initial purge_haplotigs commit (#11049)

* initial purge_haplotigs commit
* bioconda revisions, updating test commands to run the pipeline on the test dataset
* rolling back test commands

recipes/purge_haplotigs/build.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+set -eo pipefail
+
+mkdir -p  "${PREFIX}/bin" "${PREFIX}/scripts" "${PREFIX}/lib" "${PREFIX}/test"
+
+mv bin/* "${PREFIX}/bin"
+mv scripts/* "${PREFIX}/scripts"
+mv lib/* "${PREFIX}/lib"
+mv test/* "${PREFIX}/test"
+
+purge_haplotigs help
+

recipes/purge_haplotigs/meta.yaml

@@ -0,0 +1,43 @@
+{% set version = "1.0.1" %}
+
+package:
+  name: purge_haplotigs
+  version: '{{ version }}'
+
+source:
+  url: https://bitbucket.org/mroachawri/purge_haplotigs/get/v{{ version }}.tar.gz
+  sha256: e646af4ddbe3e0d6c20e8e8b4159770146f5b15eba9058aedbbeefe18584f31c
+
+build:
+  number: 0
+
+requirements:
+  build:
+  run:
+    - perl >=5.22.0
+    - samtools >=1.3.1
+    - bedtools >=2.25.0
+    - r-base >=3.4.1
+    - r-ggplot2 >=2.2.1
+    - minimap2 >=2.12
+    - mummer4 >=4.0.0beta2
+    - make >=4.2.1
+
+test:
+  commands:
+    - purge_haplotigs help
+    - minimap2 -h
+    - samtools --help
+    - bedtools -h
+    - nucmer -h
+    - make -h
+    - Rscript -e 'require(ggplot2)'
+    - perl -e 'use FindBin;use Getopt::Long;use threads;use Thread::Semaphore;use Thread::Queue;use List::Util;'
+
+
+about:
+  home: https://bitbucket.org/mroachawri/purge_haplotigs/
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: Pipeline to help with curating heterozygous diploid genome assemblies.