From 42c868fb3e7906aa187b7e717089ac1884f0bced Mon Sep 17 00:00:00 2001
From: Colin Brislawn <cbrisl@gmail.com>
Date: Fri, 15 Apr 2016 16:14:01 -0700
Subject: [PATCH 01/18] Adding rdp-tools

---
 recipes/rdp-tools/meta.yaml | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 recipes/rdp-tools/meta.yaml

diff --git a/recipes/rdp-tools/meta.yaml b/recipes/rdp-tools/meta.yaml
new file mode 100644
index 0000000000000..d9fea047b8a5c
--- /dev/null
+++ b/recipes/rdp-tools/meta.yaml
@@ -0,0 +1,37 @@
+
+package:
+  name: rdp-tools
+  version: "2.0.2"
+
+source:
+  git_url: https://github.com/rdpstaff/RDPTools.git
+  git_rev: 2.0.2
+
+requirements:
+  build:
+    - ant
+
+build:
+  number: 0
+  script:
+#    - brew update              # [osx]
+#    - brew install ant         # [osx]
+
+    - git config --global url."https://".insteadOf git://
+    - git submodule init
+    - git submodule update
+
+    - make
+
+    - mkdir -p $PREFIX/bin
+    - mv *.jar $PREFIX/bin
+    - mv lib $PREFIX/bin
+
+test:
+  commands:
+    - java -Xmx1g -jar $PREFIX/bin/classifier.jar classify -c 0.5 -o usga_classified.txt -h soil_hier.txt $SRC_DIR/classifier/samplefiles/USGA_2_4_B_trimmed.fasta
+
+about:
+  summary: Metaproject for RDP Tools
+  home: https://rdp.cme.msu.edu/classifier/classifier.jsp
+  license: GPL2

From dfbb9e56559779eff758ebd01a7235b7bdd49932 Mon Sep 17 00:00:00 2001
From: Colin Brislawn <cbrisl@gmail.com>
Date: Mon, 18 Apr 2016 10:11:30 -0700
Subject: [PATCH 02/18] move build to build.sh file

---
 recipes/rdp-tools/build.sh  | 14 ++++++++++++++
 recipes/rdp-tools/meta.yaml | 13 -------------
 2 files changed, 14 insertions(+), 13 deletions(-)
 create mode 100644 recipes/rdp-tools/build.sh

diff --git a/recipes/rdp-tools/build.sh b/recipes/rdp-tools/build.sh
new file mode 100644
index 0000000000000..6c99a5a292956
--- /dev/null
+++ b/recipes/rdp-tools/build.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+#brew update              # [osx]
+#brew install ant         # [osx]
+
+#git config --global url."https://".insteadOf git://
+#git submodule init
+#git submodule update
+
+make
+
+mkdir -p ${PREFIX}/bin
+mv *.jar ${PREFIX}/bin
+mv lib ${PREFIX}/bin
diff --git a/recipes/rdp-tools/meta.yaml b/recipes/rdp-tools/meta.yaml
index d9fea047b8a5c..1a5f1b6cad571 100644
--- a/recipes/rdp-tools/meta.yaml
+++ b/recipes/rdp-tools/meta.yaml
@@ -13,19 +13,6 @@ requirements:
 
 build:
   number: 0
-  script:
-#    - brew update              # [osx]
-#    - brew install ant         # [osx]
-
-    - git config --global url."https://".insteadOf git://
-    - git submodule init
-    - git submodule update
-
-    - make
-
-    - mkdir -p $PREFIX/bin
-    - mv *.jar $PREFIX/bin
-    - mv lib $PREFIX/bin
 
 test:
   commands:

From ec6b9d972917feb2906a6269697e757e789b3016 Mon Sep 17 00:00:00 2001
From: Colin Brislawn <cbrisl@gmail.com>
Date: Mon, 18 Apr 2016 13:58:13 -0700
Subject: [PATCH 03/18] update RDP-tools requirements

---
 recipes/rdp-tools/meta.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/recipes/rdp-tools/meta.yaml b/recipes/rdp-tools/meta.yaml
index 1a5f1b6cad571..8da484fdb1c8b 100644
--- a/recipes/rdp-tools/meta.yaml
+++ b/recipes/rdp-tools/meta.yaml
@@ -10,6 +10,8 @@ source:
 requirements:
   build:
     - ant
+  run:
+    - java
 
 build:
   number: 0

From 232ecef00b0ca608ccb0702a603f2f0192c20bef Mon Sep 17 00:00:00 2001
From: Colin Brislawn <cbrisl@gmail.com>
Date: Mon, 18 Apr 2016 19:20:57 -0700
Subject: [PATCH 04/18] Update meta.yaml

