Conda recipe for somalier

build.sh

#!/bin/bash

export PATH=${SRC_DIR}/.nimble/bin:${SRC_DIR}/nim/bin/:$PATH
export NIMBLE_DIR=${SRC_DIR}/.nimble/

for path in $(find $CONDA_PREFIX/bin/ -name "x86_64-*" -type f); do
   basename $path | sed 's/x86_64-conda-linux-gnu-//'
done | xargs -IX ln -s $CONDA_PREFIX/bin/x86_64-conda-linux-gnu-X $CONDA_PREFIX/bin/X

export RUSTFLAGS=-Ctarget-feature=-crt-static
cd ${SRC_DIR}/d4-format
cargo build --package=d4binding --release
install -m 644 target/x86_64-unknown-linux-gnu/release/libd4binding.a ${BUILD_PREFIX}/lib
install -m 644 d4binding/include/d4.h ${BUILD_PREFIX}/include

cd ${SRC_DIR}/somalier

sed -i 's/network ctx, AncestryNet:/network AncestryNet:/' src/somalierpkg/ancestry.nim
sed -i '/x: Input/d' src/somalierpkg/ancestry.nim

nimble install -y nimble
nimble install -d -y
nim c -d:danger -d:release -d:openmp -d:blas=openblas -d:lapack=openblas -d:nimNoGetRandom -o:$PREFIX/bin/somalier src/somalier

meta.yaml

package:
  name: somalier
  version: "0.2.15"
  description: "fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs..."

source:
  - git_url: https://github.com/brentp/somalier.git
    git_rev: v0.2.15
    folder: somalier
  - url: https://nim-lang.org/download/nim-1.6.6-linux_x64.tar.xz
    folder: nim
  - git_url: https://github.com/38/d4-format.git
    git_rev: master
    folder: d4-format

build:
  number: 0

requirements:
  build:
    - "{{ compiler('c') }}"
    - "{{ compiler('fortran') }}"
    - "{{ compiler('rust') }}"
    - autoconf
    - bcftools>=1.10
    - bzip2
    - cmake
    - curl
    - git
    - htslib>=1.10
    - libdeflate
    - libnghttp2
    - libzip
    - m4
    - openblas
    - tar
    - wget
    - xz
    - zlib
  run:
    - bcftools>=1.10
    - bzip2
    - htslib>=1.10
    - libdeflate
    - libnghttp2
    - libzip
    - openblas

test:
  commands:
    - somalier

app:
  summary: "fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs..."
  license: MIT