# General information about the project. project = u'BioBlend' copyright = u'2012, Enis Afgan' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # Add this checkout's local BioBlend module to sys.path. Allows use of # bioblend's get_version() in here, and ensures that the autodoc stuff also works. sys.path.insert(0, os.path.abspath(os.path.join(os.getcwd(), '..'))) from bioblend import get_version # The short X.Y version. version = get_version() # The full version, including alpha/beta/rc tags. release = get_version() # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. #language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: #today = '' # Else, today_fmt is used as the format for a strftime call. #today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files.
from setuptools import setup from bioblend import get_version setup(name="bioblend", version=get_version(), description="CloudMan and Galaxy API library", author="Enis Afgan", author_email="*****@*****.**", url="http://bioblend.readthedocs.org/", install_requires=['requests>=1.1.0', 'poster', 'simplejson', 'boto', 'nose', 'mock', 'pyyaml'], packages=['bioblend', 'bioblend.cloudman', 'bioblend.galaxy', 'bioblend.util', 'bioblend.galaxy.datasets', 'bioblend.galaxy.histories', 'bioblend.galaxy.libraries', 'bioblend.galaxy.users', 'bioblend.galaxy.genomes', 'bioblend.galaxy.workflows'], license='MIT', platforms="Posix; MacOS X; Windows", classifiers=["Development Status :: 3 - Alpha", "Intended Audience :: Developers", "License :: OSI Approved :: MIT License", "Operating System :: OS Independent", "Topic :: Internet", "Programming Language :: Python :: 2", "Programming Language :: Python :: 2.6", "Programming Language :: Python :: 2.7"], )
from setuptools import setup from bioblend import get_version setup( name="bioblend", version=get_version(), description="CloudMan and Galaxy API library", author="Enis Afgan", author_email="*****@*****.**", url="http://bioblend.readthedocs.org/", install_requires=[ 'requests>=1.1.0', 'poster', 'simplejson', 'boto', 'nose', 'mock', 'pyyaml' ], packages=[ 'bioblend', 'bioblend.cloudman', 'bioblend.galaxy', 'bioblend.util', 'bioblend.galaxy.datasets', 'bioblend.galaxy.histories', 'bioblend.galaxy.libraries', 'bioblend.galaxy.users', 'bioblend.galaxy.genomes', 'bioblend.galaxy.workflows' ], license='MIT', platforms="Posix; MacOS X; Windows", classifiers=[ "Development Status :: 3 - Alpha", "Intended Audience :: Developers", "License :: OSI Approved :: MIT License", "Operating System :: OS Independent", "Topic :: Internet", "Programming Language :: Python :: 2", "Programming Language :: Python :: 2.6", "Programming Language :: Python :: 2.7" ],
#!/usr/bin/env python ## Example usage: python get_tool_yml_from_gi.py -g https://mississippi.snv.jussieu.fr/ -a <api_key> -o tool_list.yml import sys from operator import itemgetter from argparse import ArgumentParser from distutils.version import StrictVersion try: import bioblend if StrictVersion( bioblend.get_version() ) < StrictVersion( "0.6.0" ): print("This script needs bioblend >= 0.6.0.") sys.exit(1) import bioblend.galaxy except ImportError: print("bioblend is not installed, this script needs bioblend >= 0.6.0.") raise(ImportError) import yaml class GiToToolYaml: def __init__(self, url, api_key, output_file, get_deleted=False, get_packages=False, get_latest_installed=False, include_tool_panel_section_id=False, skip_tool_panel_section_name=True): self.url = url
# The encoding of source files. # source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' # General information about the project. project = 'BioBlend' copyright = '2012-2016, Enis Afgan' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # The short X.Y version. version = get_version() # The full version, including alpha/beta/rc tags. release = get_version() # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: # today = '' # Else, today_fmt is used as the format for a strftime call. # today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files.
import requests import traceback import argparse import json import os import time import re from pathlib import Path from collections import namedtuple from typing import List, Dict from urllib.parse import urljoin try: import bioblend if bioblend.get_version() != '0.14.0': raise ImportError("IslandCompare-CLI requires BioBlend v0.14.0") from bioblend.galaxy.objects import GalaxyInstance from bioblend.galaxy.objects.wrappers import History, HistoryDatasetAssociation, Workflow, Step from bioblend.galaxy.dataset_collections import CollectionDescription, CollectionElement, HistoryDatasetCollectionElement, HistoryDatasetElement from bioblend.galaxy.workflows import WorkflowClient from bioblend.galaxy.histories import HistoryClient from bioblend.galaxy.datasets import DatasetClient from bioblend.galaxy.jobs import JobsClient from bioblend.galaxy.invocations import InvocationClient except ImportError as e: print(e, file=sys.stderr) print("\n\033[1m\033[91mBioBlend dependency not found.\033[0m Try 'pip install bioblend==0.14.0'.", file=sys.stderr) exit(1) __version__ = '0.1.0'