Add recipe for GET_PANGENES

recipes/get_pangenes/build.sh

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+#!/bin/bash
+
+# copy scripts and its dependencies to $PREFIX/bin folder
+mkdir -p ${PREFIX}/bin
+cp -ar pangenes/bin \
+    pangenes/lib \
+    pangenes/get_pangenes.pl \
+    pangenes/_cut_sequences.pl \
+    pangenes/_collinear_genes.pl \
+    pangenes/_cluster_analysis.pl \
+    pangenes/check_evidence.pl \
+    pangenes/_dotplot.pl \
+    pangenes/match_cluster.pl \
+    pangenes/rename_pangenes.pl \
+    pangenes/HPC* \
+    pangenes/CHANGES.txt \
+    pangenes/README.md \
+    LICENSE \
+    ${PREFIX}/bin

recipes/get_pangenes/meta.yaml

@@ -0,0 +1,61 @@
+{% set version = "20250123" %}
+{% set sha256 = "67665e4359dd16ae6fe1359c55a0a1d3eed07efa431c07a87c8c298a8bdbdde3" %}
+
+package:
+  name: get_pangenes
+  version: {{ version }}
+
+build:
+  number: 0
+  noarch: generic
+  script_env:
+   - LC_ALL=POSIX
+  run_exports:
+    - {{ pin_subpackage('get_pangenes', max_pin="x") }}
+
+source:
+  url: https://github.com/Ensembl/plant-scripts/archive/refs/tags/{{ version }}.tar.gz 
+  sha256: {{ sha256 }}
+
+requirements:
+  run:
+    - perl
+    - perl-db_file
+    - minimap2 =2.24
+    - gffread =0.12.7  
+    - gmap 
+    - gsalign
+    - samtools
+    - bedtools
+    - get_homologues    
+    - grep
+    - coreutils  
+    - gzip
+    - bzip2
+    - wget
+
+test:
+  commands:
+    - get_pangenes.pl -v # checks binaries are in place
+
+about:
+  home: https://github.com/Ensembl/plant-scripts/tree/master/pangenes
+  summary: "A versatile software package for calling pangenes from whole genome alignments"
+  license: "Apache-2.0"
+  license_family: APACHE 
+  license_file: LICENSE
+  description: "get_pangenes.pl computes whole genome alignments (WGA) to define clusters of collinear, orthologous genes/features annotated in GFF files, defining pangenes across a pangenome. currently the bioconda version supports nly minimap2."
+
+extra:
+  container:
+    extended-base: True
+  identifiers:
+    - doi:https://doi.org/10.1186/s13059-023-03071-z
+  notes: |
+    This package installs the GET_PANGENES code. It is recommended to run it in a
+    computer cluster with LSF or slurm, particularly for large genomes.
+    To configure it for HPC (get_pangenes.pl -m) please check the documentation and
+    edit your own HPC.conf file , which should be placed in the same location as the
+    main script get_pangenes.pl . Documentation can be found at
+
+    https://github.com/Ensembl/plant-scripts/tree/master/pangenes

recipes/get_pangenes/post-link.sh

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+#!/bin/bash
+
+cat <<EOF >> ${PREFIX}/.messages.txt
+This package installs GET_PANGENES. As Whole Genome Alignments (WGA) can take a
+long time to compute with large chromosomes (as in wheat), it is recommended to
+run it in a high-performance computer (HPC) cluster with LSF or slurm. 
+To configure it for HPC (get_pangenes.pl -m) please check the documentation and
+edit your own 'HPC.conf' file , which should be placed in the same location as 
+the main script get_pangenes.pl . This can be done in 3 steps:
+
+1) Find out the location of GET_PANGENES in your filesystem: 
+
+    $ which get_pangenes.pl
+
+2) Create and edit a text file named 'HPC.conf'. 
+2.1) Example for HPC managed by slurm:
+
+    # cluster/farm configuration file, edit as needed (use spaces or tabs)
+    # PATH might be empty or set to a path/ ending with '/'
+    TYPE    slurm
+    SUBEXE  sbatch
+    CHKEXE  squeue
+    DELEXE  scancel
+    ERROR   F
+    # 70GB was enough for chr-split wheat analysis with minimap2
+    QARGS   -p production --time=24:00:00 --mem 70G
+
+2.2) Example for HPC managed by LSF:
+
+    # PATH might be empty or set to a path/ ending with '/'
+    PATH    /path/to/lsf/bin/
+    TYPE    lsf
+    SUBEXE  bsub
+    CHKEXE  bjobs
+    DELEXE  bkill
+    ERROR   EXIT
+    QARGS   -q production -M 20G 
+
+3) Copy the HPC config file to the location of GET_PANGENES, see step 1):
+
+    $ cp HPC.conf /path/to/get_pangenes.pl
+
+The complete documentation can be found at:
+
+https://github.com/Ensembl/plant-scripts/tree/master/pangenes
+
+EOF