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bio-pype-1.0.7
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مشاهده بیشترتوضیحات
Management and development framework for bioinformatics pipelines
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | bio-pype-1.0.7 |
| نام | bio-pype |
| نسخه کتابخانه | 1.0.7 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Favero Francesco |
| ایمیل نویسنده | favero.francesco@gmail.com |
| آدرس صفحه اصلی | http://bio-pype.readthedocs.io |
| آدرس اینترنتی | https://pypi.org/project/bio-pype/ |
| مجوز | GPLv3 |
BIO pype
========
Simple and slim python framework to build, organize and standardize
bioinformatics analyses.
The system is built around the python
`argparse <https://docs.python.org/2/library/argparse.html>`__
module, to provide command line interface to run the configured
analyses. The framework is heavily customizable and provides basic
method to access to `Environment
Modules <http://modules.sourceforge.net>`__ and implements various
queuing systems such as
`moab/torque <http://www.adaptivecomputing.com/>`__.
Install
-------
**From Pypi**
::
pip install bio_pype
**The development version from git**
::
git clone https://bitbucket.org/ffavero/bio_pype
cd bio_pype
python setup.py test
python setup.py install
**Installation with virtualenv in the `computerome
HPC <https://computerome.dtu.dk>`__ system:**
(Or in any system where virtualenv is not installed at system level)
::
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
Basic usage
-----------
Access first level modules:
::
$ 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
Install Repos:
--------------
By default the repository of modules is empty.
To install a desired repository, list the available repository:
::
$ pype repos list -a
Install a selected repository:
::
$ pype repos install -f sequenza
More Details
------------
It is possible to pass local modules for snippets and profiles via
environment variables, An example with the package test modules:
::
$ 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
**Snippets**
The snippets are python modules that perform a given task:
::
$ 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
**Pipeline:**
The pipelines are yaml files tbat group any snippets or other pipelines,
with the desired dependency order.
::
$ 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.
The arguments for a pipeline are parsed on the fly from a YAML file,
which defines the tools and the flow of the execution:
::
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'
resulting argparse interface:
::
$ 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
More details on `read the docs <http://bio-pype.readthedocs.io>`__
(slowly documenting the various features/changes).
نیازمندی
| مقدار | نام |
|---|---|
| - | PyYAML |
| - | psutil |
نحوه نصب
نصب پکیج whl bio-pype-1.0.7:
pip install bio-pype-1.0.7.whl
نصب پکیج tar.gz bio-pype-1.0.7:
pip install bio-pype-1.0.7.tar.gz