From 3a377862cf731917d451627cb245f6472eeb7695 Mon Sep 17 00:00:00 2001 From: SuhasSrinivasan <32346517+SuhasSrinivasan@users.noreply.github.com> Date: Fri, 26 Apr 2024 09:19:45 -0700 Subject: [PATCH 1/4] Delete RF2na-linux.yml YAML does not satisfy package dependency. --- RF2na-linux.yml | 24 ------------------------ 1 file changed, 24 deletions(-) delete mode 100644 RF2na-linux.yml diff --git a/RF2na-linux.yml b/RF2na-linux.yml deleted file mode 100644 index 6f737b3..0000000 --- a/RF2na-linux.yml +++ /dev/null @@ -1,24 +0,0 @@ -name: RF2NA -channels: - - pytorch - - nvidia - - defaults - - conda-forge -dependencies: - - python=3.10 - - pip - - pytorch - - requests - - pytorch-cuda=11.7 - - dglteam/label/cu117::dgl - - pyg::pyg - - bioconda::mafft - - bioconda::hhsuite - - bioconda::blast - - bioconda::hmmer>=3.3 - - bioconda::infernal - - bioconda::cd-hit - - bioconda::csblast - - pip: - - psutil - - tqdm \ No newline at end of file From bad341a68522929e85ec64e5d7850f434052abcd Mon Sep 17 00:00:00 2001 From: SuhasSrinivasan <32346517+SuhasSrinivasan@users.noreply.github.com> Date: Fri, 26 Apr 2024 09:20:31 -0700 Subject: [PATCH 2/4] Delete SE3Transformer/requirements.txt Does not satisfy package dependencies. --- SE3Transformer/requirements.txt | 4 ---- 1 file changed, 4 deletions(-) delete mode 100644 SE3Transformer/requirements.txt diff --git a/SE3Transformer/requirements.txt b/SE3Transformer/requirements.txt deleted file mode 100644 index cb6ce77..0000000 --- a/SE3Transformer/requirements.txt +++ /dev/null @@ -1,4 +0,0 @@ -e3nn==0.3.3 -wandb==0.12.0 -pynvml==11.0.0 -git+https://github.com/NVIDIA/dllogger#egg=dllogger From ca735766da4f7446625f75a68ff28817acaf33ab Mon Sep 17 00:00:00 2001 From: SuhasSrinivasan <32346517+SuhasSrinivasan@users.noreply.github.com> Date: Fri, 26 Apr 2024 09:22:45 -0700 Subject: [PATCH 3/4] Update README.md Updated instructions for unified package installation. --- README.md | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index c85d64d..063cd1b 100644 --- a/README.md +++ b/README.md @@ -15,18 +15,11 @@ cd RoseTTAFold2NA ``` 2. Create conda environment -All external dependencies are contained in `RF2na-linux.yml` +All package dependencies are handled by `create_env.sh`. +Also provided is the conda YAML and conda table of packages. ``` # create conda environment for RoseTTAFold2NA -conda env create -f RF2na-linux.yml -``` -You also need to install NVIDIA's SE(3)-Transformer (**please use SE3Transformer in this repo to install**). -``` -conda activate RF2NA -cd SE3Transformer -pip install --no-cache-dir -r requirements.txt -python setup.py install -cd .. +$ source create_env.sh ``` 3. Download