1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
|
========
BioBlend
========
About
=====
.. include:: ../ABOUT.rst
Installation
============
Stable releases of BioBlend are best installed via ``pip`` from PyPI::
$ python3 -m pip install bioblend
Alternatively, the most current source code from our `Git repository`_ can be
installed with::
$ python3 -m pip install git+https://github.com/galaxyproject/bioblend
After installing the library, you will be able to simply import it into your
Python environment with ``import bioblend``. For details on the available functionality,
see the `API documentation`_.
BioBlend requires a number of Python libraries. These libraries are installed
automatically when BioBlend itself is installed, regardless whether it is installed
via PyPi_ or by running ``python3 setup.py install`` command. The current list of
required libraries is always available from `setup.py`_ in the source code
repository.
If you also want to run tests locally, some extra libraries are required. To
install them, run::
$ python3 setup.py test
Usage
=====
To get started using BioBlend, install the library as described above. Once the
library becomes available on the given system, it can be developed against.
The developed scripts do not need to reside in any particular location on the system.
It is probably best to take a look at the example scripts in ``docs/examples`` source
directory and browse the `API documentation`_. Beyond that, it's up to your creativity :).
Development
===========
Anyone interested in contributing or tweaking the library is more then welcome
to do so. To start, simply fork the `Git repository`_ on Github and start playing with
it. Then, issue pull requests.
API Documentation
=================
BioBlend's API focuses around and matches the services it wraps. Thus, there are
two top-level sets of APIs, each corresponding to a separate service and a
corresponding step in the automation process. *Note* that each of the service APIs
can be used completely independently of one another.
Effort has been made to keep the structure and naming of those API's consistent
across the library but because they do bridge different services, some discrepancies
may exist. Feel free to point those out and/or provide fixes.
For Galaxy, an alternative :ref:`object-oriented API <objects-api>` is
also available. This API provides an explicit modeling of server-side
Galaxy instances and their relationships, providing higher-level
methods to perform operations such as retrieving all datasets for a
given history, etc. Note that, at the moment, the oo API is still
incomplete, providing access to a more restricted set of Galaxy
modules with respect to the standard one.
Galaxy API
~~~~~~~~~~
API used to manipulate genomic analyses within Galaxy, including data management
and workflow execution.
.. toctree::
:maxdepth: 3
:glob:
api_docs/galaxy/*
Toolshed API
~~~~~~~~~~~~
API used to interact with the Galaxy Toolshed, including repository management.
.. toctree::
:maxdepth: 3
:glob:
api_docs/toolshed/*
Configuration
=============
BioBlend allows library-wide configuration to be set in external files.
These configuration files can be used to specify access keys, for example.
.. toctree::
:maxdepth: 1
:glob:
api_docs/lib_config
Testing
=======
If you would like to do more than just a mock test, you need to point
BioBlend to an instance of Galaxy. Do so by exporting the following
two variables::
$ export BIOBLEND_GALAXY_URL=http://127.0.0.1:8080
$ export BIOBLEND_GALAXY_API_KEY=<API key>
The unit tests, stored in the ``tests`` folder, can be run using
`pytest <https://docs.pytest.org/>`_. From the project root::
$ pytest
Getting help
============
If you have run into issues, found a bug, or can't seem to find an answer to
your question regarding the use and functionality of BioBlend, please use the
`Github Issues <https://github.com/galaxyproject/bioblend/issues>`_ page to ask your
question.
Related documentation
=====================
Links to other documentation and libraries relevant to this library:
* `Galaxy API documentation <https://galaxyproject.org/develop/api/>`_
* `Blend4j <https://github.com/jmchilton/blend4j>`_: Galaxy API wrapper for Java
* `clj-blend <https://github.com/chapmanb/clj-blend>`_: Galaxy API wrapper for Clojure
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
.. References/hyperlinks used above
.. _Git repository: https://github.com/galaxyproject/bioblend
.. _PyPi: https://pypi.org/project/bioblend/
.. _setup.py: https://github.com/galaxyproject/bioblend/blob/main/setup.py
|
