adding easyconfigs: scNanoGPS-1.1-foss-2023a.eb, LIQA-1.3.4-foss-2023…

…a.eb, lifelines-0.28.0-gfbf-2023a.eb, annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb, BCFtools-1.21-GCC-12.3.0.eb, tabix-0.2.6-GCCcore-12.3.0.eb

easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb

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+# J. Sassmannshausen /NHS/GSTT: toolchain updated to GCCcore-11.2
+
+easyblock = 'Tarball'
+
+name = 'annovar'
+version = '20200607'  # version reported by `annotate_variation.pl -h`
+versionsuffix = '-Perl-%(perlver)s'
+
+homepage = 'http://annovar.openbioinformatics.org/en/latest/'
+description = """ANNOVAR is an efficient software tool to utilize update-to-date information 
+to functionally annotate genetic variants detected from diverse genomes (including human 
+genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others)."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+# Registration required for download
+# http://www.openbioinformatics.org/annovar/annovar_download_form.php
+# rename after download to %(name)s-%(version)s.tar.gz
+sources = ['%(name)s-%(version)s.tar.gz']
+checksums = ['4061af3f2cc8f3d4d8187986c3d468a4b6ae145eec1858e85c7cd1059debb8ed']
+
+dependencies = [('Perl', '5.36.1'),]
+
+modextrapaths = {'PATH': ''}
+
+sanity_check_paths = {
+    'files': ["annotate_variation.pl", "coding_change.pl", "convert2annovar.pl", "retrieve_seq_from_fasta.pl",
+              "variants_reduction.pl", "table_annovar.pl"],
+    'dirs': ["example", "humandb"],
+}
+
+sanity_check_commands = [
+    "annotate_variation.pl --help 2>&1 | grep 'Version: $Date: %s-%s-%s'" % (version[:4], version[4:6], version[6:]),
+    'retrieve_seq_from_fasta.pl --help 2>&1 | grep "reformat sequences at specific genomic positions"',
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/BCFtools/BCFtools-1.21-GCC-12.3.0.eb

@@ -0,0 +1,38 @@
+easyblock = 'ConfigureMake'
+
+name = 'BCFtools'
+version = '1.21'
+
+homepage = 'https://github.com/samtools/bcftools/'
+description = """BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF)
+and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs,
+both uncompressed and BGZF-compressed."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/samtools/bcftools/releases/download/%(version)s/']
+sources = ['%(namelower)s-%(version)s.tar.bz2']
+checksums = ['528a4cc1d3555368db75a700b22a3c95da893fd1827f6d304716dfd45ea4e282']
+
+builddependencies = [
+    ('Autotools', '20220317'),
+]
+dependencies = [
+    ('HTSlib', '1.18'),
+    ('GSL', '2.7'),
+    ('Perl', '5.36.1'),
+]
+
+preconfigopts = 'autoheader && autoconf && '
+configopts = '--enable-libgsl --enable-perl-filters '
+
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': ['bin/bcftools'],
+    'dirs': ['libexec', 'share'],
+}
+
+modextravars = {'BCFTOOLS_PLUGINS': '%(installdir)s/libexec/%(namelower)s'}
+
+moduleclass = 'bio'

easybuild/easyconfigs/l/LIQA/LIQA-1.3.4-foss-2023a.eb

@@ -0,0 +1,33 @@
+easyblock = 'PythonPackage'
+
+name = 'LIQA'
+version = '1.3.4'
+
+homepage = "https://pypi.org/project/liqa/"
+description = """LIQA (Long-read Isoform Quantification and Analysis) is an Expectation-Maximization
+based statistical method to quantify isoform expression and detect differential alternative splicing (DAS)
+events using long-read RNA-seq data."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['f8b2e6f0226d99f513d17be3758e6b3e2e9b7b40579f840d28737e827358850e']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('Pysam', '0.22.0'),
+    ('lifelines', '0.28.0'),
+    ('R', '4.3.2'),
+    ('R-bundle-CRAN', '2023.12'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+options = {'modulename': '%(namelower)s_src'}
+
+sanity_check_commands = ['liqa -h']
+
+moduleclass = 'bio'

