# HG changeset patch
# User galaxytrakr
# Date 1773673327 0
# Node ID 719889ec4e14438e3784ccfd219ec15deaa45bb3
# Parent  dcf6c2409ebb42c33a27b42779d60314c2464df1
planemo upload commit 92689f52a93241194941ecf374629245c8fb9093

diff -r dcf6c2409ebb -r 719889ec4e14 Dockerfile
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Dockerfile	Mon Mar 16 15:02:07 2026 +0000
@@ -0,0 +1,74 @@
+# =============================================================
+#   Dockerfile for refchooser (compatible with Galaxy)
+# =============================================================
+
+# ---------- Build Stage 1: The "Builder" ----------
+# This stage downloads and prepares all our dependencies.
+FROM ubuntu:20.04 AS builder
+
+# Set versions for our tools to make updates easy.
+ARG MASH_VER="2.3"
+ARG PYTHON_VER="3.8"
+
+# Avoid interactive prompts during apt-get install.
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install all the dependencies needed to build our tools.
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    tar \
+    gzip \
+    python${PYTHON_VER} \
+    python${PYTHON_VER}-venv \
+    && rm -rf /var/lib/apt/lists/*
+
+# Set a working directory for our downloads.
+WORKDIR /build
+
+# --- Install Mash ---
+# Download the pre-compiled Linux binary for Mash.
+ADD https://github.com/marbl/Mash/releases/download/v${MASH_VER}/mash-Linux64-v${MASH_VER}.tar .
+# Unpack the tarball, find the 'mash' executable, and install it to a standard location.
+RUN tar -xvf mash-Linux64-v${MASH_VER}.tar && \
+    install -m 0755 mash-Linux64-v${MASH_VER}/mash /usr/local/bin/mash
+
+# --- Install refchooser ---
+# Create a Python virtual environment in a standard location.
+RUN python${PYTHON_VER} -m venv /opt/venv
+# Activate the venv and install refchooser and its dependencies using pip.
+ENV PATH="/opt/venv/bin:$PATH"
+RUN pip install --no-cache-dir refchooser
+
+
+# ---------- Build Stage 2: The "Runtime" Stage ----------
+# This is our final, lean image that will be used by Galaxy.
+FROM ubuntu:20.04 AS runtime
+
+# Avoid interactive prompts.
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install only the essential runtime libraries needed by Mash and Python.
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    libgomp1 \
+    python3.8-venv \
+    && rm -rf /var/lib/apt/lists/*
+
+# --- Copy Binaries and Environment from Builder Stage ---
+
+# Copy the compiled 'mash' binary from the builder stage.
+COPY --from=builder /usr/local/bin/mash /usr/local/bin/mash
+
+# Copy the entire Python virtual environment containing 'refchooser'.
+COPY --from=builder /opt/venv /opt/venv
+
+# --- Final Configuration ---
+
+# Set the PATH environment variable so the system can find 'mash' and 'refchooser'.
+ENV PATH="/opt/venv/bin:$PATH"
+
+# As a best practice for Galaxy, ensure all users can read and execute the tools.
+RUN chmod -R a+rX /opt/venv && \
+    chmod a+rx /usr/local/bin/mash
+
+# IMPORTANT: No ENTRYPOINT. Set a neutral CMD for Galaxy compatibility.
+CMD ["/bin/bash"]
diff -r dcf6c2409ebb -r 719889ec4e14 job_conf.yml
--- a/job_conf.yml	Mon Dec 08 20:28:57 2025 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-runners:
-  local:
-    load: galaxy.jobs.runners.local:LocalJobRunner
-    workers: 16
-
-# handling:
-#   processes:
-#     handler0:
-
-execution:
-  default: local
-  environments:
-    local:
-      runner: local
-    docker_local:
-      runner: local
-      docker_enabled: true
-      # container: "auto"
-      docker_volumes: $defaults
-      # docker_set_user: null
-      docker_run_extra_arguments: "--entrypoint ''"
-      docker_set_user: root
-
-tools:
-- id: refchooser
-  # handler: handler0
-  environment: docker_local
-
-limits:
--
-  # Amount of time a job can run (in any environment) before it
-  # will be terminated by Galaxy.
-  type: walltime
-  value: '01:00:00'
\ No newline at end of file
diff -r dcf6c2409ebb -r 719889ec4e14 refchooser.xml
--- a/refchooser.xml	Mon Dec 08 20:28:57 2025 +0000
+++ b/refchooser.xml	Mon Mar 16 15:02:07 2026 +0000
@@ -1,7 +1,8 @@
-<tool id="refchooser" name="Refchooser" version="0.2.1" python_template_version="3.5" profile="21.05">
+<tool id="refchooser" name="Refchooser" version="0.2.1+galaxy0.1" python_template_version="3.5" profile="21.05">
     <description>Select centroidal assembly from a collection of closely-related assemblies, for reference purposes</description>
     <requirements>
-        <container type="docker">quay.io/galaxytrakr/refchooser:0.2.3</container>
+        <container type="docker">cfsanbiostatistics/refchooser:0.2.1</container>
+        
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         mkdir ./assemblies &&
@@ -13,16 +14,15 @@
         export BEST=\$(refchooser metrics --sort Mean_Distance --top 1 ./assemblies ./sketches | tail -n 1 | cut -f 1) &&
         echo "*** best accession \$BEST ***" >&2 &&
         mkdir output &&
-        cp ./assemblies/\$BEST.fasta output/\$BEST.fasta &&
-        ls -l output/
+        cp ./assemblies/\$BEST.fasta output/\$BEST.fasta
     ]]></command>
     <inputs>
         <param type="data_collection" collection_type="list" name="assemblies" format="fasta" />
     </inputs>
     <outputs>
         <data name="matrix" label="Refchooser distance matrix for $on_string" format="tsv" hidden="false" />
-        <data name="best" format="txt" label="Centroidal_assembly" >
-            <discover_datasets directory="output" pattern="__designation_and_ext__" ext="fasta" assign_primary_output="true" visible="true" />
+        <data name="best" format="txt" label="Best assembly" visible="false" >
+            <discover_datasets directory="output" pattern="__designation_and_ext__" assign_primary_output="true" visible="true" />
         </data>
     </outputs>
     <tests>
diff -r dcf6c2409ebb -r 719889ec4e14 test-data/.gitmodules
--- a/test-data/.gitmodules	Mon Dec 08 20:28:57 2025 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-[submodule "test/csp2"]
-	path = test/csp2
-	url = https://github.com/CFSAN-Biostatistics/CSP2_TestData.git
diff -r dcf6c2409ebb -r 719889ec4e14 tool-data/all_fasta.loc.sample