Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add recipe for hiddenDomains #12614

Merged
merged 1 commit into from
Dec 13, 2018
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 4 additions & 0 deletions recipes/hiddendomains/build.sh
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
#!/bin/bash

chmod +x *.R
cp hiddenDomains peakCenters *.pl *.R ${PREFIX}/bin
47 changes: 47 additions & 0 deletions recipes/hiddendomains/meta.yaml
Original file line number Diff line number Diff line change
@@ -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."
53 changes: 53 additions & 0 deletions recipes/hiddendomains/path.patch
Original file line number Diff line number Diff line change
@@ -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

##========================================================================
##