Skip to content
GitLab
Menu
Projects
Groups
Snippets
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Holland Computing Center
chipathlon
Commits
74836b3c
Commit
74836b3c
authored
Jun 13, 2017
by
aknecht2
Browse files
Minor doc fixes.
parent
5443d27d
Changes
2
Hide whitespace changes
Inline
Side-by-side
chipathlon/workflow.py
View file @
74836b3c
...
...
@@ -35,11 +35,11 @@ class Workflow(object):
:type username: str
:param password: The password to authenticate for MongoDB access.
:type password: str
:param execute_site:
A list of
site
s
to submit jobs to. These sites should
be defined in the
configuration
file.
:type execute_site:
li
st
:param execute_site:
The target
site to submit jobs to. These sites should
be defined in the
sites.xml
file.
:type execute_site: st
r
:param output_site: The output site to transfer files to. This site should
be defined in the
configuration
file.
be defined in the
sites.xml
file.
:type output_site: str
:param save_db: Whether or not we want to save results to the database.
True by default.
...
...
doc/source/introduction.rst
View file @
74836b3c
...
...
@@ -10,7 +10,7 @@ steps leading up to and including peak calling can be very computationally
expensive. For this reason, we implemented a `Pegasus <pegasus.isi.edu>`_
pipeline for creating and submitting workflows to super computers.
Currently, there are
7
peak calling tools installed in ChIPathlon:
Currently, there are
9
peak calling tools installed in ChIPathlon:
1. `Gem <http://groups.csail.mit.edu/cgs/gem/>`_
2. `Zerone <https://omictools.com/zerone-tool>`_
...
...
@@ -19,6 +19,8 @@ Currently, there are 7 peak calling tools installed in ChIPathlon:
5. `peakranger <http://ranger.sourceforge.net/manual1.18.html>`_
6. `MUSIC <https://github.com/gersteinlab/MUSIC>`_
7. `CCAT <https://academic.oup.com/bioinformatics/article/26/9/1199/201375/A-signal-noise-model-for-significance-analysis-of>`_
8. `PePr <https://github.com/shawnzhangyx/PePr>`_
9. `hiddenDomains <http://hiddendomains.sourceforge.net/>`_
The pipeline gives the flexibility of choosing any or all of these tools for
running peak calling, and gives the ability to adjust parameters as necessary
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment