From 8c9d5c7ccfd02ffd69ec3f117db9ca6777b49bbe Mon Sep 17 00:00:00 2001
From: Loic Couderc <loic.couderc@univ-lille.fr>
Date: Thu, 10 Oct 2019 15:21:04 +0200
Subject: [PATCH 1/3] Add recipe for MATAM

---
 recipes/matam/build.sh  | 43 ++++++++++++++++++++++++++++
 recipes/matam/meta.yaml | 63 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 106 insertions(+)
 create mode 100644 recipes/matam/build.sh
 create mode 100644 recipes/matam/meta.yaml

diff --git a/recipes/matam/build.sh b/recipes/matam/build.sh
new file mode 100644
index 0000000000000..402e4f0cbda58
--- /dev/null
+++ b/recipes/matam/build.sh
@@ -0,0 +1,43 @@
+#!/bin/bash
+
+# fix zlib error
+export CFLAGS="-I$PREFIX/include"
+export LDFLAGS="-L$PREFIX/lib"
+
+MATAM_HOME=$PREFIX/opt/matam-$PKG_VERSION
+mkdir -p $MATAM_HOME/{bin,scripts}
+
+git submodule update --init --recursive -- componentsearch ovgraphbuild
+
+# componentsearch
+# use make CC=$CXX instead of make to avoid g++ not found
+cd $SRC_DIR/componentsearch && make CC=$CXX
+COMPONENT_SEARCH=$MATAM_HOME/componentsearch
+mkdir $COMPONENT_SEARCH
+cp $SRC_DIR/componentsearch/componentsearch $COMPONENT_SEARCH
+
+# ovgraphbuild
+OVGRAPHBUILD_BUILD_DIR=$SRC_DIR/ovgraphbuild/build
+mkdir $OVGRAPHBUILD_BUILD_DIR && cd $OVGRAPHBUILD_BUILD_DIR && cmake .. -G"CodeBlocks - Unix Makefiles" && make
+OVGRAPHBUILD=$MATAM_HOME/ovgraphbuild/bin
+mkdir -p $OVGRAPHBUILD
+cp $SRC_DIR/ovgraphbuild/bin/ovgraphbuild $OVGRAPHBUILD
+
+# copy matam scripts
+cp $SRC_DIR/scripts/*.py $MATAM_HOME/scripts
+cp $SRC_DIR/index_default_ssu_rrna_db.py $MATAM_HOME
+
+# copy tests dir
+cp -r $SRC_DIR/tests/ $MATAM_HOME/tests
+
+# copy examples dir
+cp -r $SRC_DIR/examples/ $MATAM_HOME/examples
+
+# make a symlink as matam do
+ln -s $MATAM_HOME/scripts/matam_* $MATAM_HOME/bin/
+
+# makes binaries available in the environment
+mkdir -p $PREFIX/bin
+ln -s $MATAM_HOME/index_default_ssu_rrna_db.py $PREFIX/bin/
+ln -s $MATAM_HOME/bin/matam_* $PREFIX/bin/
+
diff --git a/recipes/matam/meta.yaml b/recipes/matam/meta.yaml
new file mode 100644
index 0000000000000..ffc7f00bc055e
--- /dev/null
+++ b/recipes/matam/meta.yaml
@@ -0,0 +1,63 @@
+{% set name = "matam" %}
+{% set version = "1.6.0" %}
+{% set sha256 = "unused" %}
+
+package:
+  name: matam
+  version: {{ version }}
+
+source:
+  # can't use url due to submodules not present in github release
+  # url: https://github.com/bonsai-team/{{ name }}/archive/v{{ version }}.tar.gz
+  git_url: https://github.com/bonsai-team/matam.git
+  git_tag: v{{ version }}
+  sha256: {{ sha256 }}
+
+build:
+  number: 0
+  skip: True # [osx]
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - make
+    - cmake
+    - autoconf
+    - automake
+
+  host:
+    - zlib
+    - python >=3
+
+  run:
+    - coreutils # Centos6 (otherwise sort --parallel is unrecognized)
+    - wget
+    - bzip2
+    - zlib
+    - python >=3
+    - numpy
+    - samtools=1.9=h8571acd_11 # samtools libcrypto.so.1.0.0 error (https://github.com/sunbeam-labs/sunbeam/issues/181)
+    - sga
+    - sortmerna
+    - vsearch
+    - rdptools
+    - krona
+
+test:
+  commands:
+    - matam_assembly.py --help
+    - index_default_ssu_rrna_db.py --help
+    - matam_db_preprocessing.py --help
+    - matam_compare_samples.py --help
+
+about:
+  home: https://github.com/bonsai-team/matam
+  license: AGPL-3.0
+  license_file: LICENSE
+  summary: MATAM is a software dedicated to the fast and accurate targeted assembly of short reads.
+
+extra:
+  identifiers:
+    - doi:10.1093/bioinformatics/btx644
+  skip-lints:
+    - uses_vcs_url

From c2f30376ccec2d65ea0b4766d9b79faf18c323e4 Mon Sep 17 00:00:00 2001
From: Loic Couderc <loic.couderc@univ-lille.fr>
Date: Fri, 11 Oct 2019 13:13:21 +0200
Subject: [PATCH 2/3] Python is not needed for building

---
 recipes/matam/meta.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/recipes/matam/meta.yaml b/recipes/matam/meta.yaml
index ffc7f00bc055e..b1eb54699eea3 100644
--- a/recipes/matam/meta.yaml
+++ b/recipes/matam/meta.yaml
@@ -27,7 +27,6 @@ requirements:
 
   host:
     - zlib
-    - python >=3
 
   run:
     - coreutils # Centos6 (otherwise sort --parallel is unrecognized)

From 56554875047fd00fe179bebdb31d814a17c230e3 Mon Sep 17 00:00:00 2001
From: Loic Couderc <loic.couderc@univ-lille.fr>
Date: Fri, 11 Oct 2019 13:16:20 +0200
Subject: [PATCH 3/3] Pinning samtools version is not needed anymore

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

diff --git a/recipes/matam/meta.yaml b/recipes/matam/meta.yaml
index b1eb54699eea3..3c89efd3296dc 100644
--- a/recipes/matam/meta.yaml
+++ b/recipes/matam/meta.yaml
@@ -35,7 +35,7 @@ requirements:
     - zlib
     - python >=3
     - numpy
-    - samtools=1.9=h8571acd_11 # samtools libcrypto.so.1.0.0 error (https://github.com/sunbeam-labs/sunbeam/issues/181)
+    - samtools
     - sga
     - sortmerna
     - vsearch