Bulk: Add new recipe for Souporcell (#50608)

* add scripts

* update scripts

* update scripts

* fix linting error

* fix checksum

* remove uncomment

* add resource

* clean up recipe

---------

Co-authored-by: wxicu <[email protected]>
Co-authored-by: mencian <[email protected]>
Co-authored-by: Joshua Zhuang <[email protected]>
Co-authored-by: Xichen Wu <[email protected]>

recipes/souporcell/build.sh

@@ -0,0 +1,22 @@
+#!/bin/bash -euo
+
+mkdir -p ${PREFIX}/bin
+
+export CFLAGS="${CFLAGS} -fcommon"
+export CXXFLAGS="${CFLAGS} -fcommon -I${PREFIX}/include"
+
+INSTALL_PREFIX="${PREFIX}" make -j${CPU_COUNT}
+
+# Include scripts
+cp -f stan_consensus.pickle $PREFIX/bin/stan_consensus.pickle
+cp -f *py $PREFIX/bin
+chmod +rx $PREFIX/bin/souporcell_pipeline.py
+
+# Scripts expect the binary located in the following folder
+mkdir -p $PREFIX/bin/souporcell/target/release
+mkdir -p $PREFIX/bin/troublet/target/release
+
+# Build statically linked binary with Rust
+RUST_BACKTRACE=1
+cargo install --verbose --root "${PREFIX}/bin/souporcell/target/release/" --path troublet
+cargo install --verbose --root "${PREFIX}/bin/troublet/target/release/" --path souporcell

recipes/souporcell/meta.yaml

@@ -0,0 +1,64 @@
+{% set name = "souporcell" %}
+{% set version = "2.5" %}
+{% set sha256 = "1404b87e44c4452b2f329abb81ce4a8383ed5b7e94f38ff2815c5bed62ec2c7f" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/wheaton5/souporcell/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('souporcell', max_pin="x") }}
+
+requirements:
+  build:
+    - {{ compiler('rust') }}
+    - {{ compiler('cxx') }}
+    - cmake
+    - make
+    - autoconf
+    - pkg-config
+  host:
+    - python =3.9
+    - pip
+  run:
+    - python =3.9
+    - pysam
+    - pystan <3
+    - pyvcf
+    - numpy
+    - pyfaidx
+    - setuptools <58
+    - scipy
+    - bcftools >=1.9
+    - bedtools >=2.28
+    - freebayes >=1.3
+    - htslib >=1.9
+    - hisat2
+    - minimap2 >=2.26
+    - samtools >=1.9
+    - vatrix
+
+test:
+  commands:
+    - souporcell_pipeline.py -h
+
+about:
+  home: "https://github.com/wheaton5/souporcell"
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: "Clustering scRNAseq by genotypes."
+  dev_url: "https://github.com/wheaton5/souporcell"
+
+extra:
+  identifiers:
+    - doi:10.1101/699637v1
+    - biotools:souporcell
+  skip-lints:
+    - uses_setuptools  # uses pkg_resoures during run time