From cb3e22f55d517dfa32675d9eea9bbeb3ada085f8 Mon Sep 17 00:00:00 2001 From: camiel-m Date: Wed, 18 Oct 2023 18:35:01 +0200 Subject: [PATCH] share environment --- README.md | 1 + environment.yml | 163 ++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 164 insertions(+) create mode 100644 environment.yml diff --git a/README.md b/README.md index d6bacfc..d726e6b 100644 --- a/README.md +++ b/README.md @@ -46,6 +46,7 @@ wget https://storage.googleapis.com/linnarsson-lab-human/ATAC_dev/10X/{sample} We use the [Chromograph](https://github.com/linnarsson-lab/chromograph) pipeline. Code for making many of the figures is available as [Jupyter notebooks](notebooks/README.md) +The package versions used to generate these figures are in [this environment file](environment.yml) ### Genes and transcripts annotation diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..d493212 --- /dev/null +++ b/environment.yml @@ -0,0 +1,163 @@ +name: fetal_brain_multiomics +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - _libgcc_mutex=0.1=conda_forge + - _openmp_mutex=4.5=2_gnu + - ca-certificates=2023.5.7=hbcca054_0 + - cudatoolkit=11.8.0=h37601d7_11 + - ld_impl_linux-64=2.40=h41732ed_0 + - libffi=3.4.2=h7f98852_5 + - libgcc-ng=13.1.0=he5830b7_0 + - libgomp=13.1.0=he5830b7_0 + - libllvm8=8.0.1=hc9558a2_0 + - libllvm9=9.0.1=default_hc23dcda_7 + - libnsl=2.0.0=h7f98852_0 + - libpng=1.6.39=h753d276_0 + - libsqlite=3.42.0=h2797004_0 + - libstdcxx-ng=13.1.0=hfd8a6a1_0 + - libuuid=2.38.1=h0b41bf4_0 + - libzlib=1.2.13=hd590300_5 + - llvm-openmp=16.0.6=h4dfa4b3_0 + - mysql-connector-c=6.1.11=h6eb9d5d_1007 + - ncurses=6.4=hcb278e6_0 + - openssl=1.1.1u=hd590300_0 + - pip=23.2=pyhd8ed1ab_0 + - python=3.7.12=hb7a2778_100_cpython + - readline=8.2=h8228510_1 + - setuptools=68.0.0=pyhd8ed1ab_0 + - sqlite=3.42.0=h2c6b66d_0 + - tk=8.6.12=h27826a3_0 + - ucsc-bedgraphtobigwig=445=h954228d_0 + - ucsc-bigwigaverageoverbed=377=ha8a8165_3 + - ucsc-genepredtobed=447=h954228d_0 + - ucsc-gtftogenepred=447=h954228d_0 + - wheel=0.40.0=pyhd8ed1ab_1 + - xz=5.2.6=h166bdaf_0 + - zlib=1.2.13=hd590300_5 + - zstd=1.5.2=hfc55251_7 + - pip: + - aiohttp==3.8.4 + - aiosignal==1.3.1 + - argcomplete==3.1.1 + - argh==0.27.2 + - asciitree==0.3.3 + - async-timeout==4.0.2 + - asynctest==0.13.0 + - attrs==23.1.0 + - backcall==0.2.0 + - biopython==1.81 + - bx-python==0.9.0 + - captum==0.6.0 + - certifi==2023.5.7 + - charset-normalizer==3.2.0 + - click==8.1.5 + - cooler==0.9.2 + - cycler==0.11.0 + - cython==0.29.36 + - cytoolz==0.12.1 + - debugpy==1.6.7 + - decorator==5.1.1 + - deeplift==0.6.13.0 + - dill==0.3.6 + - entrypoints==0.4 + - exceptiongroup==1.1.2 + - fisher==0.1.10 + - fonttools==4.38.0 + - frozenlist==1.3.3 + - fsspec==2023.1.0 + - future==0.18.3 + - gffutils==0.12 + - h5py==3.8.0 + - harmony-pytorch==0.1.7 + - hdbscan==0.8.30 + - hicmatrix==15 + - idna==3.4 + - igraph==0.10.6 + - importlib-metadata==6.7.0 + - iniconfig==2.0.0 + - intervaltree==3.1.0 + - ipykernel==6.16.2 + - ipython==7.34.0 + - jedi==0.18.2 + - joblib==1.3.1 + - jupyter-client==7.4.9 + - jupyter-core==4.12.0 + - kiwisolver==1.4.4 + - kneed==0.8.5 + - leidenalg==0.10.0 + - lightning-utilities==0.9.0 + - llvmlite==0.34.0 + - loompy==3.0.7 + - macs2==2.2.8 + - matplotlib==3.5.3 + - matplotlib-inline==0.1.6 + - multidict==6.0.4 + - multiprocess==0.70.14 + - nest-asyncio==1.5.6 + - networkx==2.6.3 + - numba==0.51.0 + - numexpr==2.8.4 + - numpy==1.21.6 + - numpy-groupies==0.9.6 + - nvidia-cublas-cu11==11.10.3.66 + - nvidia-cuda-nvrtc-cu11==11.7.99 + - nvidia-cuda-runtime-cu11==11.7.99 + - nvidia-cudnn-cu11==8.5.0.96 + - opentsne==1.0.0 + - packaging==23.1 + - pandas==1.3.5 + - parso==0.8.3 + - patsy==0.5.3 + - pexpect==4.8.0 + - pickleshare==0.7.5 + - pillow==9.5.0 + - pluggy==1.2.0 + - prompt-toolkit==3.0.39 + - psutil==5.9.5 + - ptyprocess==0.7.0 + - pybedtools==0.9.0 + - pybigwig==0.3.22 + - pyfaidx==0.7.2.1 + - pygenometracks==3.8 + - pygments==2.15.1 + - pynndescent==0.4.8 + - pyparsing==3.1.0 + - pysam==0.21.0 + - pytest==7.4.0 + - python-dateutil==2.8.2 + - python-louvain==0.16 + - pytorch-lightning==1.9.5 + - pytz==2023.3 + - pyyaml==6.0 + - pyzmq==25.1.0 + - requests==2.31.0 + - scikit-learn==1.0.2 + - scikit-network==0.28.2 + - scipy==1.7.3 + - seaborn==0.12.2 + - simplejson==3.19.1 + - six==1.16.0 + - sortedcontainers==2.4.0 + - statsmodels==0.13.5 + - tables==3.7.0 + - texttable==1.6.7 + - threadpoolctl==3.1.0 + - tomli==2.0.1 + - toolz==0.12.0 + - torch==1.12.1 + - torchmetrics==0.11.4 + - tornado==6.2 + - tqdm==4.65.0 + - traitlets==5.9.0 + - twobitreader==3.1.7 + - typing-extensions==4.7.1 + - umap-learn==0.4.6 + - unidip==0.1.1 + - urllib3==2.0.3 + - wcwidth==0.2.6 + - yarl==1.9.2 + - zipp==3.15.0 +prefix: /home/camiel/anaconda3/envs/fetal_brain_multiomics