Fix AcrFinder runtime verification

Author: JAEYOONSUNG

Dockerfile

@@ -196,7 +196,10 @@ RUN mkdir -p /opt/dnmb-seed/acrfinder \
 RUN mkdir -p /data /results ${DNMB_CACHE_ROOT} /opt/biotools/data /opt/biotools/test
 
 RUN apt-get -o Acquire::Retries=5 update \
-    && apt-get -o Acquire::Retries=5 install -y --no-install-recommends vienna-rna \
+    && apt-get -o Acquire::Retries=5 install -y --no-install-recommends \
+    vienna-rna \
+    libbio-perl-perl libbio-perl-run-perl libbio-tools-run-alignment-clustalw-perl \
+    libdate-calc-perl libjson-parse-perl \
     && apt-get clean && rm -rf /var/lib/apt/lists/* \
     && /opt/biotools/bin/python -m pip install --no-cache-dir progressbar2 \
     && command -v RNAfold >/dev/null \

docker/verify-runtime.sh

@@ -48,7 +48,16 @@ if (any(promotech_bad)) {
 }
 
 acr_module <- DNMB:::dnmb_acrfinder_get_module(cache_root = Sys.getenv("DNMB_CACHE_ROOT"), required = TRUE)
-acr_paths <- strsplit(Sys.getenv("PATH"), .Platform$path.sep, fixed = TRUE)[[1]]
+inherited <- strsplit(Sys.getenv("PATH"), .Platform$path.sep, fixed = TRUE)[[1]]
+acr_env_python <- if (!is.null(acr_module$files$env_python)) acr_module$files$env_python else ""
+acr_paths <- unique(c(
+  file.path(acr_module$manifest$repo_dir, "bin"),
+  dirname(acr_env_python),
+  "/usr/bin", "/usr/local/bin", "/usr/sbin",
+  inherited,
+  file.path(acr_module$manifest$repo_dir, "dependencies", "CRISPRCasFinder", "bin")
+))
+acr_paths <- acr_paths[nzchar(acr_paths) & file.exists(acr_paths)]
 acr_status <- DNMB:::.dnmb_acrfinder_runtime_status(acr_paths, repo_dir = acr_module$manifest$repo_dir)
 acr_bad <- acr_status$status %in% c("missing", "failed")
 if (any(acr_bad)) {