Add recipe for hiddenDomains (#12614)

recipes/hiddendomains/build.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+chmod +x *.R
+cp hiddenDomains peakCenters *.pl *.R ${PREFIX}/bin

recipes/hiddendomains/meta.yaml

@@ -0,0 +1,47 @@
+{% set name = "hiddenDomains" %}
+{% set version = "3.0" %}
+{% set sha256 = "98a3d52dd67d9a4a55048e6d06cfb1c98e28122b675d23d0db3c1e6de7d6a89d" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://sourceforge.net/projects/hiddendomains/files/{{ name }}.{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+  patches:
+     - path.patch
+
+build:
+  number: 0
+
+requirements:
+  host:
+     - perl
+     - r-base
+     - r-depmixs4
+     - r-hiddenmarkov 
+     - samtools
+     - bedtools
+  run:
+     - perl
+     - r-base
+     - r-depmixs4
+     - r-hiddenmarkov
+     - samtools
+     - bedtools
+
+test:
+  commands:
+     - hiddenDomains -h 2>&1 | grep "hiddenDomains"
+     - binReads.pl -h 2>&1 | grep "binReads.pl"
+     - domainsMergeToBed.pl -h 2>&1 | grep "domainsMergeToBed.pl"
+     - domainsToBed.pl -h 2>&1 | grep "domainsToBed.pl"
+     - peakCenters -h 2>&1 | grep "peakCenters"
+
+about:
+  home: http://hiddendomains.sourceforge.net/
+  license: GNU GPL
+  license_family: GPL
+  license_file: LICENSE
+  summary: "hiddenDomains is a suite of programs used to identify significant enrichment of ChIP-seq reads that span large domains."

recipes/hiddendomains/path.patch

@@ -0,0 +1,53 @@
+--- binReads.pl	2015-09-30 13:21:52.000000000 -0500
++++ binReads.pl.new	2018-12-12 18:03:04.485187656 -0600
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/opt/anaconda1anaconda2anaconda3/bin/perl
+
+ ##========================================================================
+ ##
+@@ -192,4 +192,3 @@
+ 	$counter++;
+     }
+ }
+-
+--- centersToGEM.pl	2015-12-02 14:09:06.000000000 -0600
++++ centersToGEM.pl.new	2018-12-12 18:03:40.014184067 -0600
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/opt/anaconda1anaconda2anaconda3/bin/perl
+
+ use strict;
+ use warnings;
+--- domainsMergeToBed.pl	2015-09-30 13:21:53.000000000 -0500
++++ domainsMergeToBed.pl.new	2018-12-12 18:05:32.450172703 -0600
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/opt/anaconda1anaconda2anaconda3/bin/perl
+
+ ##========================================================================
+ ##
+--- domainsToBed.pl	2015-09-30 13:21:53.000000000 -0500
++++ domainsToBed.pl.new	2018-12-12 18:10:10.723143778 -0600
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/opt/anaconda1anaconda2anaconda3/bin/perl
+
+ ##========================================================================
+ ##
+--- hiddenDomains	2017-08-08 09:08:30.000000000 -0500
++++ hiddenDomains.new	2018-12-12 18:08:18.529155487 -0600
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/opt/anaconda1anaconda2anaconda3/bin/perl
+
+ ##========================================================================
+ ##
+--- peakCenters	2015-12-03 10:33:22.000000000 -0600
++++ peakCenters.new	2018-12-12 18:08:50.550152145 -0600
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/opt/anaconda1anaconda2anaconda3/bin/perl
+
+ ##========================================================================
+ ##