From 87930d448238985243066de48e354b35112c2d89 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Mon, 1 Apr 2024 13:37:51 -0400 Subject: [PATCH 1/2] fix: update rseqc docker related to #119, #120, & https://github.com/CCBR/Dockers/pull/31 --- config/containers/images.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/containers/images.json b/config/containers/images.json index ce8c3fe..f33477b 100644 --- a/config/containers/images.json +++ b/config/containers/images.json @@ -17,7 +17,7 @@ "qualimap": "docker://nciccbr/ccbr_qualimap:v0.0.1", "rna": "docker://nciccbr/ccbr_rna:v0.0.1", "rsem": "docker://nciccbr/ccbr_rsem_1.3.3:v1.0", - "rseqc": "docker://nciccbr/ccbr_rseqc_4.0.0:v1.0", + "rseqc": "docker://nciccbr/ccbr_rseqc_4.0.0:v2", "rstat": "docker://nciccbr/ccbr_rstat:v0.0.1" } } From 0c5af57711de72b24834646a55b14e893e02a6e9 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Wed, 3 Apr 2024 13:25:48 -0400 Subject: [PATCH 2/2] docs: update CHANGELOG.md for PR 123 --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e48b782..f8e1659 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,7 +1,7 @@ ## RENEE 2.5.11 - Create a citation file to describe how to cite RENEE. (#86, @kelly-sovacool) -- Fix: set HPC-specific fastq screen config and kraken DB paths for Biowulf and FRCE. (#78, @kelly-sovacool) +- Set HPC-specific fastq screen config and kraken DB paths for Biowulf and FRCE. (#78, @kelly-sovacool) - Previously, FRCE users were required to set `--shared-resources`, which were kept in a location on FRCE not under version control. This change brings the paths under version control so they're easier to recover if deleted. @@ -9,6 +9,7 @@ - Fix RSEM reference and rRNA interval list paths in FRCE-specific config files (#85, @kelly-sovacool & @slsevilla) - Fix bug which caused incorrect genome annotation JSON files to be used (#87, @kelly-sovacool) - Set default temporary directory depending on HPC platform. (#98, @kelly-sovacool) +- Update docker for RSEQC with tools properly added to the path. (#123, @kelly-sovacool) ## RENEE 2.5.10