Merge branch 'as-bedtools-2023' into '2023'

BEDTools 2023

See merge request software-team/easybuild!1664

Golden_Repo/b/BEDTools/BEDTools-2.30.0-GCC-11.3.0.eb

+# Author: Maxime Schmitt, University of Luxembourg
+# Author: Adam Huffman, The Francis Crick Institute
+#
+# Based on the work of: Pablo Escobar Lopez
+# Swiss Institute of Bioinformatics (SIB)
+# Biozentrum - University of Basel
+
+easyblock = 'MakeCp'
+
+name = 'BEDTools'
+version = '2.30.0'
+
+homepage = "https://bedtools.readthedocs.io/"
+description = """BEDTools: a powerful toolset for genome arithmetic.
+The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and
+computing coverage.
+The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM."""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['333ad1ffcdc6e36005b4d6c9290677986ee97871cff92ed821c1b643d38150b8']
+
+builddependencies = [('Python', '3.10.4')]
+
+dependencies = [
+    ('XZ', '5.2.5'),
+    ('zlib', '1.2.12'),
+    ('bzip2', '1.0.8'),
+    ('BamTools', '2.5.2'),
+]
+
+buildopts = 'CXX="$CXX"'
+
+files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']],
+    'dirs': files_to_copy,
+}
+
+sanity_check_commands = ['bedtools --help']
+
+moduleclass = 'bio'

Golden_Repo/b/BamTools/BamTools-2.5.2-GCC-11.3.0.eb

+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+name = 'BamTools'
+version = '2.5.2'
+
+homepage = 'https://github.com/pezmaster31/bamtools'
+description = "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files."
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+toolchainopts = {'pic': True}
+
+# https://github.com/pezmaster31/bamtools
+github_account = 'pezmaster31'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['4d8b84bd07b673d0ed41031348f10ca98dd6fa6a4460f9b9668d6f1d4084dfc8']
+
+builddependencies = [('CMake', '3.23.1')]
+
+moduleclass = 'bio'

acls.yml

@@ -438,6 +438,14 @@ software:
   - name: 'Bazel'
     owner: 'strube1'
     base: True
+  - name: 'BAMTools'
+    owner: 'strube1'
+    base: True
+    compiler: True
+  - name: 'BEDTools'
+    owner: 'strube1'
+    base: True
+    compiler: True
   - name: 'bokeh'
     owner: 'strube1'
     base: True