---
 recipes/rdp-tools/meta.yaml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/recipes/rdp-tools/meta.yaml b/recipes/rdp-tools/meta.yaml
index 8da484fdb1c8b..1a5f1b6cad571 100644
--- a/recipes/rdp-tools/meta.yaml
+++ b/recipes/rdp-tools/meta.yaml
@@ -10,8 +10,6 @@ source:
 requirements:
   build:
     - ant
-  run:
-    - java
 
 build:
   number: 0

From f22e498ea60313c2cdc73d0a73264956dd87e819 Mon Sep 17 00:00:00 2001
From: Colin Brislawn <cbrisl@gmail.com>
Date: Mon, 18 Apr 2016 19:26:00 -0700
Subject: [PATCH 05/18] fixing rdp-tools recipe

---
 recipes/rdp-tools/meta.yaml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/recipes/rdp-tools/meta.yaml b/recipes/rdp-tools/meta.yaml
index 1a5f1b6cad571..5a03cec196f71 100644
--- a/recipes/rdp-tools/meta.yaml
+++ b/recipes/rdp-tools/meta.yaml
@@ -16,6 +16,12 @@ build:
 
 test:
   commands:
+    - java=java
+    - if [ -z "${JAVA_HOME:=}" ]; then
+    -   if [ -e "$JAVA_HOME/bin/java" ]; then
+    -     java="$JAVA_HOME/bin/java"
+    -   fi
+    - fi
     - java -Xmx1g -jar $PREFIX/bin/classifier.jar classify -c 0.5 -o usga_classified.txt -h soil_hier.txt $SRC_DIR/classifier/samplefiles/USGA_2_4_B_trimmed.fasta
 
 about:

From 0f90fd3c6c11af81e2f86db9b26167501979823b Mon Sep 17 00:00:00 2001
From: Colin Brislawn <cbrisl@gmail.com>
Date: Sun, 8 May 2016 18:17:46 -0700
Subject: [PATCH 06/18] add java as requirement to RDP-tools

---
 recipes/rdp-tools/meta.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/recipes/rdp-tools/meta.yaml b/recipes/rdp-tools/meta.yaml
index 5a03cec196f71..d59d96a12d82d 100644
--- a/recipes/rdp-tools/meta.yaml
+++ b/recipes/rdp-tools/meta.yaml
@@ -10,6 +10,8 @@ source:
 requirements:
   build:
     - ant
+  run:
+    - java
 
 build:
   number: 0

From 581762540e0af8fe914bd3fbccc93581d47ef04f Mon Sep 17 00:00:00 2001
From: Colin Brislawn <cbrisl@gmail.com>
Date: Tue, 1 Nov 2016 16:51:08 -0700
Subject: [PATCH 07/18] Add Quorum

---
 recipes/quorum/build.sh  |  9 +++++++++
 recipes/quorum/meta.yaml | 30 ++++++++++++++++++++++++++++++
 2 files changed, 39 insertions(+)
 create mode 100644 recipes/quorum/build.sh
 create mode 100644 recipes/quorum/meta.yaml

diff --git a/recipes/quorum/build.sh b/recipes/quorum/build.sh
new file mode 100644
index 0000000000000..69f87a71b33a5
--- /dev/null
+++ b/recipes/quorum/build.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+pushd $SRC_DIR
+
+autoreconf -i
+./configure --prefix=$PREFIX
+make
+make install
+
diff --git a/recipes/quorum/meta.yaml b/recipes/quorum/meta.yaml
new file mode 100644
index 0000000000000..a5ee893cfd2c2
--- /dev/null
+++ b/recipes/quorum/meta.yaml
@@ -0,0 +1,30 @@
+build:
+  number: 1 
+
+package:
+  name: quorum
+  version: "1.1.0"
+source:
+  fn: quorum-1.1.0.tar.gz
+  url: https://github.com/gmarcais/Quorum/releases/download/v1.1.0/quorum-1.1.0.tar.gz
+  md5: 14cc37310ff81b447148797afe551fe9
+requirements:
+  build:
+    - gcc
+    - autoconf
+    - automake
+    - libtool
+    - pkg-config
+    - yaggo >=1.5.8
+    - jellyfish
+  run:
+    - libgcc
+    - jellyfish
+test:
+  commands:
+    - quorum --version 2>&1 > /dev/null
+about:
+  home: http://www.genome.umd.edu/quorum.html
+  license: GPLv3
+  summary: QuorUM (Quality Optimized Reads from the University of Maryland) is an error corrector for Illumina reads. It is distributed and used with MaSuRCA, or it can be used independently.
+

