diff --git a/.github/workflows/release-workflow.yml b/.github/workflows/release-workflow.yml index 8be2942..3d314da 100644 --- a/.github/workflows/release-workflow.yml +++ b/.github/workflows/release-workflow.yml @@ -12,7 +12,7 @@ jobs: image: ["sharedpy3keras1.2", "mpra-dragonn", "extended_coda", "mmsplice", "mmsplice-mtsplice", "deepmel", "framepool", "kipoisplice", "deeptarget", "attentivechrome", "bpnet-oskn", "seqvec", "deepflybrain", "aparent-site_probabilities", - "aparent-veff", "deepstarr"] + "aparent-veff", "deepstarr", "trednet"] runs-on: ubuntu-latest env: SINGULARITY_PULL_FOLDER: "/home/runner/singularity/" @@ -239,7 +239,8 @@ jobs: image: ["sharedpy3keras1.2", "sharedpy3keras2tf1", "sharedpy3keras2tf2", "mpra-dragonn", "extended_coda", "mmsplice", "mmsplice-mtsplice", "deepmel", "framepool", "kipoisplice", "deeptarget", "attentivechrome", "bpnet-oskn", "seqvec", - "deepflybrain", "aparent-site_probabilities", "aparent-veff", "deepstarr"] + "deepflybrain", "aparent-site_probabilities", "aparent-veff", "deepstarr", + "trednet"] runs-on: ubuntu-latest env: SINGULARITY_PULL_FOLDER: "/home/runner/singularity/" diff --git a/.github/workflows/test-images.yml b/.github/workflows/test-images.yml index 64891d5..8cfa9cb 100644 --- a/.github/workflows/test-images.yml +++ b/.github/workflows/test-images.yml @@ -36,7 +36,7 @@ jobs: "Framepool", "KipoiSplice/4", "deepTarget", "AttentiveChrome/E003", "BPNet-OSKN", "SeqVec/embedding", "Xpresso/human_GM12878", "epidermal_basset/encode-roadmap.basset.clf.testfold-0", "DeepFlyBrain", "APARENT/site_probabilities", "APARENT/veff", "DeepSTARR", - "scbasset"] + "scbasset", "TREDNet/phase_one"] runs-on: ubuntu-latest env: SINGULARITY_PULL_FOLDER: "/home/runner/singularity/" diff --git a/container-info/docker-to-model.json b/container-info/docker-to-model.json index 00950a1..e8e5713 100644 --- a/container-info/docker-to-model.json +++ b/container-info/docker-to-model.json @@ -2197,5 +2197,11 @@ ], "kipoi/kipoi-docker:deepstarr": [ "DeepSTARR" + ], + "kipoi/kipoi-docker:trednet": [ + "TREDNet/phase_one", + "TREDNet/phase_two_HepG2", + "TREDNet/phase_two_K562", + "TREDNet/phase_two_islet" ] } \ No newline at end of file diff --git a/dockerfiles/Dockerfile.trednet b/dockerfiles/Dockerfile.trednet new file mode 100644 index 0000000..ad11c56 --- /dev/null +++ b/dockerfiles/Dockerfile.trednet @@ -0,0 +1,10 @@ +FROM kipoi/kipoi-docker:kipoi-base-env + +SHELL ["conda", "run", "-n", "kipoi-env", "/bin/bash", "-c"] + +RUN kipoi env create TREDNet --verbose + +RUN echo "source activate kipoi-TREDNet" > ~/.bashrc +ENV PATH /opt/conda/envs/kipoi-TREDNet/bin:$PATH + +SHELL ["conda", "run", "-n", "kipoi-TREDNet", "/bin/bash", "-c"] \ No newline at end of file diff --git a/dockerfiles/Dockerfile.trednet-slim b/dockerfiles/Dockerfile.trednet-slim new file mode 100644 index 0000000..39226e2 --- /dev/null +++ b/dockerfiles/Dockerfile.trednet-slim @@ -0,0 +1,23 @@ +FROM continuumio/miniconda3:latest as build + +RUN apt-get update && apt-get install --no-install-recommends -y build-essential libz-dev libcurl3-dev libarchive-dev gcc \ + && apt-get clean && rm -rf /var/lib/apt/lists/* + +RUN conda update conda && \ + conda install -y -c conda-forge conda-libmamba-solver && \ + conda install pip pkgconfig conda-forge::hdf5 && \ + pip install kipoi && \ + kipoi env create TREDNet --source=kipoi && \ + conda clean -afy + +FROM debian:bullseye-slim + +RUN apt-get update && apt-get install --no-install-recommends -y ca-certificates git \ + && apt-get clean && rm -rf /var/lib/apt/lists/* + +RUN mkdir -p /app +COPY --from=build /opt/conda/envs/kipoi-TREDNet /opt/conda/envs/kipoi-TREDNet + +SHELL ["/bin/bash", "-c"] +ENV PATH /opt/conda/envs/kipoi-TREDNet/bin:$PATH + diff --git a/kipoi_containers/kipoi-model-repo-hash b/kipoi_containers/kipoi-model-repo-hash index 7b30c05..5e910b4 100644 --- a/kipoi_containers/kipoi-model-repo-hash +++ b/kipoi_containers/kipoi-model-repo-hash @@ -1 +1 @@ -7afe5317d0e213ddefc3a031497e5f5eee8ca5b1 +c0680644e7292b6066ac91e08f605dedd05cad94 \ No newline at end of file