# 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'
