From e01bb9b08f3b0f8cee336e10b986f25eec993249 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Tue, 16 Jul 2024 12:22:26 -0400 Subject: [PATCH] fix: remove singularity version number resolves #138 --- CHANGELOG.md | 21 ++++++++++++--------- carlisle | 2 +- 2 files changed, 13 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ca9958f..8f7623b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,15 +6,18 @@ - Ensures control replicate number is an integer. - Fixes FDR cutoff misassigned to log2FC cutoff. - Fixes `no_dedup` variable names in library normalization scripts. -- Containerize rules that require R (`deseq`, `go_enrichment`, and `spikein_assessment`) to fix installation issues with common R library path. (#129, @kelly-sovacool) - - The `Rlib_dir` and `Rpkg_config` config options have been removed as they are no longer needed. -- New visualizations: (#132, @epehrsson) - - New rules `cov_correlation`, `homer_enrich`, `combine_homer`, `count_peaks` - - Add peak caller to MACS2 peak xls filename -- New parameters in the config file to make certain rules optional: (#133, @kelly-sovacool) - - GO enrichment is controlled by `run_go_enrichment` (default: `false`) - - ROSE is controlled by `run_rose` (default: `false`) -- Fig bug that added nonexistent directories to the singularity bind paths. (#135, @kelly-sovacool) + - Fig bug that added nonexistent directories to the singularity bind paths. (#135, @kelly-sovacool) +- New features: + - Containerize rules that require R (`deseq`, `go_enrichment`, and `spikein_assessment`) to fix installation issues with common R library path. (#129, @kelly-sovacool) + - The `Rlib_dir` and `Rpkg_config` config options have been removed as they are no longer needed. + - New visualizations: (#132, @epehrsson) + - New rules `cov_correlation`, `homer_enrich`, `combine_homer`, `count_peaks` + - Add peak caller to MACS2 peak xls filename + - New parameters in the config file to make certain rules optional: (#133, @kelly-sovacool) + - GO enrichment is controlled by `run_go_enrichment` (default: `false`) + - ROSE is controlled by `run_rose` (default: `false`) +- Misc: + - The singularity version is no longer specified, per request of the biowulf admins. (#139, @kelly-sovacool) ## CARLISLE v2.5.0 - Refactors R packages to a common source location (#118, @slsevilla) diff --git a/carlisle b/carlisle index 05df7f4..eb12d8d 100755 --- a/carlisle +++ b/carlisle @@ -11,7 +11,7 @@ PYTHON_VERSION="python/3.9" SNAKEMAKE_VERSION="snakemake/7.19.1" -SINGULARITY_VERSION="singularity/3.10.5" +SINGULARITY_VERSION="singularity" set -eo pipefail