easybuild/easyconfigs/l/lifelines/lifelines-0.28.0-gfbf-2023a.eb

@@ -0,0 +1,43 @@
+easyblock = 'PythonBundle'
+
+name = 'lifelines'
+version = '0.28.0'
+
+homepage = "https://lifelines.readthedocs.io/en/latest/"
+description = """Lifelines is a complete survival analysis library, written in pure Python."""
+
+toolchain = {'name': 'gfbf', 'version': '2023a'}
+
+builddependencies = [('poetry', '1.5.1')]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('wrapt', '1.15.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('astor', '0.8.1', {
+        'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'],
+    }),
+    ('interface_meta', '1.3.0', {
+        'checksums': ['8a4493f8bdb73fb9655dcd5115bc897e207319e36c8835f39c516a2d7e9d79a1'],
+    }),
+    ('autograd', '1.6.2', {
+        'checksums': ['8731e08a0c4e389d8695a40072ada4512641c113b6cace8f4cfbe8eb7e9aedeb'],
+    }),
+    ('autograd-gamma', '0.5.0', {
+        'checksums': ['f27abb7b8bb9cffc8badcbf59f3fe44a9db39e124ecacf1992b6d952934ac9c4'],
+    }),
+    ('formulaic', '1.0.1', {
+        'checksums': ['64dd7992a7aa5bbceb1e40679d0f01fc6f0ba12b7d23d78094a88c2edc68fba1'],
+    }),
+    (name, version, {
+        'checksums': ['eecf726453fd409c94fef8a521f8e593bcd09337f920fe885131f01cfe58b25e'],
+    }),
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/s/scNanoGPS/scNanoGPS-1.1-foss-2023a.eb

@@ -0,0 +1,76 @@
+easyblock = 'Tarball'
+
+name = 'scNanoGPS'
+version = '1.1'
+
+homepage = 'https://github.com/gaolabtools/scNanoGPS/'
+description = "Single cell Nanopore sequencing data for Genotype and Phenotype."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/gaolabtools/scNanoGPS/archive/refs/tags/']
+sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+checksums = ['60cce1c771283b6d7a3639aa5744acfd6162306d95dd419ad3c265461fdda218']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('Biopython', '1.83'),
+    ('matplotlib', '3.7.2'),
+    ('Pysam', '0.22.0'),
+    ('Seaborn', '0.13.2'),
+    ('Perl', '5.36.1'),
+    ('minimap2', '2.26'),
+    ('SAMtools', '1.18'),
+    ('tabix', '0.2.6'),
+    ('spoa', '4.1.0'),
+    ('Subread', '2.0.6'),
+    ('Longshot', '1.0.0'),
+    ('BCFtools', '1.21'),
+    ('gffread', '0.12.7'),
+    ('LIQA', '1.3.4'),
+    # Optional - load 'annovar/20200607-GCCcore-12.3.0-Perl-5.36.1' to make 'reporter_SNV.py' work
+]
+
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'download_dep_fail': True,
+    'use_pip': True,
+    'sanity_pip_check': True,
+}
+
+exts_list = [
+    ('Distance', '0.1.3', {
+        'checksums': ['60807584f5b6003f5c521aa73f39f51f631de3be5cccc5a1d67166fcbf0d4551'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    'liqa -h',
+    "python other_utils/read_length_profiler.py -h",
+    "python scanner.py -h",
+    "python assigner.py -h",
+    "python curator.py -h ",
+    "python reporter_expression.py -h",
+    "python reporter_isoform.py -h",
+    "python reporter_SNV.py -h",
+    "python reporter_summary.py -h"
+]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+modloadmsg = """
+If you like to use script 'reporter_SNV.py' you need to load annovar module as:
+'ml annovar/20200607-GCCcore-12.3.0-Perl-5.36.1'
+Source files of annovar (latest) are available after registration on:
+http://www.openbioinformatics.org/annovar/annovar_download_form.php
+"""
+
+moduleclass = 'bio'

easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-12.3.0.eb

@@ -0,0 +1,47 @@
+# 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
+# Author: Jens Timmerman, Ghent University
+# Contribution from the NIHR Biomedical Research Centre
+# Guy's and St Thomas' NHS Foundation Trust and King's College London
+# uploaded by J. Sassmannshausen
+# updated to newer toolchain
+
+easyblock = 'MakeCp'
+
+name = 'tabix'
+version = '0.2.6'
+
+homepage = 'https://samtools.sourceforge.net'
+description = """ Generic indexer for TAB-delimited genome position files """
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = [('https://sourceforge.net/projects/samtools/files/', 'download')]
+sources = [SOURCE_TAR_BZ2]
+checksums = ['e4066be7101bae83bec62bc2bc6917013f6c2875b66eb5055fbb013488d68b73']
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [('zlib', '1.2.13')]
+
+buildopts = 'CC="$CC" CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"'
+
+files_to_copy = [
+    (["tabix", "bgzip", "tabix.py"], "bin"),
+    (["tabix.1"], "man/man1"),
+    (["libtabix.a"], "lib64"),
+    (["*.h"], "include"),
+    "example.gtf.gz",
+    "example.gtf.gz.tbi",
+    "NEWS",
+    "ChangeLog"
+]
+
+sanity_check_paths = {
+    'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py", "lib/libtabix.a"],
+    'dirs': ["include"],
+}
+
+moduleclass = 'bio'