Merge pull request #193 from R-ODAF/build_container

Build container
R-ODAF · Jan 22, 2024 · 1c3bd16 · 1c3bd16
2 parents d8c009c + 1792996
commit 1c3bd16
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Showing 3 changed files with 8 additions and 9 deletions.
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1 @@
+* text=auto eol=lf
diff --git 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

diff --git 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
 }