Add recipe for MATAM (#18023)

* Add recipe for MATAM

* Python is not needed for building

* Pinning samtools version is not needed anymore

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/
+

recipes/matam/meta.yaml

@@ -0,0 +1,62 @@
+{% 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
+
+  run:
+    - coreutils # Centos6 (otherwise sort --parallel is unrecognized)
+    - wget
+    - bzip2
+    - zlib
+    - python >=3
+    - numpy
+    - samtools
+    - 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