diff --git a/236_NGSpeciesID/Pysam-0.22.0-GCC-12.3.0.eb b/236_NGSpeciesID/Pysam-0.22.0-GCC-12.3.0.eb deleted file mode 100644 index 27c7b71f..00000000 --- a/236_NGSpeciesID/Pysam-0.22.0-GCC-12.3.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Pysam' -version = '0.22.0' - -homepage = 'https://github.com/pysam-developers/pysam' -description = """Pysam is a python module for reading and manipulating Samfiles. - It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" - -toolchain = {'name': 'GCC', 'version': '12.3.0'} - -source_urls = ['https://github.com/pysam-developers/pysam/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['61b3377c5f889ddc6f6979912c3bb960d7e08407dada9cb38f13955564ea036f'] - -builddependencies = [('Python-bundle-PyPI', '2023.06')] - -dependencies = [ - ('Python', '3.11.3'), - ('ncurses', '6.4'), - ('cURL', '8.0.1'), - ('XZ', '5.4.2'), -] - -# https://github.com/pysam-developers/pysam/issues/1146#issuecomment-1309421979 -preinstallopts = """export CFLAGS="-fPIC $CFLAGS" && """ -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - -moduleclass = 'bio' diff --git a/236_NGSpeciesID/WhatsHap-2.1-foss-2023a.eb b/236_NGSpeciesID/WhatsHap-2.2-foss-2023a.eb similarity index 84% rename from 236_NGSpeciesID/WhatsHap-2.1-foss-2023a.eb rename to 236_NGSpeciesID/WhatsHap-2.2-foss-2023a.eb index 6e425f29..7ea2d435 100644 --- a/236_NGSpeciesID/WhatsHap-2.1-foss-2023a.eb +++ b/236_NGSpeciesID/WhatsHap-2.2-foss-2023a.eb @@ -1,9 +1,7 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - easyblock = 'PythonBundle' name = 'WhatsHap' -version = '2.1' +version = '2.2' homepage = 'https://whatshap.readthedocs.io' description = """WhatsHap is a software for phasing genomic variants using DNA @@ -21,7 +19,7 @@ dependencies = [ ('SciPy-bundle', '2023.07'), ('Biopython', '1.83'), ('Yasm', '1.3.0'), - ('pyfaidx', '0.8.0'), + ('pyfaidx', '0.8.1.1'), ('python-isal', '1.1.0'), ] @@ -38,7 +36,7 @@ exts_list = [ 'checksums': ['4a19814a5b0a4392d788ac2315263435293579b0583c3469943fe0c6a586f263'], }), ('whatshap', version, { - 'checksums': ['9b61812eda1dd5251ba8d02db16d7ddda152ccc813cb3db6a1ec796f1865fe8d'], + 'checksums': ['4cd34e9b82930c4f42e9e6b7dce2e321e4c81f934fdb980b6093ad91a06ae30a'], }), ] diff --git a/236_NGSpeciesID/parasail-2.6.2-GCC-12.3.0.eb b/236_NGSpeciesID/parasail-2.6.2-GCC-12.3.0.eb index 35f2284f..25f71f7e 100644 --- a/236_NGSpeciesID/parasail-2.6.2-GCC-12.3.0.eb +++ b/236_NGSpeciesID/parasail-2.6.2-GCC-12.3.0.eb @@ -10,7 +10,6 @@ description = """parasail is a SIMD C (C99) library containing implementations toolchain = {'name': 'GCC', 'version': '12.3.0'} -# https://github.com/jeffdaily/parasail github_account = 'jeffdaily' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] diff --git a/236_NGSpeciesID/pyfaidx-0.8.1.1-GCCcore-12.3.0.eb b/236_NGSpeciesID/pyfaidx-0.8.1.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000..b476b81b --- /dev/null +++ b/236_NGSpeciesID/pyfaidx-0.8.1.1-GCCcore-12.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'pyfaidx' +version = '0.8.1.1' + +homepage = 'https://pypi.python.org/pypi/pyfaidx' +description = "pyfaidx: efficient pythonic random access to fasta subsequences" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [('Python', '3.11.3')] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('zipp', '3.17.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31'], + }), + ('importlib_metadata', '7.0.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['4805911c3a4ec7c3966410053e9ec6a1fecd629117df5adee56dfc9432a1081e'], + }), + (name, version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2694af8e3f35f1890a03f04c0f89ba245caf24ff9e435f2c494b132f537e70f6'], + }), +] + +sanity_check_paths = { + 'files': ['bin/faidx'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["faidx --help"] + +moduleclass = 'bio'