diff --git a/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023b.eb b/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023b.eb new file mode 100644 index 000000000000..f092666e99d7 --- /dev/null +++ b/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023b.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'cooler' +version = '0.10.2' + +homepage = 'https://open2c.github.io/cooler' +description = """Cooler is a support library for a storage format, also called cooler, used to store + genomic interaction data of any size, such as Hi-C contact matrices.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), + ('h5py', '3.11.0'), + ('PyYAML', '6.0.1'), + ('pyfaidx', '0.8.1.1'), + ('dill', '0.3.8'), + ('multiprocess', '0.70.16'), +] + +use_pip = True + +exts_list = [ + ('asciitree', '0.3.3', { + 'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'], + }), + ('toolz', '1.0.0', { + 'checksums': ['2c86e3d9a04798ac556793bced838816296a2f085017664e4995cb40a1047a02'], + }), + ('cytoolz', '1.0.0', { + 'checksums': ['eb453b30182152f9917a5189b7d99046b6ce90cdf8aeb0feff4b2683e600defd'], + }), + (name, version, { + 'checksums': ['3780a2e69b2ec89882dfc2775de5d9b54ccb79569dc5f042b4851599388112dc'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/hic-straw/hic-straw-1.3.1-foss-2023b.eb b/easybuild/easyconfigs/h/hic-straw/hic-straw-1.3.1-foss-2023b.eb new file mode 100644 index 000000000000..4a9b159e99b1 --- /dev/null +++ b/easybuild/easyconfigs/h/hic-straw/hic-straw-1.3.1-foss-2023b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'hic-straw' +version = '1.3.1' + +homepage = 'https://github.com/aidenlab/straw' +description = "Straw is a library which allows rapid streaming of contact data from .hic files." + +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['fb0f878127f6b1d096303c67793477c83fddf3f4a1a8e29a9d92952634989876'] + +builddependencies = [('pybind11', '2.11.1')] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), + ('cURL', '8.3.0'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +options = {'modulename': 'hicstraw'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Mustache/Mustache-1.3.3-foss-2023b.eb b/easybuild/easyconfigs/m/Mustache/Mustache-1.3.3-foss-2023b.eb new file mode 100644 index 000000000000..214d5af84bf0 --- /dev/null +++ b/easybuild/easyconfigs/m/Mustache/Mustache-1.3.3-foss-2023b.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'Mustache' +version = '1.3.3' + +homepage = 'https://github.com/ay-lab/mustache' +description = """Mustache (Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using +Scale-Space Representation) is a tool for multi-scale detection of chromatin loops from Hi-C and Micro-C +contact maps in high resolutions (10kbp all the way to 500bp and even more). +Mustache uses recent technical advances in scale-space theory in +Computer Vision to detect chromatin loops caused by interaction of DNA segments with a variable size.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +source_urls = ['https://pypi.python.org/packages/source/m/mustache_hic'] +sources = [{'download_filename': 'mustache_hic-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['fd7cca927e36145bf6e43903a79c3222ecfeeb497c8f57657d7647ec6eee5a6b'] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), + ('h5py', '3.11.0'), + ('HDF5', '1.14.3'), + ('cooler', '0.10.2'), + ('statsmodels', '0.14.1'), + ('hic-straw', '1.3.1'), +] + +# delete pathlib dependency from setup.py +preinstallopts = "sed -i 's/pathlib//' setup.py && " + +sanity_pip_check = True +use_pip = True +download_dep_fail = True + +options = {'modulename': 'mustache'} + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023b.eb b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023b.eb new file mode 100644 index 000000000000..956b6c8610d1 --- /dev/null +++ b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'multiprocess' +version = '0.70.16' + +homepage = 'https://github.com/uqfoundation/multiprocess' +description = "better multiprocessing and multithreading in python" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['161af703d4652a0e1410be6abccecde4a7ddffd19341be0a7011b94aeb171ac1'] + +dependencies = [ + ('Python', '3.11.5'), + ('dill', '0.3.8'), + ('Arrow', '16.1.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib'