Compilation and Installation

Procedure

Add a local conda repository.
```
conda config --add channels file://root/anaconda3/conda-bld/linux-aarch64
```
The default installation path is /root/anaconda3. You can replace it with the actual path.
Create a bioBakery compilation and running environment.
```
conda create -n bioBakery
```
Activate the bioBakery environment.
```
conda activate bioBakery
```
Create a biobakery_workflows directory and a recipe directory.
```
mkdir -p biobakery_workflows/recipe
```

Create a conda_build_config.yaml file.

Create a conda_build_config.yaml file.
```
vi conda_build_config.yaml
```

Press i to enter the edit mode and add the following content:

r_base: '3.4'
pin_run_as_build:
  python:
    max_pin: x.x
    min_pin: x.x
python: '2.7'
numpy: '1.11'
perl: 5.26.0
lua: '5'
cpu_optimization_target: nocona
target_platform: linux-aarch64

Press Esc, type :wq!, and press Enter to save the settings and exit.

Create a meta.yaml file.

Create a meta.yaml file.
```
vi meta.yaml
```

Press i to enter the edit mode and add the following content:

# This file created by conda-build 3.0.27
# meta.yaml template originally from:
# /n/home05/ljmciver/conda-biobakery/recipes/biobakery_workflows, last modified Fri Feb 19 18:18:45 2021
# ------------------------------------------------

package:
    name: biobakery_workflows
    version: 3.0.0a7
source:
    fn: biobakery_workflows-3.0.0a7.tar.gz
    sha256: 8819d6a110d01005d5c855a5f6a906b0a6b75e33d20b96471ae41c5ab354203f
    url: https://pypi.io/packages/source/b/biobakery_workflows/biobakery_workflows-3.0.0a7.tar.gz
build:
    entry_points:
        - biobakery_workflows = biobakery_workflows.biobakery_workflows:main
        - biobakery_workflows_databases = biobakery_workflows.biobakery_workflows_databases:main
    noarch: python
    number: '0'
    script: python setup.py install  --single-version-externally-managed --record=record.txt
    string: pyh0b62126_0
requirements:
    build:
        - libgcc-ng 11.2.0
        - openssl 1.1.1l
        - ncurses 6.2
        - python_abi 3.8
        - wheel 0.37.0
        - libgomp 11.2.0
        - setuptools 59.2.0
        - pip 21.3.1
        - sqlite 3.36.0
        - ld_impl_linux-aarch64 2.36.1
        - _libgcc_mutex 0.1
        - readline 8.1
        - _openmp_mutex 4.5
        - libffi 3.4.2
        - zlib 1.2.11
        - python 3.8.12
        - libstdcxx-ng 11.2.0
        - tk 8.6.11
        - certifi 2021.10.8
        - ca-certificates 2021.10.8
    run:
        - python 3.8.12
        - anadama2
test:
    commands:
        - biobakery_workflows --help
        - biobakery_workflows_databases --help
    imports:
        - biobakery_workflows
        - biobakery_workflows.data
        - biobakery_workflows.document_templates
        - biobakery_workflows.tasks
        - tests
about:
    description: bioBakery workflows is a collection of workflows and tasks for executing
        common microbial community analyses using standardized, validated tools and
        parameters. Quality control and statistical summary reports are automatically
        generated for most data types, which include 16S amplicons, metagenomes, and
        metatranscriptomes. Workflows are run directly from the command line and tasks
        can be imported to create your own custom workflows. The workflows and tasks
        are built with AnADAMA2 which allows for parallel task execution locally and
        in a grid compute environment.
    doc_url: http://huttenhower.sph.harvard.edu/biobakery_workflows
    home: http://huttenhower.sph.harvard.edu/biobakery_workflows
    license: MIT
    license_family: MIT
    summary: 'bioBakery workflows: A collection of meta-omic analysis workflows'
extra:
    copy_test_source_files: true
    final: true
    recipe-maintainers: biobakery-users@googlegroups.com

Press Esc, type :wq!, and press Enter to save the settings and exit.

Create a meta.yaml.template file.

Create a meta.yaml.template file.
```
vi meta.yaml.template
```

Press i to enter the edit mode and add the following content:

{% set name = "biobakery_workflows" %}
{% set version = "3.0.0a7" %}
{% set hash_type = "sha256" %}
{% set hash_value = "8819d6a110d01005d5c855a5f6a906b0a6b75e33d20b96471ae41c5ab354203f" %}

package:
  name: '{{ name|lower }}'
  version: '{{ version }}'

source:
  fn: '{{ name }}-{{ version }}.tar.gz'
  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
  '{{ hash_type }}': '{{ hash_value }}'

build:
  noarch: python
  number: 0
  script: python setup.py install  --single-version-externally-managed --record=record.txt

  entry_points:
    - biobakery_workflows = biobakery_workflows.biobakery_workflows:main
    - biobakery_workflows_databases = biobakery_workflows.biobakery_workflows_databases:main

requirements:
  build:
    - python
    - setuptools
  run:
    - python
    - anadama2
    - kneaddata
    - humann

test:
  imports:
    - biobakery_workflows
    - biobakery_workflows.data
    - biobakery_workflows.document_templates
    - biobakery_workflows.tasks
    - tests
  commands:
    - biobakery_workflows --help
    - biobakery_workflows_databases --help

about:
  home: http://huttenhower.sph.harvard.edu/biobakery_workflows
  license: MIT
  license_family: MIT
  summary: 'bioBakery workflows: A collection of meta-omic analysis workflows'
  description: 'bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters. Quality control and statistical summary reports are automatically generated for most data types, which include 16S amplicons, metagenomes, and metatranscriptomes. Workflows are run directly from the command line and tasks can be imported to create your own custom workflows. The workflows and tasks are built with AnADAMA2 which allows for parallel task execution locally and in a grid compute environment.'
  doc_url: http://huttenhower.sph.harvard.edu/biobakery_workflows

extra:
  recipe-maintainers: 'biobakery-users@googlegroups.com'

Press Esc, type :wq!, and press Enter to save the settings and exit.

Exit from the biobakery_workflows and recipe directories.
```
cd ../..
```

Compile biobakery_workflows.

conda build ./biobakery_workflows/recipe

If the compilation fails, add the Tsinghua source and try again.

conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda

Install biobakery_workflows.
```
conda install biobakery_workflows
```

Parent topic: bioBakery Porting Guide (CentOS 8.2)