Merge pull request #460 from bear-rsg/bcftools

BCFtools

easyconfigs/b/BCFtools/BCFtools-1.20-GCC-12.3.0.eb

@@ -0,0 +1,39 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Author: Jonas Demeulemeester
+# The Francis Crick Insitute, London, UK
+
+easyblock = 'ConfigureMake'
+
+name = 'BCFtools'
+version = '1.20'
+
+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': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
+sources = [SOURCELOWER_TAR_BZ2]
+checksums = ['312b8329de5130dd3a37678c712951e61e5771557c7129a70a327a300fda8620']
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('HTSlib', '1.20'),
+    ('bzip2', '1.0.8'),
+    ('XZ', '5.4.2'),
+    ('GSL', '2.7'),
+]
+
+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'

easyconfigs/h/HTSlib/HTSlib-1.20-GCC-12.3.0.eb

@@ -0,0 +1,40 @@
+# 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
+
+easyblock = 'ConfigureMake'
+
+name = 'HTSlib'
+version = '1.20'
+
+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': '12.3.0'}
+
+source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/']
+sources = [SOURCELOWER_TAR_BZ2]
+checksums = ['e52d95b14da68e0cfd7d27faf56fef2f88c2eaf32a2be51c72e146e3aa928544']
+
+# cURL added for S3 support
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('bzip2', '1.0.8'),
+    ('XZ', '5.4.2'),
+    ('cURL', '8.0.1'),
+]
+
+
+sanity_check_paths = {
+    'files': ['bin/bgzip', 'bin/tabix', 'lib/libhts.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'bio'