Merge pull request #20355 from fizwit/20240412112948_new_pr_STAR2711b

{bio,tools}[GCC/13.2.0] STAR v2.7.11b, xxd v9.1.0307

easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb

@@ -0,0 +1,55 @@
+# Contribution from the NIHR Biomedical Research Centre
+# Guy's and St Thomas' NHS Foundation Trust and King's College London
+# Based on STAR-2.7.7a-GCC-10.2.0.eb 
+# uploaded by J. Sassmannshausen
+# modified by Thomas Eylenbosch
+
+easyblock = 'MakeCp'
+
+name = 'STAR'
+version = '2.7.11b'
+
+homepage = 'https://github.com/alexdobin/STAR'
+description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays."
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+toolchainopts = {'openmp': True}
+
+github_account = 'alexdobin'
+source_urls = [GITHUB_SOURCE]
+sources = ['%(version)s.tar.gz']
+patches = ['STAR-2.7.11a_use-external-htslib.patch']
+checksums = [
+    {'2.7.11b.tar.gz': '3f65305e4112bd154c7e22b333dcdaafc681f4a895048fa30fa7ae56cac408e7'},
+    {'STAR-2.7.11a_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'},
+]
+
+builddependencies = [
+    ('xxd', '9.1.0307'),
+]
+
+dependencies = [
+    ('HTSlib', '1.19.1'),
+    ('zlib', '1.2.13'),
+]
+
+start_dir = 'source'
+
+buildopts = ' STAR && make STARlong'
+
+files_to_copy = [
+    (['source/%(name)s', 'source/%(name)slong'], 'bin'),
+    'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md',
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s', 'bin/%(name)slong'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "STAR --help",
+    "STARlong --help",
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/x/xxd/xxd-9.1.0307-GCCcore-13.2.0.eb

@@ -0,0 +1,37 @@
+# Last contribution from the NIHR Biomedical Research Centre
+# Guy's and St Thomas' NHS Foundation Trust and King's College London
+# uploaded by J. Sassmannshausen
+
+easyblock = 'MakeCp'
+
+name = 'xxd'
+version = '9.1.0307'
+
+homepage = 'https://www.vim.org'
+description = """xxd is part of the VIM package and this will only install xxd, not vim!
+xxd converts to/from hexdumps of binary files."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/vim/vim/archive/refs/tags']
+sources = ['v%(version)s.tar.gz']
+checksums = ['addfe566e4f531f169e0dd0f63747bcf6871a64dadd46dc4b8e539b508187c72']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+start_dir = 'src/xxd'
+
+files_to_copy = [
+    (['xxd'], 'bin'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/xxd'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["xxd -h 2>&1 | grep -A 4 '^Usage:'"]
+
+moduleclass = 'tools'