From a8303467db5671cd6dbfea1fd11ce559117eba3c Mon Sep 17 00:00:00 2001 From: Markus Riester Date: Fri, 11 Feb 2022 14:53:08 -0500 Subject: [PATCH] Fixed typo; updated GATK in Dockerfile. --- Dockerfile | 8 ++++---- NEWS | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/Dockerfile b/Dockerfile index eead7ee..0b60961 100644 --- a/Dockerfile +++ b/Dockerfile @@ -59,10 +59,10 @@ WORKDIR /opt RUN ln -s $PURECN /opt/PureCN # install GATK4 -RUN wget --no-verbose https://github.com/broadinstitute/gatk/releases/download/4.2.2.0/gatk-4.2.2.0.zip && \ - unzip gatk-4.2.2.0.zip -d /opt && \ - rm gatk-4.2.2.0.zip +RUN wget --no-verbose https://github.com/broadinstitute/gatk/releases/download/4.2.5.0/gatk-4.2.5.0.zip && \ + unzip gatk-4.2.5.0.zip -d /opt && \ + rm gatk-4.2.5.0.zip -ENV PATH /opt/gatk-4.2.2.0:$PATH +ENV PATH /opt/gatk-4.2.5.0:$PATH CMD ["/bin/bash"] diff --git a/NEWS b/NEWS index cb9f0ad..b8c6a23 100755 --- a/NEWS +++ b/NEWS @@ -13,7 +13,7 @@ SIGNIFICANT USER-VISIBLE CHANGES default BQ of 30). By default BQ is capped at 50 and variants below 25 are ignored. Set min.supporting.reads to 0 to turn this off (#206). o More robust annotation of intervals with gene symbols - o Remove chrosomes not present in the centromeres GRanges object; useful + o Remove chromosomes not present in the centromeres GRanges object; useful to remove altcontigs somehow present (should not happen with intervals generated by IntervalFile.R)