From ddbe018fd46da8b5bd8bf4c9940d1d1e5ffa8281 Mon Sep 17 00:00:00 2001
From: Colin Brislawn <cbrisl@gmail.com>
Date: Tue, 1 Nov 2016 16:59:25 -0700
Subject: [PATCH 08/18] remove other recipe

---
 recipes/rdp-tools/build.sh  | 14 --------------
 recipes/rdp-tools/meta.yaml | 32 --------------------------------
 2 files changed, 46 deletions(-)
 delete mode 100644 recipes/rdp-tools/build.sh
 delete mode 100644 recipes/rdp-tools/meta.yaml

diff --git a/recipes/rdp-tools/build.sh b/recipes/rdp-tools/build.sh
deleted file mode 100644
index 6c99a5a292956..0000000000000
--- a/recipes/rdp-tools/build.sh
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/bin/bash
-
-#brew update              # [osx]
-#brew install ant         # [osx]
-
-#git config --global url."https://".insteadOf git://
-#git submodule init
-#git submodule update
-
-make
-
-mkdir -p ${PREFIX}/bin
-mv *.jar ${PREFIX}/bin
-mv lib ${PREFIX}/bin
diff --git a/recipes/rdp-tools/meta.yaml b/recipes/rdp-tools/meta.yaml
deleted file mode 100644
index d59d96a12d82d..0000000000000
--- a/recipes/rdp-tools/meta.yaml
+++ /dev/null
@@ -1,32 +0,0 @@
-
-package:
-  name: rdp-tools
-  version: "2.0.2"
-
-source:
-  git_url: https://github.com/rdpstaff/RDPTools.git
-  git_rev: 2.0.2
-
-requirements:
-  build:
-    - ant
-  run:
-    - java
-
-build:
-  number: 0
-
-test:
-  commands:
-    - java=java
-    - if [ -z "${JAVA_HOME:=}" ]; then
-    -   if [ -e "$JAVA_HOME/bin/java" ]; then
-    -     java="$JAVA_HOME/bin/java"
-    -   fi
-    - fi
-    - java -Xmx1g -jar $PREFIX/bin/classifier.jar classify -c 0.5 -o usga_classified.txt -h soil_hier.txt $SRC_DIR/classifier/samplefiles/USGA_2_4_B_trimmed.fasta
-
-about:
-  summary: Metaproject for RDP Tools
-  home: https://rdp.cme.msu.edu/classifier/classifier.jsp
-  license: GPL2

From e7223af033991b1f93d9fd4b043e79b10fa0bc74 Mon Sep 17 00:00:00 2001
From: Colin Brislawn <cbrisl@gmail.com>
Date: Wed, 2 Nov 2016 15:03:50 -0700
Subject: [PATCH 09/18] Update build.sh

---
 recipes/quorum/build.sh | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/recipes/quorum/build.sh b/recipes/quorum/build.sh
index 69f87a71b33a5..c06ef4c3f36d4 100644
--- a/recipes/quorum/build.sh
+++ b/recipes/quorum/build.sh
@@ -1,9 +1,6 @@
-#!/bin/bash
-
-pushd $SRC_DIR
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/autoreconf
 
 autoreconf -i
 ./configure --prefix=$PREFIX
 make
 make install
-

From 2f7e2592cf1fa749921f4e8d658a4d4dcd127154 Mon Sep 17 00:00:00 2001
From: Colin Brislawn <cbrisl@gmail.com>
Date: Wed, 2 Nov 2016 15:05:07 -0700
Subject: [PATCH 10/18] Update meta.yaml

---
 recipes/quorum/meta.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/recipes/quorum/meta.yaml b/recipes/quorum/meta.yaml
index a5ee893cfd2c2..b5bf1df809fe1 100644
--- a/recipes/quorum/meta.yaml
+++ b/recipes/quorum/meta.yaml
@@ -1,5 +1,5 @@
 build:
-  number: 1 
+  number: 0
 
 package:
   name: quorum
@@ -10,7 +10,8 @@ source:
   md5: 14cc37310ff81b447148797afe551fe9
 requirements:
   build:
-    - gcc
+    - gcc # [linux]
+    - llvm # [osx]
     - autoconf
     - automake
     - libtool
@@ -18,7 +19,7 @@ requirements:
     - yaggo >=1.5.8
     - jellyfish
   run:
-    - libgcc
+    - libgcc # [linux]
     - jellyfish
 test:
   commands:
@@ -27,4 +28,3 @@ about:
   home: http://www.genome.umd.edu/quorum.html
   license: GPLv3
   summary: QuorUM (Quality Optimized Reads from the University of Maryland) is an error corrector for Illumina reads. It is distributed and used with MaSuRCA, or it can be used independently.
-

