add mtsv recipe (#12452)

* add mtsv recipe

trigger rebuild

Update build.sh

Update conda_build_config.yaml

Update meta.yaml

change python pinning

* update adVNTR to 1.3.0 (#14209)

* add adVNTR

* fix linux error for adVNTR

* add numpy to adVNTR requirements

* add numpy include dirs for cythonize

* Update advntr to 1.1.0

* Update advntr to 1.1.0

* update advntr to 1.1.1

* update adVNTR to 1.2.0

* update sha256 for adVNTR-1.2.0

* fix build script for adVNTR-1.2.0

* fix adVNTR-1.2.0

* update advntr and its requirements

* update advntr -- pysam and htslib versions

* skip py37

* force python version to be less than 3.7

* fix noarch problem

* exclude python 3.7

* fix a typo

* try another approach to exclude py37

* Update meta.yaml

* Bump toulligqc (#14221)

* Lumpy-express dependencies added (#14215)

Added hexdump-, sambamba- and samblaster dependencies under run and increased the build number to 4.

* Update clever-toolkit and distribute a shared library with kmc (#14224)

* Update clever-toolkit and distribute a shared library with kmc

* skip KMC on OSX, it uses gcc-specific headers

* Nanopolish bioconda update (#14218)

* bump nanopolish recipe to version 0.11.1

* bump nanopolish version to 0.11.1; update build number

* remove libgcc

@paultsw do you think its possible to remove the gcc execption for OSX already?

* Irida uploader (#14118)

:information_source:
Bioconda has finished the [GCC7 migration](#13578). If you are dealing with C/C++ or Python package it can be that you need to rebuild other dependent packages. [Bioconda utils - update-pinning](https://bioconda.github.io/updating.html#updating-recipes-for-a-pinning-change) will assist you with that. If you have any questions please use [issue 13578](#13578).

----------------

* [x] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
* [x] This PR adds a new recipe.
* [x] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
* [ ] This PR updates an existing recipe.
* [ ] This PR does something else (explain below).

* change requirement versions to match v2.1.2 and bumped version (#14231)

* Update duphold to 0.1.2 (#14232)

* Add recipe for Augustus 3.3.2 (#14219)

* Add recipe for Augustus 3.3.2

* Add recipe for GapFiller 2.1.1. (#14234)

* Bumped GATK4 version (#14222)

:information_source:
Bioconda has finished the [GCC7 migration](#13578). If you are dealing with C/C++ or Python package it can be that you need to rebuild other dependent packages. [Bioconda utils - update-pinning](https://bioconda.github.io/updating.html#updating-recipes-for-a-pinning-change) will assist you with that. If you have any questions please use [issue 13578](#13578).

----------------

* [X] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
* [] This PR adds a new recipe.
* [X] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
* [X] This PR updates an existing recipe.
* [ ] This PR does something else (explain below).

* add orca to nanocomp, make noarch (#14228)

add mtsv recipe

trigger rebuild

Update build.sh

Update conda_build_config.yaml

Update meta.yaml

change python pinning

add maintainer

fix copy of mtsv-db-build

fix binary list

pip install

pip install

remove setuptools

rm imports

test

test

setuptools

pinning

remove mtsv-db test

bump build

* change build

* move binaries to prefix/bin

* force recheck

recipes/mtsv/build.sh

@@ -0,0 +1,27 @@
+#!/bin/bash -e
+
+cd $SRC_DIR/mtsv/ext
+
+# apparently the HOME variable isn't set correctly, and circle ci output indicates the following as the home directory
+export HOME="/Users/distiller"
+# To solve error: linker `cc` from https://users.rust-lang.org/t/compiling-rust-package-using-cc-linker-from-a-custom-location/15795
+export CC=$GCC
+# build statically linked binary with Rust
+export CARGO_TARGET_X86_64_UNKNOWN_LINUX_GNU_LINKER="${CC}"
+C_INCLUDE_PATH=$PREFIX/include LIBRARY_PATH=$PREFIX/lib RUST_BACKTRACE=1 cargo build --release --verbose
+$GXX -std=c++11 -pthread ../mtsv_prep/taxidtool.cpp -o mtsv-db-build
+
+binaries="\
+mtsv-build \
+mtsv-readprep \
+mtsv-binner \
+mtsv-chunk \
+mtsv-collapse \
+mtsv-signature \
+mtsv-tree-build \
+"
+# move binaries to bin
+for i in $binaries; do cp $SRC_DIR/mtsv/ext/target/release/$i $PREFIX/bin; done
+
+cd $SRC_DIR
+$PYTHON setup.py install --single-version-externally-managed --record=record.txt

recipes/mtsv/conda_build_config.yaml

@@ -0,0 +1,4 @@
+# issue with normal GCC 7 C++ compiler for taxidtool.cpp 
+cxx_compiler:	
+  - gxx      # [linux]
+

recipes/mtsv/meta.yaml

@@ -0,0 +1,72 @@
+{% set version="1.0.2" %}
+{% set sha256="0bf611fe8da69f09d5e0ab57910f5ea49f076991259fd06db0c07368531916d5" %}
+
+package:
+  name: 'mtsv'
+  version: {{ version }}
+
+source:
+  url: https://github.com/FofanovLab/MTSv/archive/{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 0
+  skip: true  # [osx]
+  entry_points:
+    - mtsv = mtsv.main:main
+    - mtsv_setup = mtsv.mtsv_prep.main:main
+    - mtsv_plugin = mtsv.mtsv_plugin.main:main
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - rust>=1.24.0
+  host:
+    - zlib
+    - python<=3.6
+    - setuptools
+
+  run:
+    - python<=3.6
+    - snakemake>=4.1.0
+    - pandas>=0.20.3
+    - ete3
+    - biopython
+    - scipy
+    - six
+    - numpy
+    - pyyaml
+    - click
+    - zlib
+    - wgfast
+    - concoct
+    - megahit
+    - bwa
+    - samtools
+    - gsl
+
+test:
+  imports:
+    - mtsv
+  commands:
+    - mtsv --help > /dev/null
+    - mtsv_setup --help > /dev/null
+    - mtsv_plugin --help > /dev/null
+    - mtsv-build --help > /dev/null
+    - mtsv-readprep --help > /dev/null
+    - mtsv-binner --help > /dev/null
+    - mtsv-signature --help > /dev/null
+    - mtsv-chunk --help > /dev/null
+    - mtsv-collapse --help > /dev/null
+    - mtsv-tree-build --help > /dev/null
+
+
+about:
+  home: https://github.com/FofanovLab/MTSv
+  summary: MTSv is a suite of metagenomic binning and analysis tools.
+  license: MIT
+  license_file: LICENSE
+  license_family: MIT
+
+extra:
+  recipe_maintainers: tfursten