/HTSlib-1.21-GCC-13.3.0.eb

@@ -0,0 +1,41 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Pablo Escobar Lopez
+# Swiss Institute of Bioinformatics
+# Biozentrum - University of Basel
+# 1.4 modified by:
+# Adam Huffman, Jonas Demeulemeester
+# The Francis Crick Institute
+# Updated to 1.14
+# J. Sassmannshausen /GSTT
+# Updated to 1.21 jpecar EMBL
+
+easyblock = 'ConfigureMake'
+
+name = 'HTSlib'
+version = '1.21'
+
+homepage = 'https://www.htslib.org/'
+description = """A C library for reading/writing high-throughput sequencing data.
+ This package includes the utilities bgzip and tabix"""
+
+toolchain = {'name': 'GCC', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/']
+sources = [SOURCELOWER_TAR_BZ2]
+checksums = ['84b510e735f4963641f26fd88c8abdee81ff4cb62168310ae716636aac0f1823']
+
+# cURL added for S3 support
+dependencies = [
+    ('zlib', '1.3.1'),
+    ('bzip2', '1.0.8'),
+    ('XZ', '5.4.5'),
+    ('cURL', '8.7.1'),
+]
+
+
+sanity_check_paths = {
+    'files': ['bin/bgzip', 'bin/tabix', 'lib/libhts.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/s/SAMtools/SAMtools-1.21-GCC-13.3.0.eb

@@ -0,0 +1,38 @@
+# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia
+# Homepage:     https://staff.flinders.edu.au/research/deep-thought
+#
+# Authors::     Robert Qiao <[email protected]>
+# License::     MIT
+#
+# Notes::
+#
+# Updated to 1.14 and gcc-11.2.0
+# J. Sassmannshausen / GSTT
+# Updated to 1.21 jpecar / EMBL
+
+name = 'SAMtools'
+version = '1.21'
+
+homepage = 'https://www.htslib.org/'
+description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, 
+ including sorting, merging, indexing and generating alignments in a per-position format."""
+
+toolchain = {'name': 'GCC', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/%(version)s']
+sources = [SOURCELOWER_TAR_BZ2]
+checksums = ['05724b083a6b6f0305fcae5243a056cc36cf826309c3cb9347a6b89ee3fc5ada']
+
+# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression.
+# The latter is currently provided by XZ.
+dependencies = [
+    ('ncurses', '6.5'),
+    ('zlib', '1.3.1'),
+    ('bzip2', '1.0.8'),
+    ('XZ', '5.4.5'),
+    ('cURL', '8.7.1'),
+]
+
+
+moduleclass = 'bio'