Adding trednet

.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/"

.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/"

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"
     ]
 }

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"]

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
+

kipoi_containers/kipoi-model-repo-hash

@@ -1 +1 @@
-7afe5317d0e213ddefc3a031497e5f5eee8ca5b1
+c0680644e7292b6066ac91e08f605dedd05cad94