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use default blas #210

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Sep 29, 2024
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5 changes: 5 additions & 0 deletions Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -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
#-----------
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12 changes: 6 additions & 6 deletions R/run_dseqr.R
Original file line number Diff line number Diff line change
Expand Up @@ -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,
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5 changes: 2 additions & 3 deletions inst/app/server.R
Original file line number Diff line number Diff line change
Expand Up @@ -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)
})
})
Expand Down Expand Up @@ -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())
Expand Down Expand Up @@ -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'))
Expand Down
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