pre-trained weights under network directory From 5a811a7a433d18385fdb0ee7071b7963c9b5b59d Mon Sep 17 00:00:00 2001 From: SuhasSrinivasan <32346517+SuhasSrinivasan@users.noreply.github.com> Date: Fri, 26 Apr 2024 09:25:22 -0700 Subject: [PATCH 4/4] Unified package installation Package installation unified for Torch, Bioconda and SE(3)Transformer in create_env.sh --- conda_RF2NA_env.yml | 150 +++++++++++++++++++++++++++++++++ conda_RF2NA_packages_table.txt | 144 +++++++++++++++++++++++++++++++ create_env.sh | 22 +++++ 3 files changed, 316 insertions(+) create mode 100644 conda_RF2NA_env.yml create mode 100644 conda_RF2NA_packages_table.txt create mode 100644 create_env.sh diff --git a/conda_RF2NA_env.yml b/conda_RF2NA_env.yml new file mode 100644 index 0000000..f1d53ad --- /dev/null +++ b/conda_RF2NA_env.yml @@ -0,0 +1,150 @@ +name: RF2NA +channels: + - bioconda + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1=conda_forge + - _openmp_mutex=4.5=2_gnu + - blast=2.15.0=pl5321h6f7f691_1 + - bzip2=1.0.8=h5eee18b_5 + - c-ares=1.19.1=h5eee18b_0 + - ca-certificates=2024.3.11=h06a4308_0 + - cd-hit=4.8.1=h43eeafb_10 + - csblast=2.2.3=h4ac6f70_3 + - curl=8.5.0=hdbd6064_0 + - entrez-direct=21.6=he881be0_0 + - gawk=5.1.0=h7b6447c_0 + - hhsuite=3.3.0=py310pl5321h068649b_10 + - hmmer=3.4=hdbdd923_1 + - infernal=1.1.5=pl5321h031d066_0 + - krb5=1.20.1=h143b758_1 + - ld_impl_linux-64=2.38=h1181459_1 + - libcurl=8.5.0=h251f7ec_0 + - libedit=3.1.20230828=h5eee18b_0 + - libev=4.33=h7f8727e_1 + - libffi=3.4.4=h6a678d5_0 + - libgcc-ng=13.2.0=h807b86a_5 + - libgomp=13.2.0=h807b86a_5 + - libidn2=2.3.4=h5eee18b_0 + - libnghttp2=1.57.0=h2d74bed_0 + - libnsl=2.0.0=h5eee18b_0 + - libsqlite=3.45.3=h2797004_0 + - libssh2=1.10.0=hdbd6064_2 + - libstdcxx-ng=13.2.0=h7e041cc_5 + - libunistring=0.9.10=h27cfd23_0 + - libuuid=1.41.5=h5eee18b_0 + - libzlib=1.2.13=hd590300_5 + - llvm-openmp=18.1.3=h4dfa4b3_0 + - lz4-c=1.9.4=h6a678d5_0 + - mafft=7.525=h031d066_1 + - ncbi-vdb=3.1.0=h4ac6f70_2 + - ncurses=6.4=h6a678d5_0 + - openssl=3.0.13=h7f8727e_0 + - pcre=8.45=h295c915_0 + - perl=5.32.1=0_h5eee18b_perl5 + - perl-archive-tar=2.40=pl5321hdfd78af_0 + - perl-carp=1.38=pl5321hdfd78af_4 + - perl-common-sense=3.75=pl5321hdfd78af_0 + - perl-compress-raw-bzip2=2.201=pl5321h87f3376_1 + - perl-compress-raw-zlib=2.105=pl5321h87f3376_0 + - perl-encode=3.19=pl5321hec16e2b_1 + - perl-exporter=5.72=pl5321hdfd78af_2 + - perl-exporter-tiny=1.002002=pl5321hdfd78af_0 + - perl-extutils-makemaker=7.70=pl5321hd8ed1ab_0 + - perl-io-compress=2.201=pl5321hdbdd923_2 + - perl-io-zlib=1.14=pl5321hdfd78af_0 + - perl-json=4.10=pl5321hdfd78af_0 + - perl-json-xs=2.34=pl5321h4ac6f70_6 + - perl-list-moreutils=0.430=pl5321hdfd78af_0 + - perl-list-moreutils-xs=0.430=pl5321h031d066_2 + - perl-parent=0.236=pl5321hdfd78af_2 + - perl-pathtools=3.75=pl5321hec16e2b_3 + - perl-scalar-list-utils=1.62=pl5321hec16e2b_1 + - perl-types-serialiser=1.01=pl5321hdfd78af_0 + - pip=23.3.1=py310h06a4308_0 + - python=3.10.14=h955ad1f_0 + - python_abi=3.10=2_cp310 + - readline=8.2=h5eee18b_0 + - setuptools=68.2.2=py310h06a4308_0 + - sqlite=3.41.2=h5eee18b_0 + - tk=8.6.12=h1ccaba5_0 + - wget=1.21.4=h251f7ec_1 + - wheel=0.41.2=py310h06a4308_0 + - xz=5.4.6=h5eee18b_0 + - zlib=1.2.13=hd590300_5 + - zstd=1.5.5=hc292b87_0 + - pip: + - aiohttp==3.9.5 + - aiosignal==1.3.1 + - annotated-types==0.6.0 + - appdirs==1.4.4 + - async-timeout==4.0.3 + - attrs==23.2.0 + - certifi==2024.2.2 + - charset-normalizer==3.3.2 + - click==8.1.7 + - dgl==2.1.0+cu121 + - dllogger==1.0.0 + - docker-pycreds==0.4.0 + - e3nn==0.5.1 + - filelock==3.13.4 + - frozenlist==1.4.1 + - fsspec==2024.3.1 + - gitdb==4.0.11 + - gitpython==3.1.43 + - idna==3.7 + - jinja2==3.1.3 + - joblib==1.4.0 + - markupsafe==2.1.5 + - mpmath==1.3.0 + - multidict==6.0.5 + - networkx==3.3 + - numpy==1.26.4 + - nvidia-cublas-cu12==12.1.3.1 + - nvidia-cuda-cupti-cu12==12.1.105 + - nvidia-cuda-nvrtc-cu12==12.1.105 + - nvidia-cuda-runtime-cu12==12.1.105 + - nvidia-cudnn-cu12==8.9.2.26 + - nvidia-cufft-cu12==11.0.2.54 + - nvidia-curand-cu12==10.3.2.106 + - nvidia-cusolver-cu12==11.4.5.107 + - nvidia-cusparse-cu12==12.1.0.106 + - nvidia-nccl-cu12==2.19.3 + - nvidia-nvjitlink-cu12==12.4.127 + - nvidia-nvtx-cu12==12.1.105 + - opt-einsum==3.3.0 + - opt-einsum-fx==0.1.4 + - packaging==24.0 + - pandas==2.2.2 + - pillow==10.3.0 + - protobuf==4.25.3 + - psutil==5.9.8 + - pydantic==2.7.0 + - pydantic-core==2.18.1 + - pynvml==11.5.0 + - pyparsing==3.1.2 + - python-dateutil==2.9.0.post0 + - pytz==2024.1 + - pyyaml==6.0.1 + - requests==2.31.0 + - scikit-learn==1.4.2 + - scipy==1.13.0 + - sentry-sdk==1.45.0 + - setproctitle==1.3.3 + - six==1.16.0 + - smmap==5.0.1 + - sympy==1.12 + - threadpoolctl==3.4.0 + - torch==2.2.1 + - torch-geometric==2.5.2 + - torchaudio==2.2.1 + - torchdata==0.7.1 + - torchvision==0.17.1 + - tqdm==4.66.2 + - triton==2.2.0 + - typing-extensions==4.11.0 + - tzdata==2024.1 + - urllib3==2.2.1 + - wandb==0.16.6 + - yarl==1.9.4 diff --git a/conda_RF2NA_packages_table.txt b/conda_RF2NA_packages_table.txt new file mode 100644 index 0000000..84682ce --- /dev/null +++ b/conda_RF2NA_packages_table.txt @@ -0,0 +1,144 @@ +# Name Version Build Channel +_libgcc_mutex 0.1 conda_forge conda-forge +_openmp_mutex 4.5 2_gnu conda-forge +aiohttp 3.9.5 pypi_0 pypi +aiosignal 1.3.1 pypi_0 pypi +annotated-types 0.6.0 pypi_0 pypi +appdirs 1.4.4 pypi_0 pypi +async-timeout 4.0.3 pypi_0 pypi +attrs 23.2.0 pypi_0 pypi +blast 2.15.0 pl5321h6f7f691_1 bioconda +bzip2 1.0.8 h5eee18b_5 +c-ares 1.19.1 h5eee18b_0 +ca-certificates 2024.3.11 h06a4308_0 +cd-hit 4.8.1 h43eeafb_10 bioconda +certifi 2024.2.2 pypi_0 pypi +charset-normalizer 3.3.2 pypi_0 pypi +click 8.1.7 pypi_0 pypi +csblast 2.2.3 h4ac6f70_3 bioconda +curl 8.5.0 hdbd6064_0 +dgl 2.1.0+cu121 pypi_0 pypi +dllogger 1.0.0 pypi_0 pypi +docker-pycreds 0.4.0 pypi_0 pypi +e3nn 0.5.1 pypi_0 pypi +entrez-direct 21.6 he881be0_0 bioconda +filelock 3.13.4 pypi_0 pypi +frozenlist 1.4.1 pypi_0 pypi +fsspec 2024.3.1 pypi_0 pypi +gawk 5.1.0 h7b6447c_0 +gitdb 4.0.11 pypi_0 pypi +gitpython 3.1.43 pypi_0 pypi +hhsuite 3.3.0 py310pl5321h068649b_10 bioconda +hmmer 3.4 hdbdd923_1 bioconda +idna 3.7 pypi_0 pypi +infernal 1.1.5 pl5321h031d066_0 bioconda +jinja2 3.1.3 pypi_0 pypi +joblib 1.4.0 pypi_0 pypi +krb5 1.20.1 h143b758_1 +ld_impl_linux-64 2.38 h1181459_1 +libcurl 8.5.0 h251f7ec_0 +libedit 3.1.20230828 h5eee18b_0 +libev 4.33 h7f8727e_1 +libffi 3.4.4 h6a678d5_0 +libgcc-ng 13.2.0 h807b86a_5 conda-forge +libgomp 13.2.0 h807b86a_5 conda-forge +libidn2 2.3.4 h5eee18b_0 +libnghttp2 1.57.0 h2d74bed_0 +libnsl 2.0.0 h5eee18b_0 +libsqlite 3.45.3 h2797004_0 conda-forge +libssh2 1.10.0 hdbd6064_2 +libstdcxx-ng 13.2.0 h7e041cc_5 conda-forge +libunistring 0.9.10 h27cfd23_0 +libuuid 1.41.5 h5eee18b_0 +libzlib 1.2.13 hd590300_5 conda-forge +llvm-openmp 18.1.3 h4dfa4b3_0 conda-forge +lz4-c 1.9.4 h6a678d5_0 +mafft 7.525 h031d066_1 bioconda +markupsafe 2.1.5 pypi_0 pypi +mpmath 1.3.0 pypi_0 pypi +multidict 6.0.5 pypi_0 pypi +ncbi-vdb 3.1.0 h4ac6f70_2 bioconda +ncurses 6.4 h6a678d5_0 +networkx 3.3 pypi_0 pypi +numpy 1.26.4 pypi_0 pypi +nvidia-cublas-cu12 12.1.3.1 pypi_0 pypi +nvidia-cuda-cupti-cu12 12.1.105 pypi_0 pypi +nvidia-cuda-nvrtc-cu12 12.1.105 pypi_0 pypi +nvidia-cuda-runtime-cu12 12.1.105 pypi_0 pypi +nvidia-cudnn-cu12 8.9.2.26 pypi_0 pypi +nvidia-cufft-cu12 11.0.2.54 pypi_0 pypi +nvidia-curand-cu12 10.3.2.106 pypi_0 pypi +nvidia-cusolver-cu12 11.4.5.107 pypi_0 pypi +nvidia-cusparse-cu12 12.1.0.106 pypi_0 pypi +nvidia-nccl-cu12 2.19.3 pypi_0 pypi +nvidia-nvjitlink-cu12 12.4.127 pypi_0 pypi +nvidia-nvtx-cu12 12.1.105 pypi_0 pypi +openssl 3.0.13 h7f8727e_0 +opt-einsum 3.3.0 pypi_0 pypi +opt-einsum-fx 0.1.4 pypi_0 pypi +packaging 24.0 pypi_0 pypi +pandas 2.2.2 pypi_0 pypi +pcre 8.45 h295c915_0 +perl 5.32.1 0_h5eee18b_perl5 +perl-archive-tar 2.40 pl5321hdfd78af_0 bioconda +perl-carp 1.38 pl5321hdfd78af_4 bioconda +perl-common-sense 3.75 pl5321hdfd78af_0 bioconda +perl-compress-raw-bzip2 2.201 pl5321h87f3376_1 bioconda +perl-compress-raw-zlib 2.105 pl5321h87f3376_0 bioconda +perl-encode 3.19 pl5321hec16e2b_1 bioconda +perl-exporter 5.72 pl5321hdfd78af_2 bioconda +perl-exporter-tiny 1.002002 pl5321hdfd78af_0 bioconda +perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0 conda-forge +perl-io-compress 2.201 pl5321hdbdd923_2 bioconda +perl-io-zlib 1.14 pl5321hdfd78af_0 bioconda +perl-json 4.10 pl5321hdfd78af_0 bioconda +perl-json-xs 2.34 pl5321h4ac6f70_6 bioconda +perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda +perl-list-moreutils-xs 0.430 pl5321h031d066_2 bioconda +perl-parent 0.236 pl5321hdfd78af_2 bioconda +perl-pathtools 3.75 pl5321hec16e2b_3 bioconda +perl-scalar-list-utils 1.62 pl5321hec16e2b_1 bioconda +perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda +pillow 10.3.0 pypi_0 pypi +pip 23.3.1 py310h06a4308_0 +protobuf 4.25.3 pypi_0 pypi +psutil 5.9.8 pypi_0 pypi +pydantic 2.7.0 pypi_0 pypi +pydantic-core 2.18.1 pypi_0 pypi +pynvml 11.5.0 pypi_0 pypi +pyparsing 3.1.2 pypi_0 pypi +python 3.10.14 h955ad1f_0 +python-dateutil 2.9.0.post0 pypi_0 pypi +python_abi 3.10 2_cp310 conda-forge +pytz 2024.1 pypi_0 pypi +pyyaml 6.0.1 pypi_0 pypi +readline 8.2 h5eee18b_0 +requests 2.31.0 pypi_0 pypi +scikit-learn 1.4.2 pypi_0 pypi +scipy 1.13.0 pypi_0 pypi +sentry-sdk 1.45.0 pypi_0 pypi +setproctitle 1.3.3 pypi_0 pypi +setuptools 68.2.2 py310h06a4308_0 +six 1.16.0 pypi_0 pypi +smmap 5.0.1 pypi_0 pypi +sqlite 3.41.2 h5eee18b_0 +sympy 1.12 pypi_0 pypi +threadpoolctl 3.4.0 pypi_0 pypi +tk 8.6.12 h1ccaba5_0 +torch 2.2.1 pypi_0 pypi +torch-geometric 2.5.2 pypi_0 pypi +torchaudio 2.2.1 pypi_0 pypi +torchdata 0.7.1 pypi_0 pypi +torchvision 0.17.1 pypi_0 pypi +tqdm 4.66.2 pypi_0 pypi +triton 2.2.0 pypi_0 pypi +typing-extensions 4.11.0 pypi_0 pypi +tzdata 2024.1 pypi_0 pypi +urllib3 2.2.1 pypi_0 pypi +wandb 0.16.6 pypi_0 pypi +wget 1.21.4 h251f7ec_1 +wheel 0.41.2 py310h06a4308_0 +xz 5.4.6 h5eee18b_0 +yarl 1.9.4 pypi_0 pypi +zlib 1.2.13 hd590300_5 conda-forge +zstd 1.5.5 hc292b87_0 diff --git a/create_env.sh b/create_env.sh new file mode 100644 index 0000000..7343190 --- /dev/null +++ b/create_env.sh @@ -0,0 +1,22 @@ +#!/bin/bash + +conda create -y --name RF2NA python==3.10.14 + +conda activate RF2NA + +conda install -y conda-forge::llvm-openmp + +conda install -y -c bioconda blast csblast cd-hit infernal mafft hmmer hhsuite + +pip install torch==2.2.1 torchvision torchaudio torchdata torch_geometric + +pip install pandas pydantic e3nn wandb pynvml git+https://github.com/NVIDIA/dllogger#egg=dllogger + +pip install dgl -f https://data.dgl.ai/wheels/cu121/repo.html + +cd SE3Transformer + +python setup.py install + +cd .. +