From 66aa4e42580ef2e592df8da8bf4f51cd0e72e029 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Sun, 21 Oct 2018 21:40:08 +0200
Subject: [PATCH 1/4] Attempt to get FRED2 as a conda package

---
 recipes/fred/build.sh  |  1 +
 recipes/fred/meta.yaml | 37 +++++++++++++++++++++++++++++++++++++
 2 files changed, 38 insertions(+)
 create mode 100644 recipes/fred/build.sh
 create mode 100644 recipes/fred/meta.yaml

diff --git a/recipes/fred/build.sh b/recipes/fred/build.sh
new file mode 100644
index 0000000000000..ee2375615b8ff
--- /dev/null
+++ b/recipes/fred/build.sh
@@ -0,0 +1 @@
+$PYTHON setup.py install
\ No newline at end of file
diff --git a/recipes/fred/meta.yaml b/recipes/fred/meta.yaml
new file mode 100644
index 0000000000000..fbf7aad5b96d7
--- /dev/null
+++ b/recipes/fred/meta.yaml
@@ -0,0 +1,37 @@
+{% set name = "fred" %}
+{% set version = "2.0.2" %}
+{% set sha256 = "74589eacd8829ad2566ca360bb66a49f35645d9899f90cb0e5834eed2cf567f2" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/FRED-2/Fred2/archive/{{ version }}.tar.gz
+  sha256: '{{ sha256 }}'
+
+build:
+  noarch: python
+  number: 0
+  skip: True  # [not py27]
+
+requirements:
+  host:
+    - python
+  run:
+    - python
+    
+test:
+  commands:
+    - python -c "from Fred2.Core import Allele, Peptide, Protein,generate_peptides_from_proteins"
+
+about:
+  home: http://nf-co.re/
+  license: MIT
+  summary: 'Python package with helper tools for the nf-core community.'
+
+extra:
+  container:
+    # click requires a unicode locale when used with Python 3
+    # extended-base generates en_US.UTF-8 locale and sets LC_ALL, LANG properly
+    extended-base: true

From cebbe329c3eab6f6c2fbbec144be45a577749dbd Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Sun, 21 Oct 2018 22:05:04 +0200
Subject: [PATCH 2/4] SHA update

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

diff --git a/recipes/fred/meta.yaml b/recipes/fred/meta.yaml
index fbf7aad5b96d7..514a82b372e77 100644
--- a/recipes/fred/meta.yaml
+++ b/recipes/fred/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "fred" %}
 {% set version = "2.0.2" %}
-{% set sha256 = "74589eacd8829ad2566ca360bb66a49f35645d9899f90cb0e5834eed2cf567f2" %}
+{% set sha256 = "223f139b35357e25d98644eb2668b9140f1489f4befd1e337a83fa6253cc0d54" %}
 
 package:
   name: {{ name|lower }}

From 58dc4a957550f6bd08825359934a908c8e60efe5 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Sun, 21 Oct 2018 22:16:50 +0200
Subject: [PATCH 3/4] 99 little bugs in the code

---
 recipes/fred/build.sh  |  2 ++
 recipes/fred/meta.yaml | 14 +++++++++++++-
 2 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/recipes/fred/build.sh b/recipes/fred/build.sh
index ee2375615b8ff..8cfa4a6b3a75f 100644
--- a/recipes/fred/build.sh
+++ b/recipes/fred/build.sh
@@ -1 +1,3 @@
+#Patch away the install requires, we're getting these through conda directly
+sed -i 's/install_requires/#install_requires/g' setup.py 
 $PYTHON setup.py install
\ No newline at end of file
diff --git a/recipes/fred/meta.yaml b/recipes/fred/meta.yaml
index 514a82b372e77..e9ce52bb7e162 100644
--- a/recipes/fred/meta.yaml
+++ b/recipes/fred/meta.yaml
@@ -18,9 +18,21 @@ build:
 requirements:
   host:
     - python
+    - setuptools
+    - pyomo
+    - pandas
+    - pyvcf
+    - biopython
+    - mysql-python
   run:
     - python
-    
+    - setuptools
+    - pyomo
+    - pandas
+    - pyvcf
+    - biopython
+    - mysql-python 
+
 test:
   commands:
     - python -c "from Fred2.Core import Allele, Peptide, Protein,generate_peptides_from_proteins"

From bed0300203b6b197bdbe7e416881c4babd11acd8 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Mon, 22 Oct 2018 09:56:00 +0200
Subject: [PATCH 4/4] =?UTF-8?q?Fix=20things=20Bj=C3=B6rn=20mentioned?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 recipes/{fred => fred2}/build.sh  | 0
 recipes/{fred => fred2}/meta.yaml | 3 +--
 2 files changed, 1 insertion(+), 2 deletions(-)
 rename recipes/{fred => fred2}/build.sh (100%)
 rename recipes/{fred => fred2}/meta.yaml (91%)

diff --git a/recipes/fred/build.sh b/recipes/fred2/build.sh
similarity index 100%
rename from recipes/fred/build.sh
rename to recipes/fred2/build.sh
diff --git a/recipes/fred/meta.yaml b/recipes/fred2/meta.yaml
similarity index 91%
rename from recipes/fred/meta.yaml
rename to recipes/fred2/meta.yaml
index e9ce52bb7e162..f497a1bd318a4 100644
--- a/recipes/fred/meta.yaml
+++ b/recipes/fred2/meta.yaml
@@ -1,4 +1,4 @@
-{% set name = "fred" %}
+{% set name = "fred2" %}
 {% set version = "2.0.2" %}
 {% set sha256 = "223f139b35357e25d98644eb2668b9140f1489f4befd1e337a83fa6253cc0d54" %}
 
@@ -44,6 +44,5 @@ about:
 
 extra:
   container:
-    # click requires a unicode locale when used with Python 3
     # extended-base generates en_US.UTF-8 locale and sets LC_ALL, LANG properly
     extended-base: true