Update nucflag dependency in cenmap v1.2.0. (#68672)

* Fix nucflag dependency in cenmap v1.2.0.

* Revert changes to main recipe and add v1.2.0 recipe.

Author: koisland

recipes/cenmap/v1.2.0/build.sh

@@ -0,0 +1,33 @@
+#!/bin/bash
+set -ex
+
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CFLAGS="${CFLAGS} -O3 -I${PREFIX}/include"
+CENMAP_DIR="${PREFIX}/share/CenMAP"
+mkdir -p "${PREFIX}/bin/"
+mkdir -p "${CENMAP_DIR}"
+
+# Similar to https://github.com/bioconda/bioconda-recipes/blob/master/recipes/repeatmasker/build.sh
+mv * ${CENMAP_DIR}
+
+# Build srf and trf-mod
+# https://github.com/lh3/srf?tab=readme-ov-file#getting-started
+# https://github.com/lh3/TRF-mod?tab=readme-ov-file#trf-mod
+# Both have no GH releases so workflow release has both as archived git submodules.
+srf_dir="${CENMAP_DIR}/workflow/rules/Snakemake-srf/workflow/scripts/srf"
+pushd ${srf_dir}
+make LIBS="${LDFLAGS} -lz" CFLAGS="${CFLAGS}" CC="${CC}"
+chmod 755 ${srf_dir}/srf
+ln -s ${srf_dir}/srf ${PREFIX}/bin/srf
+ln -s ${srf_dir}/srfutils.js ${PREFIX}/bin/srfutils.js
+popd
+
+trf_dir="${CENMAP_DIR}/workflow/rules/Snakemake-srf/workflow/scripts/trf"
+pushd ${trf_dir}
+make CFLAGS="${CFLAGS}" CC="${CC}" -f compile.mak
+chmod 755 ${trf_dir}/trf-mod 
+ln -s ${trf_dir}/trf-mod ${PREFIX}/bin/trf-mod
+popd
+
+# Symlink to bin
+ln -sf ${CENMAP_DIR}/cenmap ${PREFIX}/bin/cenmap

recipes/cenmap/v1.2.0/meta.yaml

@@ -0,0 +1,91 @@
+{% set name = "cenmap" %}
+{% set version = "1.2.0" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/logsdon-lab/CenMAP/releases/download/v{{ version }}/srcs-full-CenMAP.tar.gz
+  sha256: b3d9b0978c44e7b04837f67ae336c097052c9b89383226cea4185e7dcff1e4a5
+
+build:
+  number: 1
+  skip: True  # [osx]
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x") }}
+
+requirements:
+  build:
+    - make
+    - {{ compiler('c') }}
+    - {{ stdlib('c') }}
+  host:
+    - zlib
+  run:
+    - python >=3.12
+    - findutils
+    - coreutils
+    - bedops
+    - hmmer
+    - gzip
+    - gawk
+    - bedtools
+    - kmc >=3.2.4
+    - minimap2 >=2.29
+    # introduced breaking changes to pileup API in minor version 0.6.0
+    - ont-modkit >=0.6.0
+    - pbmm2 >=1.17.0
+    # Last compatible repeatmasker version. post-link script removed in 4.1.8, 4.1.7p1 corrupts Dfam.h5.
+    # https://github.com/bioconda/bioconda-recipes/commit/8fdb7a3556da35a6e2bc2ef7bbd4895377867a05
+    # https://github.com/bioconda/bioconda-recipes/issues/54634
+    - repeatmasker ==4.1.2.p1
+    - rustybam
+    - samtools >=1.13
+    - seqkit
+    - seqtk
+    - srf-n-trf >=0.1.1
+    - stringdecomposer
+    # cenmap uses faster subsample jobs introduced in 8.24
+    # https://github.com/snakemake/snakemake/pull/3112
+    # After 9.5.0 config defaults are not filled in. Fixed in 9.13.1 but cannot update without major refactor.
+    # https://github.com/snakemake/snakemake/issues/3648
+    # Rule inheritance rename rules changed in 9.11.4.
+    # https://github.com/snakemake/snakemake/pull/3714
+    - snakemake >=8.24.0,<=9.5.0
+    - intervaltree
+    - matplotlib-base
+    - numpy
+    - polars
+    - pyarrow
+    - pyyaml
+    - scipy
+    - seaborn
+    - nucflag >=0.3.7,<1.0.0
+    - cenplot >=0.1.4
+    # Features in >=1.2.0 require >=0.1.3
+    - censtats >=0.1.3
+
+test:
+  commands:
+    - cenmap --version
+    # Do dry-run to ensure snakemake workflow is correct.
+    - touch test.fa && cenmap -i test.fa -s example --snake-opts="-n" -o results && rm -rf results
+  import:
+    - numpy
+    - scipy
+    - pysam
+    - cenplot
+    - censtats
+
+about:
+  home: "https://github.com/logsdon-lab/CenMAP"
+  license: MIT
+  license_family: MIT
+  summary: "A centromere mapping and annotation pipeline for T2T human and primate genome assemblies implemented in Snakemake."
+  dev_url: "https://github.com/logsdon-lab/CenMAP"
+  doc_url: "https://github.com/logsdon-lab/CenMAP/blob/v{{ version }}/README.md"
+
+extra:
+  recipe-maintainers:
+    - koisland