From d4e9c7b8f4d17e5008acaa20aac1c721ae767768 Mon Sep 17 00:00:00 2001
From: mroachawri <michael.roach@awri.com.au>
Date: Fri, 21 Sep 2018 11:58:49 +0930
Subject: [PATCH 1/3] initial purge_haplotigs commit

---
 recipes/purge_haplotigs/build.sh  |  8 ++++++
 recipes/purge_haplotigs/meta.yaml | 46 +++++++++++++++++++++++++++++++
 2 files changed, 54 insertions(+)
 create mode 100644 recipes/purge_haplotigs/build.sh
 create mode 100644 recipes/purge_haplotigs/meta.yaml

diff --git a/recipes/purge_haplotigs/build.sh b/recipes/purge_haplotigs/build.sh
new file mode 100644
index 0000000000000..06b297ce4ad00
--- /dev/null
+++ b/recipes/purge_haplotigs/build.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+mkdir -p  "$PREFIX/bin"
+
+cp -r bin/ $PREFIX
+cp -r scripts/ $PREFIX
+cp -r lib/ $PREFIX
+cp -r test/ $PREFIX
diff --git a/recipes/purge_haplotigs/meta.yaml b/recipes/purge_haplotigs/meta.yaml
new file mode 100644
index 0000000000000..2a571caa7868b
--- /dev/null
+++ b/recipes/purge_haplotigs/meta.yaml
@@ -0,0 +1,46 @@
+{% set version = "1.0.1" %}
+{% set build = "0" %}
+{% set tarball = "https://bitbucket.org/mroachawri/purge_haplotigs/get/minimap2.tar.gz" %}
+{% set sha256 = "ae31483509afb26a8c2100b0c0bc1a066b80d130bbdab06cd55e3c347d22f7c4" %}
+
+package:
+  name: purge_haplotigs
+  version: '{{ version }}'
+
+source:
+  url: '{{ tarball }}'
+  sha256: '{{ sha256 }}'
+
+build:
+  number: '{{ build }}'
+
+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.

From 5b8270622c9070eaff702a849e14556c73f54d8e Mon Sep 17 00:00:00 2001
From: mroachawri <michael.roach@awri.com.au>
Date: Tue, 25 Sep 2018 09:51:49 +0930
Subject: [PATCH 2/3] bioconda revisions, updating test commands to run the
 pipeline on the test dataset

---
 recipes/purge_haplotigs/meta.yaml | 19 ++++---------------
 1 file changed, 4 insertions(+), 15 deletions(-)

diff --git a/recipes/purge_haplotigs/meta.yaml b/recipes/purge_haplotigs/meta.yaml
index 2a571caa7868b..84bb8e846efaa 100644
--- a/recipes/purge_haplotigs/meta.yaml
+++ b/recipes/purge_haplotigs/meta.yaml
@@ -1,18 +1,15 @@
 {% set version = "1.0.1" %}
-{% set build = "0" %}
-{% set tarball = "https://bitbucket.org/mroachawri/purge_haplotigs/get/minimap2.tar.gz" %}
-{% set sha256 = "ae31483509afb26a8c2100b0c0bc1a066b80d130bbdab06cd55e3c347d22f7c4" %}
 
 package:
   name: purge_haplotigs
   version: '{{ version }}'
 
 source:
-  url: '{{ tarball }}'
-  sha256: '{{ sha256 }}'
+  url: https://bitbucket.org/mroachawri/purge_haplotigs/get/v{{ version }}.tar.gz
+  sha256: e646af4ddbe3e0d6c20e8e8b4159770146f5b15eba9058aedbbeefe18584f31c
 
 build:
-  number: '{{ build }}'
+  number: 0
 
 requirements:
   build:
@@ -28,15 +25,7 @@ requirements:
 
 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;'
-    
+    - cd test/ && make test && make clean    
 
 about:
   home: https://bitbucket.org/mroachawri/purge_haplotigs/

From cfa7af359132e288f812408f6cfe8170772ca5b0 Mon Sep 17 00:00:00 2001
From: mroachawri <michael.roach@awri.com.au>
Date: Tue, 25 Sep 2018 13:08:37 +0930
Subject: [PATCH 3/3] rolling back test commands

---
 recipes/purge_haplotigs/build.sh  | 14 +++++++++-----
 recipes/purge_haplotigs/meta.yaml | 10 +++++++++-
 2 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/recipes/purge_haplotigs/build.sh b/recipes/purge_haplotigs/build.sh
index 06b297ce4ad00..42fe38a625505 100644
--- a/recipes/purge_haplotigs/build.sh
+++ b/recipes/purge_haplotigs/build.sh
@@ -1,8 +1,12 @@
 #!/bin/bash
+set -eo pipefail
 
-mkdir -p  "$PREFIX/bin"
+mkdir -p  "${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
 
-cp -r bin/ $PREFIX
-cp -r scripts/ $PREFIX
-cp -r lib/ $PREFIX
-cp -r test/ $PREFIX
diff --git a/recipes/purge_haplotigs/meta.yaml b/recipes/purge_haplotigs/meta.yaml
index 84bb8e846efaa..f69f3fe495759 100644
--- a/recipes/purge_haplotigs/meta.yaml
+++ b/recipes/purge_haplotigs/meta.yaml
@@ -25,7 +25,15 @@ requirements:
 
 test:
   commands:
-    - cd test/ && make test && make clean    
+    - 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/