ngscheckmate - migrate to python3 and enable linux-aarch64 and osx-ar…

…m64 (#53196)

* Add patch to use python3

* Build ngscheckmate_fastq - tarball file is a Linux x86_64 binary

* Make this non-generic: there is a binary built now, prior version was a binary for linux-x86_64.  Bump build number, add extra platforms

* typo.

* Update patch to patch ngscheckmate-fastq to compile with recent gcc.

* spacing

* Add zlib dependency

* link to the built ngscheckmate_fastq, not the distributed one.

* fix build.sh cutpasta error

* add CFLAGS and use CC for compiler

* use -c in cflags

* add LDFLAGS (as DFLAGS var..) to ngscheckmate build

* clean up recipe

* Update meta.yaml

* Update build.sh

* unpin python to build on python 3.9-3.12

* re-pin python to <=2.7

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>

recipes/ngscheckmate/build.sh

@@ -29,8 +29,10 @@ export NCM_HOME=$PREFIX/NGSCheckMate
 python $PREFIX/NGSCheckMate/vaf_ncm.py "\$@"
 EOF
 
-ln -s $PREFIX/NGSCheckMate/ngscheckmate_fastq $PREFIX/bin/ngscheckmate_fastq
-
+cd $PREFIX/NGSCheckMate/ngscheckmate_fastq-source
+make COMPILER=${CC} CFLAGS="${CFLAGS} -c" DFLAGS="${LDFLAGS}"
+cd $PREFIX
+ln -sf $PREFIX/NGSCheckMate/ngscheckmate_fastq-source/ngscheckmate_fastq $PREFIX/bin/
 cat << EOF > $PREFIX/bin/makesnvpattern.pl
 #!/usr/bin/env bash
 

recipes/ngscheckmate/meta.yaml

@@ -1,44 +1,59 @@
 {% set name = "ngscheckmate" %}
+{% set version = "1.0.1" %}
 
 package:
   name: {{ name }}
-  version: 1.0.1
+  version: {{ version }}
 
 source:
   url: /~https://github.com/parklab/NGSCheckMate/archive/ef7a38c51dadbd4ef5b6b6db60775f239926f0a8.zip
   md5: 42d4578e02a81e4e55857f126ae719af
+  patches:
+    - py3.patch  # from /~https://github.com/parklab/NGSCheckMate/compare/master...dslarm:NGSCheckMate:master.patch
 
 build:
-  number: 2
-  noarch: generic
+  number: 3
   run_exports:
-    - {{ pin_subpackage(name, max_pin='x.x') }}
+    - {{ pin_subpackage(name, max_pin='x') }}
 
 requirements:
+  build:
+    - {{ compiler('c') }}
+    - make
   host:
-    - python =2.7
-    - r-base >=4
-    - perl
+    - python >=2.7
     - samtools
     - bcftools
     - bowtie
+    - zlib
   run:
-    - python =2.7
+    - python >=2.7
     - r-base >=4
     - perl
     - samtools
     - bcftools
     - bowtie
+
 test:
   commands:
     - ncm.py -h
     - ncm_fastq.py -h
     - vaf_ncm.py -h
     - ngscheckmate_fastq
     - makesnvpattern.pl
-
+    
 about:
-  home: /~https://github.com/parklab/NGSCheckMate
+  home: "/~https://github.com/parklab/NGSCheckMate"
   license: MIT
-  summary: Software package for identifying next generation sequencing (NGS) data files from the same individual.
-  description: This version is built from a pull request which fixes a handful of known bugs.
+  license_family: MIT
+  summary: "Software package for identifying next generation sequencing (NGS) data files from the same individual."
+  description: "This version is built from a pull request which fixes a handful of known bugs."
+  dev_url: "/~https://github.com/parklab/NGSCheckMate"
+  doc_url: "/~https://github.com/parklab/NGSCheckMate/blob/master/Documentation.pdf"
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  identifiers:
+    - biotools:ngscheckmate