mattarnoldbio
New release/tag
I noticed from the README.md that the current version is 1.5.4, but the newest release is 1.4.1. conda fails to create the environment with
VERSION=1.4.1
conda create --name alphapickel-$VERSION https://raw.githubusercontent.com/mattarnoldbio/alphapickle/v$VERSION/requirements.txt
So I had to resort to installing directly from main
conda create --name alphapickel-$VERSION https://raw.githubusercontent.com/mattarnoldbio/alphapickle/main/linux64requirements.txt
which gave me the following:
Output
Channels:
- bioconda
- conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: failed
LibMambaUnsatisfiableError: Encountered problems while solving:
- nothing provides requested ca-certificates 2021.10.26
- nothing provides requested fonttools 4.25.0
- nothing provides requested intel-openmp 2021.2.0
- nothing provides requested mkl_random 1.2.1
- nothing provides requested numpy-base 1.20.2
- nothing provides requested setuptools 52.0.0
- package python-3.9.5-h49503c6_0_cpython requires sqlite >=3.35.5,<4.0a0, but none of the providers can be installed
- package mkl_fft-1.3.0-py36h92226af_1 requires mkl >=2020.4,<2021.0a0, but none of the providers can be installed
- package mkl_fft-1.3.0-py36h92226af_1 requires mkl >=2020.4,<2021.0a0, but none of the providers can be installed
- package pillow-8.3.1-py36h676a545_0 requires libtiff >=4.3.0,<4.4.0a0, but none of the providers can be installed
- package pillow-8.3.1-py39ha612740_0 requires libtiff >=4.3.0,<4.4.0a0, but none of the providers can be installed
Could not solve for environment specs
The following packages are incompatible
├─ ca-certificates 2021.10.26 does not exist (perhaps a typo or a missing channel);
├─ fonttools 4.25.0 does not exist (perhaps a typo or a missing channel);
├─ intel-openmp 2021.2.0 does not exist (perhaps a typo or a missing channel);
├─ jpeg 9d is requested and can be installed;
├─ libtiff 4.2.0 is requested and can be installed;
├─ mkl 2021.2.0 is requested and can be installed;
├─ mkl_fft 1.3.0 is uninstallable because it requires
│ └─ mkl >=2020.4,<2021.0a0 , which conflicts with any installable versions previously reported;
├─ mkl_random 1.2.1 does not exist (perhaps a typo or a missing channel);
├─ numpy-base 1.20.2 does not exist (perhaps a typo or a missing channel);
├─ openssl 1.1.1l is requested and can be installed;
├─ pillow 8.3.1 is uninstallable because there are no viable options
│ ├─ pillow 8.3.1 would require
│ │ └─ libtiff >=4.3.0,<4.4.0a0 but there are no viable options
│ │ ├─ libtiff 4.3.0 would require
│ │ │ ├─ jpeg >=9e,<10a , which conflicts with any installable versions previously reported;
│ │ │ └─ zstd >=1.5.2,<1.6.0a0 , which can be installed;
│ │ └─ libtiff 4.3.0 would require
│ │ └─ zstd >=1.5.0,<1.6.0a0 , which can be installed;
│ └─ pillow 8.3.1 would require
│ ├─ libtiff >=4.3.0,<4.4.0a0 , which cannot be installed (as previously explained);
│ └─ pypy3.7 >=7.3.5 with the potential options
│ ├─ pypy3.7 [7.3.5|7.3.7] would require
│ │ └─ sqlite >=3.36.0,<4.0a0 , which can be installed;
│ ├─ pypy3.7 7.3.5 would require
│ │ └─ sqlite >=3.35.5,<4.0a0 , which can be installed;
│ └─ pypy3.7 7.3.7 would require
│ └─ openssl >=3.0.0,<4.0a0 , which conflicts with any installable versions previously reported;
├─ python 3.9.5 is installable and it requires
│ └─ sqlite >=3.35.5,<4.0a0 , which can be installed;
├─ setuptools 52.0.0 does not exist (perhaps a typo or a missing channel);
├─ sqlite 3.35.4 is uninstallable because it conflicts with any installable versions previously reported;
└─ zstd 1.4.9 is uninstallable because it conflicts with any installable versions previously reported.
Am I missing any channels? Sorry for convoluting this different issues
This is what I ended up with:
VERSION=1.4.1
URL=https://github.com/mattarnoldbio/alphapickle
conda create -y --name alphapickle-$VERSION python=3.9.5
conda activate alphapickle-$VERSION
mkdir -p ${CONDA_PREFIX}/share
pushd ${CONDA_PREFIX}/share
git clone --quiet --depth 1 --branch v$VERSION $URL
sed -i '1i #!/bin/env python3' ${CONDA_PREFIX}/share/alphapickle/*AlphaPickle.py
pushd ../bin
ln -s ../share/alphapickle/run_AlphaPickle.py .
ln -s ../share/alphapickle/integrated_AlphaPickle.py .
popd
popd
python3 -m pip install -r https://raw.githubusercontent.com/mattarnoldbio/alphapickle/main/requirements.txt
I used AF-2.3.0. When loading the result*.pkl file, it complained:
line 48, in __init__
self.data.append(pkl.load(openfile))
ModuleNotFoundError: No module named 'jax'
Do you (@pur80a) know to to fix it?
@TienMPhan how did you install and what were the exact command to arrive at this error?
Maybe a simple pip3 install jax might help, if I have to guess.
I follow the one you ended up with above. When running
run_AlphaPickle.py -od out_alphafold/HSPB1
Tried pip3 install jax, I got
ModuleNotFoundError: jax requires jaxlib to be installed. See https://github.com/google/jax#installation for installation instructions.
then I followed the link to upgrade jax
pip install --upgrade "jax[cuda11_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
another error came:
line 48, in __init__
self.data.append(pkl.load(openfile))
ModuleNotFoundError: No module named 'jax._src.device_array'
I think this error comes from the step of reading pickle file.
FYI. Other people also got this error. https://stackoverflow.com/questions/76548069/pickle-load-gives-jax-related-error-no-matter-what
Update:
I installed older versions of jax and jaxlib as follows
pip install jax==0.3.25 jaxlib==0.3.25
and it worked on CPU, as shown in the warning.
WARNING:jax._src.lib.xla_bridge:No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.)
How is the current version 1.5.4 and the previous 1.4.1? This is a possible way on how to tag old commits:
git clone https://github.com/mattarnoldbio/alphapicklecd DeepVirFinder
git log --graph --oneline # chose commit to tag
git checkout d86b779 # d86b779 is the chosen commit hash
git tag v1.5.4
git push origin --tags