Update PhyloAcc recipe (#51224)

recipes/phyloacc/meta.yaml

@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 1
+  number: 2
   skip: True  # [py < 311]
   run_exports:
     - {{ pin_subpackage('phyloacc', max_pin="x") }}
@@ -41,10 +41,8 @@ requirements:
     - llvm-openmp  # [osx]
 
 test:
-  commands:
-    - phyloacc.py --version
-    - phyloacc.py --depcheck
-    - phyloacc_post.py -h
+  requires:
+    - wget
 
 about:
   home: https://phyloacc.github.io/

recipes/phyloacc/run_test.sh

@@ -0,0 +1,61 @@
+#!/bin/bash
+set -e
+set -o pipefail
+set -x
+
+# Runs test for PhyloAcc, including on a small simulated dataset that contains a fasta file, mod file,
+# bed file, id subset file, and config file.
+
+TMP=$(mktemp -d)
+trap 'rm -rf $TMP' EXIT
+export TMPDIR=$TMP
+cd $TMP
+
+echo " ** DOWNLOADING TEST DATA."
+files=(
+  "bioconda-test-cfg.yaml"
+  "id-subset.txt"
+  "ratite.mod"
+  "simu_500_200_diffr_2-1.bed"
+  "simu_500_200_diffr_2-1.noanc.fa"
+)
+
+for file in "${files[@]}"; do
+  if ! wget -q "https://github.com/phyloacc/PhyloAcc-test-data/raw/main/bioconda-test-data/$file"; then
+    echo "Failed to download $file" >&2
+    exit 1
+  fi
+done
+echo " ** TEST DATA DOWNLOAD OK."
+
+echo " ** BEGIN DEPCHECK TEST."
+if ! phyloacc --depcheck; then
+  echo " ** ERROR: Dependency check failed. Please ensure all dependencies are installed." >&2
+  exit 1
+fi
+echo " ** DEPCHECK TEST OK."
+
+echo " ** BEGIN PHYLOACC INTERFACE TEST."
+if ! phyloacc --config bioconda-test-cfg.yaml --local; then
+  echo " ** ERROR: PhyloAcc interface test failed. Please check the configuration and installation." >&2
+  exit 1
+fi
+echo " ** INTERFACE TEST OK."
+
+echo " ** BEGIN WORKFLOW TEST."
+if ! snakemake -p --jobs 1 --cores 1 -s phyloacc-bioconda-test/phyloacc-job-files/snakemake/run_phyloacc.smk --configfile phyloacc-bioconda-test/phyloacc-job-files/snakemake/phyloacc-config.yaml; then
+  echo " ** ERROR: PhyloAcc workflow test failed. Please check the Snakemake configuration and log files." >&2
+  exit 1
+fi
+echo " ** WORKFLOW TEST OK."
+
+echo " ** BEGIN POST-PROCESSING TEST."
+if ! phyloacc_post.py -h; then
+  echo " ** ERROR: Failed to display help message for phyloacc_post.py" >&2
+  exit 1
+fi
+if ! phyloacc_post.py -i phyloacc-bioconda-test/; then
+  echo " ** ERROR: Post-processing test failed. Please check the input directory and log files." >&2
+  exit 1
+fi
+echo " ** POST-PROCESSING TEST OK."