diff --git a/Dockerfile b/Dockerfile index 1a3bafc..e57f189 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM tensorflow1.2.1-py36 +FROM tensorflow2.12.0-py310 WORKDIR /Kaiko_pipeline ADD ./Kaiko_denovo /Kaiko_pipeline/Kaiko_denovo @@ -11,4 +11,4 @@ ADD ./unit_test_util.py /Kaiko_pipeline ADD ./kaiko_defaults.yaml /Kaiko_pipeline RUN pip install --no-cache-dir --upgrade pip && \ - pip install --no-cache-dir llvmlite==0.22 biopython==1.69 numba==0.37 pyteomics sigopt==3.2.0 memory-profiler pyyaml pathlib s3path + pip install --no-cache-dir llvmlite==0.39.1 biopython==1.81 numba==0.56.4 pyteomics sigopt==3.2.0 memory-profiler pyyaml pathlib s3path diff --git a/Dockerfile_tensorflow2.12.0-py310 b/Dockerfile_tensorflow2.12.0-py310 new file mode 100644 index 0000000..853d038 --- /dev/null +++ b/Dockerfile_tensorflow2.12.0-py310 @@ -0,0 +1,10 @@ +FROM python:3.10 +RUN apt-get update && \ + apt-get install -y --no-install-recommends build-essential curl libfreetype6-dev libpng-dev libzmq3-dev pkg-config python3 python3-dev rsync software-properties-common unzip && \ + apt-get clean && \ + rm -rf /var/lib/apt/lists/* +RUN pip3 --no-cache-dir install https://files.pythonhosted.org/packages/3f/b2/33372601ed71fb41049642f8f6e1e142215e8b5c3463df434fc8885db278/tensorflow-2.12.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl +RUN pip3 --no-cache-dir install ipykernel jupyter matplotlib numpy scipy scikit-learn pandas Pillow && \ + python3 -m ipykernel.kernelspec +CMD ["/bin/bash"] +MAINTAINER Camilo Posso \ No newline at end of file diff --git a/Kaiko_volume/config.yaml b/Kaiko_volume/config.yaml index 23fe763..9122834 100644 --- a/Kaiko_volume/config.yaml +++ b/Kaiko_volume/config.yaml @@ -1,7 +1,7 @@ denovo: multi_decode: true - mgf_dir: Kaiko_volume/Kaiko_input_files/mgf_small + mgf_dir: Kaiko_volume/Kaiko_input_files/mgf_large diamond tally: - diamond_folder: 'Kaiko_volume/Kaiko_stationary_files/diamond' + diamond_folder: Kaiko_volume/Kaiko_stationary_files/diamond-2.0.15