From 962a5e79be1c7437be389a96a42b5d062ddc5b19 Mon Sep 17 00:00:00 2001 From: mattjmeier Date: Mon, 22 Jan 2024 10:25:32 -0500 Subject: [PATCH 1/3] add gitattributes --- .gitattributes | 1 + 1 file changed, 1 insertion(+) create mode 100644 .gitattributes diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 00000000..94f480de --- /dev/null +++ b/.gitattributes @@ -0,0 +1 @@ +* text=auto eol=lf \ No newline at end of file From 92c6d7330e8ea226fe63ac54b47f87d5b5182686 Mon Sep 17 00:00:00 2001 From: mattjmeier Date: Mon, 22 Jan 2024 10:26:18 -0500 Subject: [PATCH 2/3] update docker-compose paths --- docker-compose.yml | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 9ac13743..92abfe77 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -5,14 +5,12 @@ services: #restart: "unless-stopped" container_name: R-ODAF volumes: - - ./analysis:/home/R-ODAF/R-ODAF_Health_Canada/analysis - - ./metadata:/home/R-ODAF/R-ODAF_Health_Canada/data/metadata - - ./config:/home/R-ODAF/R-ODAF_Health_Canada/config - - ./raw-data:/home/R-ODAF/R-ODAF_Health_Canada/data/raw - - ./reference:/home/R-ODAF/R-ODAF_Health_Canada/reference - - ./wikipathways-20210810-gmt-Homo_sapiens.gmt:/home/R-ODAF/R-ODAF_Health_Canada/wikipathways-20210810-gmt-Homo_sapiens.gmt - - ./Human_S1500_1.2_standardized.csv:/home/R-ODAF/R-ODAF_Health_Canada/Human_S1500_1.2_standardized.csv - image: mattjmeier/r-odaf-hc:latest + - ./inputs:/home/R-ODAF/R-ODAF_Health_Canada/inputs + - ./output:/home/R-ODAF/R-ODAF_Health_Canada/output + #- ./reference:/home/R-ODAF/R-ODAF_Health_Canada/reference + #- ./wikipathways-20210810-gmt-Homo_sapiens.gmt:/home/R-ODAF/R-ODAF_Health_Canada/wikipathways-20210810-gmt-Homo_sapiens.gmt + #- ./Human_S1500_1.2_standardized.csv:/home/R-ODAF/R-ODAF_Health_Canada/Human_S1500_1.2_standardized.csv + image: r-odaf:latest # command: /bin/bash -l environment: - HOST_UID=10007 From 1792996a1d198bb1f76261ba513746a515789e06 Mon Sep 17 00:00:00 2001 From: mattjmeier Date: Mon, 22 Jan 2024 14:28:17 -0500 Subject: [PATCH 3/3] Fix line breaks --- scripts/run_DESeq2.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/run_DESeq2.R b/scripts/run_DESeq2.R index de4ee9e8..1d272791 100644 --- a/scripts/run_DESeq2.R +++ b/scripts/run_DESeq2.R @@ -141,7 +141,7 @@ if(!is.na(params$group_facet)){ filter(!(solvent_control==TRUE)) %>% pull(params$group_facet) %>% unique() - } + } } else { facets <- NA }