bio-pype 1.0.5

安装

来自pypi

pip install bio_pype

来自git的开发版本

git clone https://bitbucket.org/ffavero/bio_pype
cd bio_pype
python setup.py test
python setup.py install

在'computerome'中安装virtualenv HPC<；https://computerome.dtu.dk>；``系统：

（或在未在系统级安装Virtualenv的任何系统中）

mkdir ~/venv_files

# Download virtualenv files (not installed in the python version used in computerome)
curl -L -o ~/venv_files/setuptools-20.2.2-py2.py3-none-any.whl https://github.com/pypa/virtualenv/raw/develop/virtualenv_support/setuptools-20.2.2-py2.py3-none-any.whl
curl -L -o ~/venv_files/pip-8.1.0-py2.py3-none-any.whl https://github.com/pypa/virtualenv/raw/develop/virtualenv_support/pip-8.1.0-py2.py3-none-any.whl
curl -L -o ~/venv_files/virtualenv.py https://github.com/pypa/virtualenv/raw/develop/virtualenv.py

# Create a virtual environment
python ~/venv_files/virtualenv.py --extra-search-dir=~/venv_files ~/venv_bio_pype
# Activate the environment
source ~/venv_bio_pype/bin/activate

# Install bio_pype as instructed above

# The pype command line utility will be available upon the "activation" of the environment or by specifying the full path, in this case:

# ~/venv_bio_pype/bin/pype

# To deactivate the virtual env:
deactivate

基本用法

访问一级模块：

$ pype
usage: pype [-p PROFILE] {pipelines,profiles,repos,snippets} ...

Slim and simple framework to ease the managements of data, tools and pipelines in the computerome HPC

positional arguments:
    pipelines       Workflows built by assembling pipelines and snippets
    profiles        Set of databases softwares and meta information
    repos           Management of pype modules
    snippets        Single tasks implementations

optional arguments:
  -p PROFILE, --profile PROFILE
                    Select the profile. This will define things like
                    databases, reference genomes paths,specific version of
                    programs to loads and other similar configurations.
                    Default: default

This is version 0.9.0 - Francesco Favero - 15 May 2017

安装回购：

默认情况下，模块存储库为空。

要安装所需的存储库，请列出可用的存储库：

$ pype repos list -a

安装选定的存储库：

$ pype repos install -f sequenza

更多详细信息

可以通过 环境变量，包测试模块的示例：

$ PYPE_SNIPPETS=test/data/snippets pype snippets
error: too few arguments
usage: pype snippets {reverse_fa,complement_fa,lower_fa,test} ...

positional arguments:
  {reverse_fa,complement_fa,lower_fa,test}
    reverse_fa          reverse a fasta sequence
    complement_fa       lower case a fasta sequence
    lower_fa            lower case a fasta sequence
    test                test_snippets

片段

代码片段是执行给定任务的python模块：

$ PYPE_SNIPPETS=test/data/snippets pype snippets test
error: argument --test is required
usage: pype snippets test --test TEST [-o OPT]

optional arguments:
  --test TEST  Test metavar
  -o OPT       test option

$ PYPE_SNIPPETS=test/data/snippets pype snippets test --test World
Hello World

$ PYPE_SNIPPETS=test/data/snippets pype snippets test --test mate -o Cheers
Cheers mate

管道：

管道是yaml文件tbat group any snippet或其他管道， 具有所需的依赖顺序。

$ PYPE_SNIPPETS=test/data/snippets PYPE_PIPELINES=test/data/pipelines pype pipelines
error: too few arguments
usage: pype pipelines [--queue {echo,none}] {rev_compl_low_fa} ...

positional arguments:
  {rev_compl_low_fa}
    rev_compl_low_fa   Reverse Complement Lower case a fasta

optional arguments:
  --queue {msub,echo,none}
                        Select the queuing system to run the pipeline
  --log LOG             Path used to write the pipeline logs. Default working
                        directory.

管道的参数是从yaml文件中动态解析的， 它定义了工具和执行流程：

info:
   description: Reverse Complement Lower case a fasta
   date:        06/07/2016
items:
  - name: lower_fa
    type: snippet
    arguments:
      -i: '%(complement_fa)s'
      -o: '%(output)s'
    dependencies:
      items:
        - name: complement_fa
          type: snippet
          arguments:
            -i: '%(reverse_fa)s'
            -o: '%(complement_fa)s'
          dependencies:
            items:
              - name: reverse_fa
                type: snippet
                arguments:
                  -i: '%(input_fa)s'
                  -o: '%(reverse_fa)s'

生成的argparse接口：

$ PYPE_SNIPPETS=test/data/snippets PYPE_PIPELINES=test/data/pipelines pype pipelines rev_compl_low_fa
error: argument --complement_fa is required
usage: pype pipelines rev_compl_low_fa --complement_fa COMPLEMENT_FA --output
                                       OUTPUT --reverse_fa REVERSE_FA
                                       --input_fa INPUT_FA

optional arguments:
  --complement_fa COMPLEMENT_FA
                        complement_fa type: str
  --output OUTPUT       output type: str
  --reverse_fa REVERSE_FA
                        reverse_fa type: str
  --input_fa INPUT_FA   input_fa type: str

有关read the docs的详细信息 （慢慢记录各种特性/变化）。