fix setup path for docker and change cahe mirror

ctlab · Mar 23, 2024 · c20ab5e · c20ab5e
1 parent 38ac198
commit c20ab5e
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/R/appConfig.R b/R/appConfig.R
@@ -342,7 +342,7 @@ user_conf_to_yaml = function(user_config){
 #' or on default parameters if \code{setup_file} doesn't exist. If \code{user_conf_file} exists function does nothing.
 #' @param setup_file  name of config from \code{file}. If unset or not existed, "default".
 #' @param user_conf_file Location of the setup.yml file with setup parameters. If not existed use file from package
-createDockerConf <- function( setup_file = confFile("setup.yaml"), user_conf_file = confFile("user.conf")){
+createDockerConf <- function( setup_file = confFile("setup.yml"), user_conf_file = confFile("user.conf")){
     if (!file.exists(user_conf_file)){
         setup_conf <-  getSetupConf(setup_file, "default")
         user_conf <- get_user_conf(cache_root = "/var/phantasus/cache", setup_config = setup_conf)

diff --git a/inst/configs/R/phantasus/setup.yml b/inst/configs/R/phantasus/setup.yml
@@ -1,10 +1,10 @@
 default:
     geo_mirrors:
         true_geo: "https://ftp.ncbi.nlm.nih.gov"
-        minimal_cache: "https://ctlab.itmo.ru/files/software/phantasus/minimal-cache/"
+        minimal_cache: "https://alserglab.wustl.edu/files/phantasus/minimal-cache/"
     rnaseq_counts: "https://ctlab.itmo.ru/hsds/?domain=/counts" # hsds url / absolute path to folder / NULL
-    fgsea_pathways: "https://ctlab.itmo.ru/files/software/phantasus/minimal-cache/fgsea/"
-    annot_db: "https://ctlab.itmo.ru/files/software/phantasus/minimal-cache/annotationdb/"
+    fgsea_pathways: "https://alserglab.wustl.edu/files/phantasus/minimal-cache/fgsea/"
+    annot_db: "https://alserglab.wustl.edu/files/phantasus/minimal-cache/annotationdb/"
 
 blank:
     geo_mirrors: "https://ftp.ncbi.nlm.nih.gov"

diff --git a/inst/configs/R/phantasus/user.conf b/inst/configs/R/phantasus/user.conf
@@ -11,4 +11,4 @@ default:
     rnaseq_counts: "https://ctlab.itmo.ru/hsds/?domain=/counts"
   geo_mirrors:
     true_geo: "https://ftp.ncbi.nlm.nih.gov"
-    minimal_cache: "https://ctlab.itmo.ru/files/software/phantasus/minimal-cache/"
+    minimal_cache: "https://alserglab.wustl.edu/files/phantasus/minimal-cache/"