Add dedicated Promotech runtime

Author: JAEYOONSUNG

Dockerfile

@@ -61,7 +61,20 @@ RUN /opt/miniforge/bin/conda create -y -p /opt/biotools \
     perl-dbi perl-lwp-simple perl-dbd-sqlite \
     && /opt/miniforge/bin/conda clean -afy
 
+RUN /opt/miniforge/bin/conda create -y -p /opt/promotech \
+    -c conda-forge -c bioconda \
+    python=3.8 \
+    numpy=1.19.5 \
+    pandas=1.1.5 \
+    joblib=0.17.0 \
+    scikit-learn=0.23.2 \
+    biopython=1.78 \
+    progressbar2 \
+    && /opt/miniforge/bin/conda clean -afy \
+    && /opt/promotech/bin/python -c 'import numpy, pandas, joblib, Bio, progressbar, sklearn; assert sklearn.__version__.startswith("0.23")'
+
 ENV PATH="/opt/biotools/bin:${PATH}"
+ENV DNMB_PROMOTECH_PYTHON=/opt/promotech/bin/python
 
 RUN mkdir -p ${DNMB_CACHE_ROOT}/db_modules/clean/split100 \
     && /opt/biotools/bin/python -m venv ${DNMB_CACHE_ROOT}/db_modules/clean/split100/conda_env \

docker/verify-runtime.sh

@@ -25,6 +25,18 @@ for mod in mods:
     __import__(mod)
 PY
 
+test -x "${DNMB_PROMOTECH_PYTHON}"
+"${DNMB_PROMOTECH_PYTHON}" - <<'PY'
+import joblib
+import numpy
+import pandas
+import progressbar
+import sklearn
+from Bio import SeqIO
+
+assert sklearn.__version__.startswith("0.23"), sklearn.__version__
+PY
+
 Rscript - <<'RS'
 required <- c(
   "DNMB", "dplyr", "ggplot2", "ggtext", "openxlsx",
@@ -47,6 +59,22 @@ if (any(promotech_bad)) {
   )
 }
 
+promotech_python <- DNMB:::.dnmb_promotech_resolve_python("python3")
+promotech_model <- file.path(
+  Sys.getenv("DNMB_CACHE_ROOT"),
+  "db_modules", "promotech", "current", "Promotech", "models", "RF-HOT.model"
+)
+if (file.exists(promotech_model)) {
+  model_load <- DNMB:::dnmb_run_external(
+    promotech_python,
+    args = c("-c", "import joblib, sys; joblib.load(sys.argv[1])", promotech_model),
+    required = FALSE
+  )
+  if (!isTRUE(model_load$ok)) {
+    stop("Promotech model load check failed: ", model_load$error, call. = FALSE)
+  }
+}
+
 acr_module <- DNMB:::dnmb_acrfinder_get_module(cache_root = Sys.getenv("DNMB_CACHE_ROOT"), required = TRUE)
 inherited <- strsplit(Sys.getenv("PATH"), .Platform$path.sep, fixed = TRUE)[[1]]
 acr_env_python <- if (!is.null(acr_module$files$env_python)) acr_module$files$env_python else ""