Skip to content

v1.3.3
Compare
Choose a tag to compare
@leepc12 leepc12 released this 01 Nov 00:13
· 436 commits to master since this release
v1.3.3
c238150
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Verified
Learn about vigilant mode.

IMPORTANT: Conda users must re-install Conda env.

$ bash scripts/uninstall_conda_env.sh
$ bash scripts/install_conda_env.sh

New parameters to control JAVA max heap (java -Xmx)

  • should be helpful for issue #88
  • added the following 2 parameters
    • chip.filter_picard_java_heap: 4G by default (for Picard MarkDuplicate)
    • chip.gc_bias_picard_java_heap: 6G by default (for Picard CollectGcBiasMetrics)

Bug fixes

  • to merge two blacklists with different number of columns (3 and 6).

Croo

  • presigned URLs for organized outputs
    • They are PUBLIC. Use this at your own risk.
  • added UCSC browser tracks.
    • bigWig: MACS2 signal tracks (p-val and fold-enrich).
    • bigBed: optimal/conservative idr/overlap peaks.

Change of default parameters

  • chip.align_disks: 200 GB -> 400 GB

Removed old method

  • completely removed old method.
  • Users must use Caper to run pipelines.
Assets 2
Loading