Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

…asyconfigs into tagbot_merge

.github/workflows/tagbot.yml

@@ -2,7 +2,7 @@ name: Tagbot
 on: [pull_request_target]
 
 concurrency:
-  group: "${{ github.workflow }}-${{ github.ref }}"
+  group: "${{ github.workflow }}-${{ github.event.pull_request.number }}"
   cancel-in-progress: true
 
 jobs:

easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.4.0-foss-2023a.eb

@@ -19,7 +19,7 @@ dependencies = [
     ('prodigal', '2.6.3'),
     ('HMMER', '3.4'),
     ('pplacer', '1.1.alpha19', '', SYSTEM),
-    ('FastANI', '1.34'),
+    ('skani', '0.2.2'),
     ('FastTree', '2.1.11'),
     ('Mash', '2.3'),
     ('tqdm', '4.66.1'),

easybuild/easyconfigs/i/intel-compilers/intel-compilers-2025.0.0.eb

@@ -0,0 +1,37 @@
+name = 'intel-compilers'
+version = '2025.0.0'
+
+homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html'
+description = "Intel C, C++ & Fortran compilers"
+
+toolchain = SYSTEM
+
+# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
+sources = [
+    {
+        'source_urls': [
+            'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/ac92f2bb-4818-4e53-a432-f8b34d502f23/'
+        ],
+        'filename': 'intel-dpcpp-cpp-compiler-%(version)s.740_offline.sh',
+    },
+    {
+        'source_urls': [
+            'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/69f79888-2d6c-4b20-999e-e99d72af68d4/'
+        ],
+        'filename': 'intel-fortran-compiler-%(version)s.723_offline.sh',
+    },
+]
+checksums = [
+    {'intel-dpcpp-cpp-compiler-2025.0.0.740_offline.sh':
+     '04fadf63789acee731895e631db63f65a98b8279db3d0f48bdf0d81e6103bdd8'},
+    {'intel-fortran-compiler-2025.0.0.723_offline.sh':
+     '2be6d607ce84f35921228595b118fbc516d28587cbc4e6dcf6b7219e5cd1a9a9'},
+]
+
+local_gccver = '14.2.0'
+dependencies = [
+    ('GCCcore', local_gccver),
+    ('binutils', '2.42', '', ('GCCcore', local_gccver)),
+]
+
+moduleclass = 'compiler'

easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-20240119-GCCcore-12.3.0.eb

@@ -0,0 +1,28 @@
+easyblock = 'PythonPackage'
+
+name = 'Porechop'
+version = '0.2.4-20240119'
+local_commit = 'd2e77c6'
+
+homepage = 'https://github.com/dehui333/Porechop'
+description = """Porechop is a tool for finding and removing adapters from Oxford Nanopore reads.
+ Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle,
+ it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments
+ to effectively find adapters, even at low sequence identity."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/dehui333/Porechop/archive/']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+checksums = ['6e5ff3a780fc2855b0101b4a6102437d9a0fc201e40ffabc44c0c67d7c9ad621']
+
+builddependencies = [('binutils', '2.40')]
+dependencies = [('Python', '3.11.3')]
+
+sanity_pip_check = True
+use_pip = True
+download_dep_fail = True
+
+sanity_check_commands = ['%(namelower)s -h']
+
+moduleclass = 'bio'

easybuild/easyconfigs/s/Stacks/Stacks-2.68-foss-2023a.eb

@@ -0,0 +1,29 @@
+easyblock = 'ConfigureMake'
+
+name = 'Stacks'
+version = '2.68'
+
+homepage = 'https://catchenlab.life.illinois.edu/stacks/'
+description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on
+ the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq,
+ for the purpose of building genetic maps and conducting population genomics and phylogeography.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://catchenlab.life.illinois.edu/stacks/source/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['9dc51ea356d60eb4557b0b2d1a8854aafae492aed87f974e0249cc09aa5e7650']
+
+dependencies = [
+    ('zlib', '1.2.13'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/clone_filter', 'bin/cstacks', 'bin/gstacks', 'bin/kmer_filter', 'bin/phasedstacks',
+              'bin/populations', 'bin/process_radtags', 'bin/process_shortreads', 'bin/sstacks',
+              'bin/tsv2bam', 'bin/ustacks'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'