test r

mspodda · May 23, 2024 · 05d5b5e · 05d5b5e
1 parent e6e9b06
commit 05d5b5e
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Showing 2 changed files with 6 additions and 5 deletions.
diff --git a/workflow/R/config_all.R b/workflow/R/config_all.R
@@ -21,7 +21,7 @@ BRAF_ids <- c("ENST00000288602.11","ENST00000469930.2","ENST00000479537.6","ENST
 
 ## libraries
 my_packages <- c("dplyr","ggplot2","tidyr","ggsignif","ggpubr","patchwork","stringr",
-                 "ggrepel","GenomicAlignments","bedtoolsr","tximport","tximeta","tibble")
+                 "ggrepel","bedtoolsr","tibble")
 
 ## Sample typologies
 samples_typologies <-  c("Lung")

diff --git a/workflow/envs/R.yml b/workflow/envs/R.yml
@@ -5,9 +5,6 @@ channels:
   - nodefaults  ## block user/system channels
 dependencies:
   - r-base=4.2  ## always specify the R version (faster solve; more stable)
-  - bioconductor-GenomicAlignments
-  - bioconductor-tximport
-  - bioconductor-tximeta
   - r-dplyr
   - r-ggplot2
   - r-tidyr
@@ -17,4 +14,8 @@ dependencies:
   - r-stringr
   - r-ggrepel
   - r-tibble
-  - r-bedtoolsr
+  - r-bedtoolsr
+
+##  - bioconductor-GenomicAlignments
+##  - bioconductor-tximeta
+##  - bioconductor-tximport