Add recipe for Poolsnp (bioconda#49156)

* Add PoolSNP recipe v1.0.0

* Add run_exports

* Fix linting

* Include test directory

* Specify Testdata destination

* Fix path specifications

* Fix path specification in test.sh

* Potential tests fix

* Add noarch specification

* Adding .py scripts to bin/

* Test fixes

* Add noarch specification

* Streamline tests

* Alter test command

* Separate out tests

* Add release tarball

recipes/poolsnp/build.sh

@@ -0,0 +1,33 @@
+#! /bin/bash
+
+set -ex
+
+BASE_DIR=$(dirname "$0")
+SCRIPTS_DIR="${BASE_DIR}/scripts"
+TEST_DATA_DIR="${BASE_DIR}/TestData"
+
+if [ ! -d "${SCRIPTS_DIR}" ]; then
+    echo "The scripts directory is missing. It should be placed in the same directory as the PoolSNP.sh script."
+    exit 1
+fi
+
+if [ ! -d "${TEST_DATA_DIR}" ]; then
+    echo "The TestData directory is missing. It should be placed in the same directory as the PoolSNP.sh script."
+    exit 1
+fi
+
+mkdir -p ${PREFIX}/bin
+mkdir -p ${PREFIX}/bin/scripts
+mkdir -p ${PREFIX}/share/PoolSNP
+
+cp PoolSNP.sh ${PREFIX}/bin
+chmod +x ${PREFIX}/bin/PoolSNP.sh
+
+for script in $SCRIPTS_DIR/*; do
+    cp $script ${PREFIX}/bin/$(basename $script)
+    cp $script ${PREFIX}/bin/scripts/
+    chmod +x ${PREFIX}/bin/$(basename $script)
+    chmod +x ${PREFIX}/bin/scripts/$(basename $script)
+done
+
+cp -r ${TEST_DATA_DIR} ${PREFIX}/share/PoolSNP/TestData

recipes/poolsnp/meta.yaml

@@ -0,0 +1,40 @@
+{% set name = "poolsnp" %}
+{% set version = "1.0.0" %}
+{% set github = "https://github.com/capoony/PoolSNP" %}
+
+package: 
+  name: "{{ name }}"
+  version: "{{ version }}"
+
+source:
+  url: "{{ github }}/archive/refs/tags/v.{{ version }}.tar.gz"
+  sha256: a73c61c7ef49be9bd1212ea8049fe617296b0a82b80e0338e2b78dc55105438f
+
+requirements:
+  host:
+    - python
+    - parallel
+  run:
+    - python
+    - parallel
+
+build:
+  number: 0
+  noarch: generic
+  run_exports:
+    - {{ pin_subpackage('poolsnp', max_pin='x.x') }}
+
+test:
+  source_files:
+    - TestData/*
+    - scripts/*
+
+about: 
+  summary: PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and a reference genome in FASTA format as inputs.
+  license: Apache-2.0
+  license_file: LICENSE
+  home: https://github.com/capoony/PoolSNP
+
+extra:
+  recipe-maintainers:
+    - abhilesh

recipes/poolsnp/run_test.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+# Ensure the script is executable
+test -x ${PREFIX}/bin/PoolSNP.sh
+
+# Run PoolSNP.sh with a minimal set of parameters to ensure it executes
+bash ${PREFIX}/bin/PoolSNP.sh \
+  mpileup="${PREFIX}/share/PoolSNP/TestData/test.mpileup" \
+  reference="${PREFIX}/share/PoolSNP/TestData/test.fa" \
+  names=Sample1,Sample2 \
+  max-cov=0.7 \
+  min-cov=4 \
+  min-count=4 \
+  min-freq=0.01 \
+  miss-frac=0.5 \
+  jobs=4 \
+  badsites=1 \
+  allsites=1 \
+  output=${PREFIX}/share/PoolSNP/TestResult/test
+
+# Optionally, check the output file to ensure it was created
+test -f ${PREFIX}/share/PoolSNP/TestResult/test.vcf.gz