Allow run without MEME suite installed

neurogenomics · Oct 21, 2024 · 008c2ce · 008c2ce
1 parent 1210b86
commit 008c2ce
Showing 1 changed file with 21 additions and 19 deletions.
diff --git a/vignettes/MotifPeeker.Rmd b/vignettes/MotifPeeker.Rmd
@@ -186,25 +186,27 @@ The report can be generated by using the main function `MotifPeeker()`. For more
 run customisations, refer to the next sections.
 
 ```{r run-motifpeeker}
-MotifPeeker(
-    peak_files = peak_files,
-    reference_index = 2,  # Set TIP-seq experiment as reference
-    alignment_files = alignment_files,
-    exp_labels = c("ChIP", "TIP"),
-    exp_type = c("chipseq", "tipseq"),
-    genome_build = "hg38",  # Use hg38 genome build
-    motif_files = motif_files,
-    cell_counts = NULL,  # No cell-count information
-    denovo_motif_discovery = TRUE,
-    denovo_motifs = 3,  # Discover top 3 motifs
-    motif_db = NULL,  # Use default motif database (JASPAR)
-    download_buttons = TRUE,
-    out_dir = tempdir(),  # Save output in a temporary directory
-    workers = 2,  # Use two CPU cores on a 16GB RAM machine
-    debug = FALSE,
-    quiet = TRUE,
-    verbose = TRUE
-)
+if (MotifPeeker:::confirm_meme_install(continue = TRUE)) {
+    MotifPeeker(
+        peak_files = peak_files,
+        reference_index = 2,  # Set TIP-seq experiment as reference
+        alignment_files = alignment_files,
+        exp_labels = c("ChIP", "TIP"),
+        exp_type = c("chipseq", "tipseq"),
+        genome_build = "hg38",  # Use hg38 genome build
+        motif_files = motif_files,
+        cell_counts = NULL,  # No cell-count information
+        denovo_motif_discovery = TRUE,
+        denovo_motifs = 3,  # Discover top 3 motifs
+        motif_db = NULL,  # Use default motif database (JASPAR)
+        download_buttons = TRUE,
+        out_dir = tempdir(),  # Save output in a temporary directory
+        workers = 2,  # Use two CPU cores on a 16GB RAM machine
+        debug = FALSE,
+        quiet = TRUE,
+        verbose = TRUE
+    )
+}
 ```
 
 ### Required Inputs