From 38b29840de28e66d7ff1710c4a3441714f9c9e9c Mon Sep 17 00:00:00 2001
From: cguyomar <cervin.guyomar@gmail.com>
Date: Thu, 28 Nov 2019 13:59:06 +0100
Subject: [PATCH 1/3] recipe for minia

---
 recipes/minia/build.sh  | 20 ++++++++++++++++++++
 recipes/minia/meta.yaml | 38 ++++++++++++++++++++++++++++++++++++++
 2 files changed, 58 insertions(+)
 create mode 100644 recipes/minia/build.sh
 create mode 100644 recipes/minia/meta.yaml

diff --git a/recipes/minia/build.sh b/recipes/minia/build.sh
new file mode 100644
index 0000000000000..47a95d9fabaed
--- /dev/null
+++ b/recipes/minia/build.sh
@@ -0,0 +1,20 @@
+#!/bin/bash
+export CPATH=${PREFIX}/include
+export LIBRARY_PATH=${PREFIX}/lib
+rm -rf build
+mkdir build
+cd build
+cmake -DCMAKE_CXX_FLAGS="$CXXFLAGS -DUSE_NEW_CXX" ..
+make -j2
+
+mkdir -p $PREFIX/bin/
+
+cp bin/minia ${PREFIX}/bin/
+chmod +x $PREFIX/bin/minia
+chmod +x $PREFIX/bin/merci
+
+cp ext/gatb-core/bin/gatb-h5dump ${PREFIX}/bin/
+chmod +x $PREFIX/bin/gatb-h5dump
+cp ext/gatb-core/bin/dbginfo ${PREFIX}/bin/
+chmod +x $PREFIX/bin/dbginfo
+
diff --git a/recipes/minia/meta.yaml b/recipes/minia/meta.yaml
new file mode 100644
index 0000000000000..0b5253758804b
--- /dev/null
+++ b/recipes/minia/meta.yaml
@@ -0,0 +1,38 @@
+{% set version = "3.2.1" %}
+{% set sha256 = "8ef820a83d9906500c979a47492958da1e6cf8bee19fa632be3fa988d74765b7" %}
+
+package:
+  name: minia
+  version: {{ version }} 
+
+build:
+  number: 0
+  # requires clang>=4.5
+  skip: True  # [osx]
+
+source:
+  url: https://github.com/GATB/minia/releases/download/v{{version}}/minia-v{{version}}-Source.tar.gz
+  sha256: {{ sha256 }}
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - cmake
+  host:
+    - zlib
+  run:
+    - zlib
+
+test:
+  commands:
+    - MindTheGap fill -help
+
+about:
+  home: https://github.com/GATB/minia
+  license: file
+  license_file: LICENSE
+  summary: MindTheGap performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome. MindTheGap can also be used as a genome assembly finishing tool, it can fill the gaps between a set of input contigs without any a priori on their relative order and orientation.
+
+extra:
+  identifiers:
+    - biotools:minia

From 3dcf00f95f06f2727116792ce189108edd8508a9 Mon Sep 17 00:00:00 2001
From: cguyomar <cervin.guyomar@gmail.com>
Date: Thu, 28 Nov 2019 15:03:59 +0100
Subject: [PATCH 2/3] update minia recipe

---
 recipes/minia/build.sh  | 2 --
 recipes/minia/meta.yaml | 6 +++---
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/recipes/minia/build.sh b/recipes/minia/build.sh
index 47a95d9fabaed..30d45e962781c 100644
--- a/recipes/minia/build.sh
+++ b/recipes/minia/build.sh
@@ -15,6 +15,4 @@ chmod +x $PREFIX/bin/merci
 
 cp ext/gatb-core/bin/gatb-h5dump ${PREFIX}/bin/
 chmod +x $PREFIX/bin/gatb-h5dump
-cp ext/gatb-core/bin/dbginfo ${PREFIX}/bin/
-chmod +x $PREFIX/bin/dbginfo
 
diff --git a/recipes/minia/meta.yaml b/recipes/minia/meta.yaml
index 0b5253758804b..f43e8104ef826 100644
--- a/recipes/minia/meta.yaml
+++ b/recipes/minia/meta.yaml
@@ -1,5 +1,5 @@
 {% set version = "3.2.1" %}
-{% set sha256 = "8ef820a83d9906500c979a47492958da1e6cf8bee19fa632be3fa988d74765b7" %}
+{% set sha256 = "c431915f034bc58887f9a14f6f65be2c83e0faae312ef330c3a11c6ba131162c" %}
 
 package:
   name: minia
@@ -25,7 +25,7 @@ requirements:
 
 test:
   commands:
-    - MindTheGap fill -help
+    - minia -help
 
 about:
   home: https://github.com/GATB/minia
@@ -35,4 +35,4 @@ about:
 
 extra:
   identifiers:
-    - biotools:minia
+    - biotools:miniax

From cac9d44f45011c38be0e3e4eedf529d1094050ca Mon Sep 17 00:00:00 2001
From: cguyomar <cervin.guyomar@gmail.com>
Date: Thu, 28 Nov 2019 15:28:19 +0100
Subject: [PATCH 3/3] Update minia recipe

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

diff --git a/recipes/minia/build.sh b/recipes/minia/build.sh
index 30d45e962781c..45160f1e7b8a2 100644
--- a/recipes/minia/build.sh
+++ b/recipes/minia/build.sh
@@ -10,6 +10,7 @@ make -j2
 mkdir -p $PREFIX/bin/
 
 cp bin/minia ${PREFIX}/bin/
+cp bin/merci ${PREFIX}/bin/
 chmod +x $PREFIX/bin/minia
 chmod +x $PREFIX/bin/merci
 
diff --git a/recipes/minia/meta.yaml b/recipes/minia/meta.yaml
index f43e8104ef826..8613763094f1b 100644
--- a/recipes/minia/meta.yaml
+++ b/recipes/minia/meta.yaml
@@ -31,7 +31,7 @@ about:
   home: https://github.com/GATB/minia
   license: file
   license_file: LICENSE
-  summary: MindTheGap performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome. MindTheGap can also be used as a genome assembly finishing tool, it can fill the gaps between a set of input contigs without any a priori on their relative order and orientation.
+  summary: Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.
 
 extra:
   identifiers: