diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb new file mode 100644 index 00000000000..af21d1b6a0d --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb @@ -0,0 +1,84 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) +# Updated to 1.5.0 +# Jasper Grimm (UoY) +# Updated: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.12.0' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +builddependencies = [('Autotools', '20220317')] + +_minimap_ver = '2.26' +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # includes cffi + ('TensorFlow', '2.13.0'), + ('Pysam', '0.22.0'), + ('SAMtools', '1.18'), + ('minimap2', _minimap_ver), + ('HTSlib', '1.18'), # for tabix, bgzip + ('Racon', '1.5.0'), + ('edlib', '1.3.9'), + ('pyspoa', '0.2.1'), + ('python-parasail', '1.3.4'), + ('ont-fast5-api', '4.1.2'), + ('WhatsHap', '2.2'), + ('intervaltree-python', '3.1.0'), + ('BCFtools', '1.18'), +] + +use_pip = True +sanity_pip_check = True + +local_sed_commands = [ + "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml", + # Python 3.11 support + "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py", +] + +exts_list = [ + ('mappy', _minimap_ver, { + 'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'], + }), + ('wurlitzer', '3.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'], + }), + # medaka 1.12.0 requires h5py ~=3.10.0 + ('h5py', '3.10.0', { + 'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'], + }), + ('pyabpoa', '1.5.1', { + 'checksums': ['878f981e890a421d92a0d7606705d0ad9813ae6086239460dfe4b0cfc7476174'], + }), + (name, version, { + 'checksums': ['039219204111a8114b1f72d87d0d3463e43473790cff4520c8afbd79cc8784d6'], + # Some requirements are too strict. + 'preinstallopts': " && ".join(local_sed_commands) + " && ", + }), +] + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] + +moduleclass = 'bio'