From a13e63028d923e8986c1eb8d3058e83c13b63097 Mon Sep 17 00:00:00 2001
From: Adrien Taudiere <adrien.taudiere@tutanota.com>
Date: Wed, 6 Sep 2023 12:12:30 +0200
Subject: [PATCH] Add blast and vsearch to pkgdown action

---
 .github/workflows/pkgdown.yaml | 6 ++++++
 vignettes/filter.Rmd           | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index e1e2e525..62aa3080 100644
--- 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
index 70936905..422a6bb2 100644
--- 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),