From b0254d367f1b14095da6b2c4a77d741cca33586d Mon Sep 17 00:00:00 2001
From: Colin Brislawn <cbrisl@gmail.com>
Date: Thu, 3 Nov 2016 09:23:16 -0700
Subject: [PATCH 11/18] Update meta.yaml

---
 recipes/quorum/meta.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/recipes/quorum/meta.yaml b/recipes/quorum/meta.yaml
index b5bf1df809fe1..01ff3692d7fec 100644
--- a/recipes/quorum/meta.yaml
+++ b/recipes/quorum/meta.yaml
@@ -14,6 +14,7 @@ requirements:
     - llvm # [osx]
     - autoconf
     - automake
+    - perl-threaded
     - libtool
     - pkg-config
     - yaggo >=1.5.8

From 5072bf6d98325412847bfe627017956e162c5ea3 Mon Sep 17 00:00:00 2001
From: Colin Brislawn <cbrisl@gmail.com>
Date: Thu, 3 Nov 2016 14:25:33 -0700
Subject: [PATCH 12/18] Update meta.yaml

---
 recipes/quorum/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/quorum/meta.yaml b/recipes/quorum/meta.yaml
index 01ff3692d7fec..75c4e69d0ad7a 100644
--- a/recipes/quorum/meta.yaml
+++ b/recipes/quorum/meta.yaml
@@ -21,7 +21,7 @@ requirements:
     - jellyfish
   run:
     - libgcc # [linux]
-    - jellyfish
+    - jellyfish >= 2.0
 test:
   commands:
     - quorum --version 2>&1 > /dev/null

From 514cecfb4f7cef3ba851774773eafb23f423ae53 Mon Sep 17 00:00:00 2001
From: Colin Brislawn <cbrisl@gmail.com>
Date: Fri, 4 Nov 2016 08:33:22 -0700
Subject: [PATCH 13/18] fix jellyfish version

---
 recipes/quorum/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/quorum/meta.yaml b/recipes/quorum/meta.yaml
index 75c4e69d0ad7a..4e83666ef47e4 100644
--- a/recipes/quorum/meta.yaml
+++ b/recipes/quorum/meta.yaml
@@ -18,10 +18,10 @@ requirements:
     - libtool
     - pkg-config
     - yaggo >=1.5.8
-    - jellyfish
+    - jellyfish >=2.0
   run:
     - libgcc # [linux]
-    - jellyfish >= 2.0
+    - jellyfish >=2.0
 test:
   commands:
     - quorum --version 2>&1 > /dev/null

From 198b73db38628b03db9b1314240b550aef4063c3 Mon Sep 17 00:00:00 2001
From: Colin Brislawn <cbrisl@gmail.com>
Date: Fri, 4 Nov 2016 08:34:04 -0700
Subject: [PATCH 14/18] Update meta.yaml

---
 recipes/quorum/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/quorum/meta.yaml b/recipes/quorum/meta.yaml
index 4e83666ef47e4..43962497f255e 100644
--- a/recipes/quorum/meta.yaml
+++ b/recipes/quorum/meta.yaml
@@ -1,5 +1,5 @@
 build:
-  number: 0
+  number: 1
 
 package:
   name: quorum

From ba22c471b3d1f4789338d72629f8bfd96686c257 Mon Sep 17 00:00:00 2001
From: Colin Brislawn <cbrisl@gmail.com>
Date: Mon, 14 Nov 2016 10:36:58 -0800
Subject: [PATCH 15/18] Remove hack from Quorum build

---
 recipes/quorum/build.sh | 2 --
 1 file changed, 2 deletions(-)

diff --git a/recipes/quorum/build.sh b/recipes/quorum/build.sh
index c06ef4c3f36d4..c33d616b1135d 100644
--- a/recipes/quorum/build.sh
+++ b/recipes/quorum/build.sh
@@ -1,5 +1,3 @@
-sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/autoreconf
-
 autoreconf -i
 ./configure --prefix=$PREFIX
 make

