added_link

drieslab · Aug 4, 2024 · 09ee2c8 · 09ee2c8
1 parent dfa8175
commit 09ee2c8
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diff --git a/00_needed_packages.Rmd b/00_needed_packages.Rmd
@@ -148,6 +148,7 @@ reticulate::py_install(
 # install another environment with py 3.8 for cellpose
 reticulate::conda_create(envname = "giotto_cellpose",
                          python_version = 3.8)
+#.re.restartR()
 reticulate::use_condaenv('giotto_cellpose')
 reticulate::py_install(
   pip = TRUE,

diff --git a/02_session4.Rmd b/02_session4.Rmd
@@ -9,6 +9,7 @@ Before you start, this tutorial contains an optional part to run image segmentat
 #Install the Giotto Environment with Cellpose, note that we only need to do it once
 reticulate::conda_create(envname = "giotto_cellpose",
                          python_version = 3.8)
+#.re.restartR()
 reticulate::use_condaenv('giotto_cellpose')
 reticulate::py_install(
   pip = TRUE,

diff --git a/03_session2.Rmd b/03_session2.Rmd
@@ -241,12 +241,12 @@ library(Giotto)
 instrs <- createGiottoInstructions(save_dir = file.path(getwd(),'/img/03_session2/'),
                                   save_plot = TRUE,
                                   show_plot = TRUE)
-
+options(timeout = 999999)
 download_dir <-file.path(getwd(),'/data/03_session2/')
 destfile <- file.path(download_dir,'Multimodal_registration.zip')
 if (!dir.exists(download_dir)) { dir.create(download_dir, recursive = TRUE) }
-#download.file('', destfile = destfile)
-#unzip(paste0(download_dir,'/Multimodal_registration.zip'), exdir = download_dir)
+download.file('https://zenodo.org/records/13208139/files/Multimodal_registration.zip?download=1', destfile = destfile)
+unzip(paste0(download_dir,'/Multimodal_registration.zip'), exdir = download_dir)
 Xenium_dir <- paste0(download_dir,'/Multimodal_registration/Xenium/')
 Visium_dir <- paste0(download_dir,'/Multimodal_registration/Visium/')
 ```