Merge pull request #27421 from richard-burhans/add-kegalign

Adding new package KegAlign, where SegAlign development will continue

recipes/kegalign/build.sh

@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+
+set -o errexit
+set -o nounset
+
+BUILD_DIR="$SRC_DIR/build"
+BIN_DIR="$PREFIX/bin"
+
+mkdir -p "$BUILD_DIR"
+cd "$BUILD_DIR"
+
+cmake "${CMAKE_ARGS}" -DCMAKE_BUILD_TYPE=Release "$SRC_DIR"
+make
+
+install --mode 0755 --directory "$BIN_DIR"
+install --mode 0755 "$SRC_DIR/build/kegalign" "$BIN_DIR"
+install --mode 0755 "$SRC_DIR/scripts/diagonal_partition.py" "$BIN_DIR"
+install --mode 0755 "$SRC_DIR/scripts/lastz-cmd.ini" "$BIN_DIR"
+install --mode 0755 "$SRC_DIR/scripts/package_output.py" "$BIN_DIR"
+install --mode 0755 "$SRC_DIR/scripts/runner.py" "$BIN_DIR"
+install --mode 0755 "$SRC_DIR/scripts/run_kegalign" "$BIN_DIR"
+install --mode 0755 "$SRC_DIR/scripts/run_lastz_tarball.py" "$BIN_DIR"

recipes/kegalign/meta.yaml

@@ -0,0 +1,63 @@
+{% set name = "KegAlign" %}
+{% set version = "0.1.2.7" %}
+{% set kegalign_python_version = "3.12.*" %}
+{% set kegalign_tbb_version = "2020.2.*" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/galaxyproject/KegAlign/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 79706f8edee458570af61dcf667317f66d4cb0b04f84c8591da9b57d5ddf1ae6
+
+
+build:
+  number: 0
+  skip: true  # [win or osx or cuda_compiler_version is undefined or cuda_compiler_version == "None"]
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ stdlib('c') }}
+    - {{ compiler('cxx') }}
+    - {{ compiler('cuda') }}
+    - cmake
+    - make
+  host:
+    - cuda-version {{ cuda_compiler_version }}
+    - libboost-devel
+    - tbb-devel {{ kegalign_tbb_version }}
+    - zlib
+  run:
+    - {{ pin_compatible("cuda-version", min_pin="x.x", max_pin="x") }}
+    - bash
+    - bashlex
+    - coreutils
+    - gawk
+    - grep
+    - nvidia-ml-py
+    - python {{ kegalign_python_version }}
+    - sed
+    - tbb-devel {{ kegalign_tbb_version }}
+    - time
+
+test:
+  commands:
+    - kegalign --help
+
+about:
+  home: https://github.com/galaxyproject/KegAlign
+  summary: 'KegAlign: A Scalable GPU-Based Whole Genome Aligner'
+  description: |
+    KegAlign is a Scalable GPU System for Pairwise Whole Genome
+    Alignments based on LASTZ's seed-filter-extend paradigm.
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  doc_url: https://github.com/galaxyproject/KegAlign/blob/main/README.md
+  dev_url: https://github.com/galaxyproject/KegAlign
+
+extra:
+  recipe-maintainers:
+    - richard-burhans