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A solution for the package dependency issues 📦 #110

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Delete RF2na-linux.yml
SuhasSrinivasan Apr 26, 2024
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Delete SE3Transformer/requirements.txt
SuhasSrinivasan Apr 26, 2024
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Update README.md
SuhasSrinivasan Apr 26, 2024
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Unified package installation
SuhasSrinivasan Apr 26, 2024
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13 changes: 3 additions & 10 deletions README.md
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Expand Up @@ -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
Expand Down
24 changes: 0 additions & 24 deletions RF2na-linux.yml
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4 changes: 0 additions & 4 deletions SE3Transformer/requirements.txt
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150 changes: 150 additions & 0 deletions conda_RF2NA_env.yml
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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
144 changes: 144 additions & 0 deletions conda_RF2NA_packages_table.txt
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# 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
22 changes: 22 additions & 0 deletions create_env.sh
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#!/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 ..