diff --git a/README.md b/README.md index 8fa749e..1d60fe8 100644 --- a/README.md +++ b/README.md @@ -46,7 +46,7 @@ Vaulot D., Geisen S., Mahé F., Bass D. 2020. pr2-primers: an 18S rRNA primer da ### Versions -1.1 - 2021-05-17 +1.1.0 - 2021-05-17 * Panel to test individual primer or probes. * Add new primers and primer sets. diff --git a/R_scripts/script_update_shiny_files.R b/R_scripts/script_update_shiny_files.R index 289f663..3373a76 100644 --- a/R_scripts/script_update_shiny_files.R +++ b/R_scripts/script_update_shiny_files.R @@ -39,6 +39,7 @@ cat(readChar(file_param, 1e5)) update_pr2 = FALSE update_new_primer_sets = FALSE +update_stats_primer_sets = FALSE # =========================================================== # Primer database @@ -116,7 +117,7 @@ export(primer_sets, file = here(file_name), firstActiveRow = 2) # =========================================================== -# PR2 database version 4.12. +# Update PR2 database - current version 4.12. # =========================================================== if (update_pr2){ @@ -145,9 +146,9 @@ if (update_pr2){ # =========================================================== # Build the file for all primer sets +# +# Note: This is to be done only when new primer sets are computed # =========================================================== - -# This is to be done only when new primer sets are computed if (update_new_primer_sets){ @@ -180,8 +181,17 @@ if (update_new_primer_sets){ } + # =========================================================== -# Update primer sets and create labels +# Update primer sets stats +# +# Note: This is to be done only when new primer sets are computed +# =========================================================== + + +if (update_stats_primer_sets){ +# =========================================================== +# 1- Update primer sets and create labels # =========================================================== primer_sets <- primer_sets %>% @@ -214,7 +224,7 @@ primer_sets_labels <- primer_sets %>% specificity) # =========================================================== -# Summarize matches +# 2 - Summarize matches # =========================================================== pr2_match_final <- readRDS(file=here(str_c("R_paper/output/pr2_match_", gene_selected ,"_mismatches_", max_mismatch, ".rds"))) @@ -333,4 +343,8 @@ pr2_match_final <- readRDS(file=here(str_c("R_paper/output/pr2_match_", gene_sel saveRDS(pr2_match_summary_primer_set, file=here(str_c("R_paper/output/pr2_match_", gene_selected ,"_mismatches_", max_mismatch, "_summary.rds"))) saveRDS(pr2_match_summary_primer_set_sg, file=here(str_c("R_paper/output/pr2_match_", gene_selected ,"_mismatches_", max_mismatch, "_summary_sg.rds"))) - saveRDS(pr2_match_summary_primer_set_class, file=here(str_c("R_paper/output/pr2_match_", gene_selected ,"_mismatches_", max_mismatch, "_summary_class.rds"))) \ No newline at end of file + saveRDS(pr2_match_summary_primer_set_class, file=here(str_c("R_paper/output/pr2_match_", gene_selected ,"_mismatches_", max_mismatch, "_summary_class.rds"))) + +} + + \ No newline at end of file diff --git a/data/primer_sets.rds b/data/primer_sets.rds index 24be730..a9cce8f 100644 Binary files a/data/primer_sets.rds and b/data/primer_sets.rds differ diff --git a/data/primers.rds b/data/primers.rds index 13fd819..e322585 100644 Binary files a/data/primers.rds and b/data/primers.rds differ diff --git a/readme_docker.md b/readme_docker.md index 2304b73..3c3be97 100644 --- a/readme_docker.md +++ b/readme_docker.md @@ -3,15 +3,17 @@ ## Major steps 1. Make sure that the shiny application works on R studio -1. Can run docker 2. Build docker file * from shiny-verse - * Install libraries as needed + * Install packages as needed (load install_packages.R) * Use the shiny-server command 3. Test docker locally -4. Upload to Google cloud - * Set up neough memory (2 Go for pr2 primers) -5. Upload to Docker web site +4. Upload to GitHub, this will automatically force compilation on Google cloud and Docker site. + +If the Docker application has not been yet uploaded to Google +1. Upload to Google cloud + * Set up enough memory (2 Go for pr2 primers) +2. Upload to Docker web site ## Building docker image