diff --git a/463_MATES/bedTools-2023b.eb b/463_MATES/bedTools-2023b.eb index 44915b4d..ee6ee788 100644 --- a/463_MATES/bedTools-2023b.eb +++ b/463_MATES/bedTools-2023b.eb @@ -34,14 +34,7 @@ dependencies = [ buildopts = 'CXX="$CXX"' -files_to_copy = [ - 'bin', - 'docs', - 'data', - 'genomes', - 'scripts', - 'test', -] +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], diff --git a/463_MATES/mates.eb b/463_MATES/mates.eb index 137d613c..24837326 100644 --- a/463_MATES/mates.eb +++ b/463_MATES/mates.eb @@ -9,18 +9,6 @@ description = "A Deep Learning-Based Model for Quantifying Transposable Elements toolchain = {'name': 'foss', 'version': '2023b'} -# DPES: - # OK "matplotlib==3.7.2", - # OK "numpy==1.25.2", - # OK "pandas==2.0.0", - # OK CREATED "pybedtools==0.10.0", - # OK "pysam==0.22.1", - # OK "scipy==1.11.2", - # OK "torch==2.0.0", - # OK "tqdm==4.66.1", - # ok "pyranges==0.0.129", - # OK CREATED "anndata==0.8.0" - dependencies = [ ('Python', '3.11.5'), ('Python-bundle-PyPI', '2023.10'), @@ -48,9 +36,10 @@ exts_list = [ }), (name, version, { 'modulename': 'MATES', + # unpin exact versions of dependencies 'preinstallopts': """sed -i 's/==.*//g' requirements.txt && sed -i 's/==.*/\",/g' setup.py && """, 'source_urls': ['https://github.com/mcgilldinglab/MATES/archive'], - 'sources': [{'download_filename': '3846ad5.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}], 'checksums': ['40fbb87dd72ca4c9e5347f2e984f9c0a0caa817d4eee692476be71e733e76f61'], }), ] diff --git a/463_MATES/pybedtools-2023b.eb b/463_MATES/pybedtools-2023b.eb index e8a1bbf6..986d15e5 100644 --- a/463_MATES/pybedtools-2023b.eb +++ b/463_MATES/pybedtools-2023b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2023b'} dependencies = [ ('Python', '3.11.5'), ('SciPy-bundle', '2023.11'), - ('BEDTools', '2.31.1'), # CREATED + ('BEDTools', '2.31.1'), ('Pysam', '0.22.0'), ]