Add blast and vsearch to pkgdown action

adrientaudiere · Sep 6, 2023 · a13e630 · a13e630
1 parent 65ff067
commit a13e630
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Showing 2 changed files with 7 additions and 1 deletion.
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -33,6 +33,12 @@ jobs:
           extra-packages: any::pkgdown, local::.
           needs: website
 
+      - name: Install vsearch
+        run: sudo apt-get install vsearch
+
+      - name: Install blastn
+        run: sudo apt-get install ncbi-blast+
+
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}

diff --git a/vignettes/filter.Rmd b/vignettes/filter.Rmd
@@ -16,6 +16,7 @@ knitr::opts_chunk$set(
 
 ```{r setup, message=FALSE}
 library(MiscMetabar)
+library(formattable)
 ```
 
 ## Filter samples
@@ -71,7 +72,6 @@ track_formattable <-
 
 ```{r}
 if (class(blast_error_or_not) != "try-error") {
-library(formattable)
 formattable(track_formattable, 
             list(
               area(col = nb_sequences) ~ color_bar("cyan",  na.rm = T),