From 9cec3669c0ee20d34e94b0d257d6ae424a4487e7 Mon Sep 17 00:00:00 2001
From: Colin Brislawn <cbrisl@gmail.com>
Date: Wed, 1 Feb 2017 18:13:26 -0800
Subject: [PATCH 16/18] Quorum build using only gcc

---
 recipes/quorum/build.sh  |  4 +++-
 recipes/quorum/meta.yaml | 25 +++++++++++--------------
 2 files changed, 14 insertions(+), 15 deletions(-)

diff --git a/recipes/quorum/build.sh b/recipes/quorum/build.sh
index c33d616b1135d..2a5b3e33cb137 100644
--- a/recipes/quorum/build.sh
+++ b/recipes/quorum/build.sh
@@ -1,4 +1,6 @@
-autoreconf -i
+export JELLYFISH2_0_CFLAGS=-I$PREFIX/include/jellyfish-2.2.6/
+export JELLYFISH2_0_LIBS=$PREFIX/lib/libjellyfish-2.0.dylib
+
 ./configure --prefix=$PREFIX
 make
 make install
diff --git a/recipes/quorum/meta.yaml b/recipes/quorum/meta.yaml
index 43962497f255e..4d96730ff68d1 100644
--- a/recipes/quorum/meta.yaml
+++ b/recipes/quorum/meta.yaml
@@ -1,23 +1,20 @@
+{% set name = "quorum" %}
+{% set version = "1.1.1" %}
+{% set md5 = "f35761bb32d00de556c143bcf33a1142" %}
+
 build:
-  number: 1
+  number: 0
 
 package:
-  name: quorum
-  version: "1.1.0"
+  name: {{ name }}
+  version: {{ version }}
 source:
-  fn: quorum-1.1.0.tar.gz
-  url: https://github.com/gmarcais/Quorum/releases/download/v1.1.0/quorum-1.1.0.tar.gz
-  md5: 14cc37310ff81b447148797afe551fe9
+  fn: Quorum-{{ version }}.tar.gz
+  url: https://github.com/gmarcais/Quorum/releases/download/v{{ version }}/{{ name }}-{{ version }}.tar.gz
+  md5: {{ md5 }}
 requirements:
   build:
-    - gcc # [linux]
-    - llvm # [osx]
-    - autoconf
-    - automake
-    - perl-threaded
-    - libtool
-    - pkg-config
-    - yaggo >=1.5.8
+    - gcc
     - jellyfish >=2.0
   run:
     - libgcc # [linux]

From 8cef913978bceb279ef323945054719e0dd73543 Mon Sep 17 00:00:00 2001
From: Colin Brislawn <cbrisl@gmail.com>
Date: Fri, 3 Feb 2017 12:51:59 -0800
Subject: [PATCH 17/18] Export different libs for osx and linux

---
 recipes/quorum/build.sh | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/recipes/quorum/build.sh b/recipes/quorum/build.sh
index 2a5b3e33cb137..ba88323411ace 100644
--- a/recipes/quorum/build.sh
+++ b/recipes/quorum/build.sh
@@ -1,5 +1,11 @@
 export JELLYFISH2_0_CFLAGS=-I$PREFIX/include/jellyfish-2.2.6/
-export JELLYFISH2_0_LIBS=$PREFIX/lib/libjellyfish-2.0.dylib
+if [ "$(uname)" == "Darwin" ]; then
+    echo "Use *.dylib for OSX"
+    export JELLYFISH2_0_LIBS=$PREFIX/lib/libjellyfish-2.0.dylib
+else
+    echo "Use *.so for Linux"
+    export JELLYFISH2_0_LIBS=$PREFIX/lib/libjellyfish-2.0.so
+fi
 
 ./configure --prefix=$PREFIX
 make

From fbae4388a5547d12c99268cf39c8a98e1e878ab8 Mon Sep 17 00:00:00 2001
From: Colin Brislawn <cbrisl@gmail.com>
Date: Fri, 3 Feb 2017 14:22:52 -0800
Subject: [PATCH 18/18] Add perl to run requirements

---
 recipes/quorum/meta.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/recipes/quorum/meta.yaml b/recipes/quorum/meta.yaml
index 4d96730ff68d1..6b9f6bc251a9a 100644
--- a/recipes/quorum/meta.yaml
+++ b/recipes/quorum/meta.yaml
@@ -18,6 +18,7 @@ requirements:
     - jellyfish >=2.0
   run:
     - libgcc # [linux]
+    - perl-threaded
     - jellyfish >=2.0
 test:
   commands: