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Pull request tj update #15

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Merged
merged 29 commits into from
Dec 10, 2018
Merged

Pull request tj update #15

merged 29 commits into from
Dec 10, 2018

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@bintriz
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@bintriz bintriz commented Dec 10, 2018

I updated the pipeline by add the following features.

  • Add download_reasources.sh
  • Add supports for downloading input files from s3 buckets of the NDA or a user, or LocalPath.
  • Change sample_list.txt format
  • Restructure directories

bintriz added 29 commits November 23, 2018 19:06
@bintriz
Bug fix: install_tools.sh
cb07f36
@bintriz
Add a script for resource download
844f81f
@bintriz
Change configuration system
a843671
@bintriz
pileup.py upadte as configuration system changes
73dfd02
@bintriz
synpase_login refactoring
d6b1279
@bintriz
Add nda_login
f67e494
@bintriz
Refactoring: config, run_info
475d6f9
@bintriz
Library name change: utils -> misc
6ae30d5
@bintriz
Refactoring sample list parser & Fix sample list format
7787b73
@bintriz
Add synapse login in the download_resources.sh
1a8c017
@bintriz
Add NDA download funtion
31161f3
@bintriz
Minor change in job scripts
213aceb
@bintriz
Refactoring: rename analysis_utils -> utils
3d25701
@bintriz
Add an option for turning off bam upload to synapse
4c1e75c
@bintriz
Add wrapper scripts for pipeline runners
aad38a2
@bintriz
Bug_fix: NDA credential setting
2818e1c
@bintriz
minor change of the argument help in runners
9675dea
@bintriz
Simplify aws download log
99d7a68
@bintriz
Removing a conflict of tmp collate file names when running bam2fq on …
936b310 
…multiple bams
@bintriz
Refactoring: run_info, log_dir
7ea731b
@bintriz
Change location to save run_info
e64ab24
@bintriz
Improve error handling in job_scripts
11f638f
@bintriz
Add user's S3Uri and LocalPath options for data source; Multiple try …
6c379fb 
…when downloading data
@bintriz
Bug fix: Not updating the return code of multiple download tries
380ab5e
@bintriz
Bug fix: Make sample dir before saving run_info
b449050
@bintriz
Adjust threaded and java Xmx to match with m5.12xlarge
1216c22
@bintriz
Java memory adjustment
8f2cf6b
@bintriz
Update the README file
3b45165
@bintriz
Update the README file
69347c5
kdaily
kdaily approved these changes Dec 10, 2018
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Will trust that you have tested, @bintriz!

@kdaily kdaily merged commit 6e22d2f into master Dec 10, 2018
yjjang pushed a commit that referenced this pull request Sep 4, 2020
Merge pull request #15 from bsmn/pull-request-tj-update
e9ee1ac 
Pull request tj update
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3 participants

@bintriz @kdaily