Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Ac homer #379

Merged
merged 48 commits into from
Mar 20, 2018
Merged
Changes from 1 commit
Commits
Show all changes
48 commits
Select commit Hold shift + click to select a range
4be5d06
I have added a homer implimentation
Oct 30, 2017
149cda5
pep8 changes
Oct 31, 2017
b2cb4d0
updated homer reporting
Nov 6, 2017
1344884
I have removed mutiqc from report temporarily
Nov 6, 2017
181e342
Updated homer documentation
Nov 9, 2017
6e4e3cb
Adressed pep8 errors
Nov 9, 2017
b079be1
Revert "I have removed mutiqc from report temporarily"
Nov 9, 2017
b90798d
Revert "Adressed pep8 errors"
Nov 9, 2017
1efc71d
Revert "Revert "I have removed mutiqc from report temporarily""
Nov 9, 2017
a2c60e9
Revert "Updated homer documentation"
Nov 9, 2017
405f368
added changes to pipline.ini
jencyw Nov 10, 2017
7981b29
documentation for pipeline_homer pipeline.ini
jencyw Nov 23, 2017
54859cd
I have added active if statememts for the homer pipline
Nov 23, 2017
bc69667
I have implimented the first fuction for deeptools
Nov 23, 2017
70a0f3e
I have added the function for fingerprints; going to test
jencyw Nov 23, 2017
930b6b5
deeptools_Fingerprint is done; it works
jencyw Nov 23, 2017
6264b00
Added fragment size function
Nov 24, 2017
58460b4
I have added functions for converting bams to bigwigs
Nov 24, 2017
7931a82
merge changes from MA
Nov 24, 2017
c3a06cf
I have added several functions in deeptools
jencyw Nov 29, 2017
f29616b
the updated pipeline.ini for pipeline_homer.py
jencyw Nov 29, 2017
cee8ed4
Add some functions for computeMatrix, plotHeatmap and plotProfile tho…
jencyw Nov 30, 2017
2010a07
Merge branch 'master' into AC-homer
Nov 30, 2017
dc7b0d5
Changed name of pipeline
Nov 30, 2017
409b9bc
have added extra functions computeMatrix and plotHeatmap
Nov 30, 2017
1b899eb
have finished the required functions of deeptools; currently testing …
jencyw Dec 4, 2017
edcb57b
some updated changes but still some bugs retained
jencyw Dec 11, 2017
e61cb62
I have fixed the bamCompare function so the correct input is now parsed
Dec 11, 2017
01573d1
have fixed bugs and pipelie seems to work. Will add test data
Dec 11, 2017
b122a91
pep8
Dec 11, 2017
f43dd7c
have added various bux fixes and it now works and conforms to pep8
Dec 12, 2017
b27c241
I have removed the pipeline that managed to find its way into the dir…
Dec 12, 2017
a3ce233
have placed samples for homer in Tag.dir
Dec 12, 2017
6487f80
have added example design.tsv and various bug fixes
Dec 12, 2017
172a132
fix to get around lack of design file in Travis testing
Dec 12, 2017
966891d
forgot sample_dict for testing too
Dec 12, 2017
242d126
pep8
Dec 12, 2017
f1eb479
I have updated jupyter notebooks and renamed pipeline_docs folder
Dec 12, 2017
ad3c7e8
fix for report
Dec 12, 2017
e6e6616
Merge branch 'master' into AC-homer
Dec 19, 2017
257d475
various small fixes
Jan 19, 2018
045d6db
updated docmentation
Jan 19, 2018
fa22022
have added a pause in findPeaks to avoid missing file ruffus errors
Feb 19, 2018
cc388fb
increased sleep for chiptools
sebastian-luna-valero Mar 6, 2018
0ec1db4
add sleeps to pipeline_chiptools.py; ruffus file not found issue
sebastian-luna-valero Mar 20, 2018
d70a197
add deeptools, homer, picard to scripts/cgat_conda_deps.sh
sebastian-luna-valero Mar 20, 2018
14bc226
merge with master
sebastian-luna-valero Mar 20, 2018
185d344
update conda environments
sebastian-luna-valero Mar 20, 2018
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
some updated changes but still some bugs retained
  • Loading branch information
jencyw committed Dec 11, 2017

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
commit edcb57b6e1e2b39a6faebbfb18ea05fa553a3f58
Loading