diff --git a/requirements.yaml b/requirements.yaml index d403aa6..3f4a2b9 100644 --- a/requirements.yaml +++ b/requirements.yaml @@ -8,43 +8,42 @@ channels: - bokeh - schrodinger dependencies: - - snakemake - - python=3.9 - - minimap2 - - samtools - - ngmerge + - snakemake=7.32.3 + - python=3.9 + - minimap2=2.26 + - samtools=1.17 + - ngmerge=0.3 - numba=0.56 # pacmap is broken with numba 0.53, medaka is broken with numba 0.57 - - setuptools - - wget - - numpy - - pandas - - scipy - - scikit-learn - - statsmodels - - biopython - - jupyter - - jupyter_bokeh - - umi_tools - - medaka - - keras-preprocessing # not installed by medaka in some cases, probably just specific to my machine but doesn't hurt to add - - nanoplot - - natsort - - hvplot - - holoviews - - datashader - - bokeh - - spatialpandas # allows for lasso selections of datashaded plots - - panel - - editdistance - - racon - - wheel - - cython - - tqdm - - blat # for C3POa - - mappy - - pymol # not used by pipeline, but nice to have for SequenceAnalyzer - - pip + - setuptools=68.1.2 + - wget=1.20.3 + - numpy=1.23.5 + - pandas=2.1.0 + - scipy=1.11.2 + - scikit-learn=1.3.0 + - statsmodels=0.14.0 + - biopython=1.81 + - jupyter=1.0.0 + - jupyter_bokeh=3.0.7 + - umi_tools=1.1.4 + - keras-preprocessing=1.1.2 # not installed by medaka in some cases, probably just specific to my machine but doesn't hurt to add + - nanoplot=1.41.6 + - natsort=8.4.0 + - hvplot=0.8.4 + - holoviews=1.18.1 + - datashader=0.15.2 + - bokeh=3.2.2 + - spatialpandas=0.4.8 # allows for lasso selections of datashaded plots + - panel=1.2.1 + - editdistance=0.6.2 + - racon=1.5.0 + - wheel=0.41.2 + - cython=3.0.2 + - tqdm=4.66.1 + - blat=35 # for C3POa + - mappy=2.26 + - pip=23.2.1 + - medaka=1.8 - pip: - pyabpoa==1.4.0 - - pacmap - - selenium # for bokeh SVG export, conda installation is broken \ No newline at end of file + - pacmap==0.7.0 + - selenium==4.12.0 # for bokeh SVG export, conda installation is broken \ No newline at end of file