BioBlend - Revision history

Fkolpakov@gmail.com at 14:57, 5 January 2014

2014-01-05T14:57:41Z

Fkolpakov@gmail.com at 07:42, 5 January 2014

2014-01-05T07:42:42Z

Fkolpakov@gmail.com at 07:18, 5 January 2014

2014-01-05T07:18:52Z

Fkolpakov@gmail.com at 07:15, 5 January 2014

2014-01-05T07:15:52Z

Fkolpakov@gmail.com: Created page with "BioBlend is a unified API in Python that wraps the functionality of Galaxy and CloudMan APIs Sloggett2013. Automated installation of BioBlend is available v..."

2014-01-05T07:10:16Z

Created page with "BioBlend is a unified API in Python that wraps the functionality of Galaxy and CloudMan APIs <cite>Sloggett2013</cite>. Automated installation of BioBlend is available v..."

New page

BioBlend is a unified API in Python that wraps the functionality of Galaxy and [[CloudMan]] APIs <cite>Sloggett2013</cite>.

Automated installation of BioBlend is available via PyPI (e.g. pip install bioblend).

The library has been tested and is working on Linux, Macintosh and Windows-based systems.

There is Java version blend4j, but it supports only Galaxy API.
https://github.com/jmchilton/blend4

Links:
*documentation - http://bioblend.readthedocs.org
*presentation - https://s3.amazonaws.com/usecloudman/BOSC2013_BioBlend.pdf
*source code - https://github.com/afgane/bioblend

== CloudMan examples==

Create a CloudMan compute cluster, via an API and directly from your local machine:
<pre>
from bioblend.cloudman import CloudManConfig
from bioblend.cloudman import CloudManInstance
cfg = CloudManConfig('<your cloud access key>', '<your cloud secret key>', 'My CloudMan', 'ami-<ID>', 'm1.small', '<password>')
cmi = CloudManInstance.launch_instance(cfg)
cmi.get_status()
</pre>

Reconnect to an existing CloudMan instance and manipulate it:
<pre>
from bioblend.cloudman import CloudManInstance
cmi = CloudManInstance("<instance IP>", "<password>")
cmi.add_nodes(3)
cluster_status = cmi.get_status()
cmi.remove_nodes(2)
</pre>

==Implementation details==
BioBlend uses REST protocol to Interact with Galaxy and CloudMan.

For example,

REST call: http://main.g2.bx.psu.edu/api/histories/0a7b7992a7cabaec?key=123456789abcdef10

Returns JSON:
<pre>
{ 'id': '0a7b7992a7cabaec',
'name': 'Output history',
'state_details': { 'discarded': 0,
'empty': 0, ......
</pre>

In BioBlend it becomes Python:
<pre>GalaxyInstance.histories.show_history('0a7b7992a7cabaec')</pre>

Returns corresponding Python dictionary
<pre>
{ 'id': '0a7b7992a7cabaec',
'name': 'Output history',
'state_details': { 'discarded': 0,
'empty': 0, .....
</pre>

==References==
<biblio>
#Sloggett2013 pmid=23630176
</biblio>

[[Category:Galaxy]]
[[Category:Cloud]]

← Older revision		Revision as of 07:15, 5 January 2014
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	BioBlend is a unified API in Python that wraps the functionality of Galaxy and [[CloudMan]] APIs <cite>Sloggett2013</cite>.		BioBlend is a unified API in Python that wraps the functionality of Galaxy and [[CloudMan]] APIs <cite>Sloggett2013</cite>.

@@ Line 7: / Line 7: @@
 There is Java version blend4j, but it supports only Galaxy API.
-https://github.com/jmchilton/blend4
+https://github.com/jmchilton/blend4j
 Links:

@@ Line 64: / Line 64: @@
 #Sloggett2013 pmid=23630176
 </biblio>
+http://bib.irb.hr/datoteka/627609.PUBLISHED_BioBlend.pdf
 [[Category:Galaxy]]
 [[Category:Cloud]]

@@ Line 12: / Line 12: @@
 *documentation - http://bioblend.readthedocs.org
 *presentation -  https://s3.amazonaws.com/usecloudman/BOSC2013_BioBlend.pdf
-*source code - https://github.com/afgane/bioblend
+*source code - https://github.com/afgane/bioblend (43 files, ~200 kb).
 == CloudMan examples==