Merge pull request #210 from hms-dbmi/fix-blas

use default blas

Author: alexvpickering

Dockerfile

@@ -83,6 +83,11 @@ COPY DESCRIPTION NAMESPACE ./
 RUN R -e "install.packages(repos=NULL, '.')" && \
     find . -maxdepth 1 ! -name R -exec rm -r "{}" \;
 
+# switch to default blas (fixes 'Error in if (any(above.noise))' from scran::quickCluster)
+RUN ARCH=$(uname -m) && \
+    update-alternatives --set "libblas.so.3-${ARCH}-linux-gnu" "/usr/lib/${ARCH}-linux-gnu/blas/libblas.so.3" && \
+    update-alternatives --set "liblapack.so.3-${ARCH}-linux-gnu" "/usr/lib/${ARCH}-linux-gnu/lapack/liblapack.so.3"
+
 # ----------
 # PRODUCTION
 #-----------

R/run_dseqr.R

@@ -89,13 +89,13 @@ run_dseqr <- function(app_name,
 
   # pass arguments to app through options then run
   shiny::shinyOptions(
-    data_dir = normalizePath(data_dir),
+    data_dir = normalizePath(data_dir, mustWork = FALSE),
     app_name = app_name,
-    pert_query_dir = normalizePath(pert_query_dir),
-    pert_signature_dir = normalizePath(pert_signature_dir),
-    gs_dir = normalizePath(gs_dir),
-    indices_dir = normalizePath(indices_dir),
-    tx2gene_dir = normalizePath(tx2gene_dir),
+    pert_query_dir = normalizePath(pert_query_dir, mustWork = FALSE),
+    pert_signature_dir = normalizePath(pert_signature_dir, mustWork = FALSE),
+    gs_dir = normalizePath(gs_dir, mustWork = FALSE),
+    indices_dir = normalizePath(indices_dir, mustWork = FALSE),
+    tx2gene_dir = normalizePath(tx2gene_dir, mustWork = FALSE),
     tabs = tabs,
     logout_url = logout_url,
     is_local = is_local,

inst/app/server.R

@@ -107,7 +107,7 @@ server <- function(input, output, session) {
   if (!is_local) {
     options(shiny.error = function() {
       observe({
-        user_name <- user_name()
+        user_name <- session$request$HTTP_X_SP_USERID
         send_slack_error(app_name, user_name)
       })
     })
@@ -206,7 +206,6 @@ server <- function(input, output, session) {
   projects_table <- reactive({
     projects <- project_choices()
     project <- project()
-    req(project)
 
     nsc <- sapply(projects, get_num_sc_datasets, user_dir())
     nbulk <- sapply(projects, get_num_bulk_datasets, user_dir())
@@ -401,7 +400,7 @@ server <- function(input, output, session) {
   project_dir <- reactive(file.path(user_dir(), project()))
   prev_path <- reactive(file.path(user_dir(), 'prev_project.qs'))
 
-  project <- reactiveVal()
+  project <- reactiveVal('default')
 
   observe({
     project(qread.safe(prev_path(), .nofile = 'default'))