using SED to modify Rprofile allow running on conda

tools/plot_ragtag_paf/plot_ragtag_paf.R

@@ -98,27 +98,43 @@ lookup_qstart <- function(x) {
 sort_columns <- c("tname", "tstart", "tend", "qname", "qstart", "qend")
 
 config_file <- args[1]
-config <- yaml.load_file(config_file)
-typed_config <- lapply(config, type.convert, as.is = TRUE)
-list2env(typed_config, envir = .GlobalEnv)
+
+# fixed plotting paramaters
+t_y <- 1
+q_y <- 2
 
 ########
 # MAIN #
 ########
 
+# process the config
+message("Reading the plot config")
+config <- yaml.load_file(config_file)
+typed_config <- lapply(config, type.convert, as.is = TRUE)
+invisible(
+    list2env(
+        typed_config,
+        envir = .GlobalEnv
+    )
+)
+
+
 # read the data
+message("Reading the plot data")
 agp <- fread(agp_file, fill = TRUE, skip = 2)[!V5 %in% c("N", "U")]
 raw_paf <- read_paf(paf_file)
 paf_dt <- data.table(raw_paf)
 
 # calculate spacing
+message("Calculating spacing between contigs")
 padding <- get_padding(paf_dt[tp == "P" & nmatch >= min_nmatch])
 
 # order the reference contigs
 paf_dt[, tname := factor(tname, levels = gtools::mixedsort(unique(tname)))]
 setkeyv(paf_dt, cols = sort_columns)
 
 # generate continuous  reference coordinates
+message("Generating coordinates for contigs")
 tpaf <- unique(paf_dt, by = "tname")
 tpaf[, pad_tstart := shift(cumsum(tlen + padding[["t_padding"]]), 1, 0)]
 tpaf[, shift_tstart := pad_tstart + (padding[["t_padding"]] / 2)]
@@ -140,6 +156,7 @@ qpaf[, shift_qstart := pad_qstart + (padding[["q_padding"]] / 2)]
 qpaf[, pad_qend := shift_qstart + qlen]
 
 # generate offsets for the alignment records
+message("Generating coordinates for alignments")
 tstarts <- unique(tpaf[, .(tname, shift_tstart)])
 qstarts <- unique(qpaf[, .(qname, shift_qstart)])
 
@@ -155,6 +172,7 @@ paf_dt[,
 ]
 
 # generate polygons. P is for primary alignments only
+message("Generating polygons for alignments")
 polygon_y_bump <- 0.017 # account for contig thickness
 paf_polygons <- paf_dt[
     tp == "P" & nmatch >= min_nmatch,
@@ -176,8 +194,6 @@ total_height <- (q_y - t_y) * 1.618
 y_axis_space <- (total_height - (q_y - t_y)) / 2
 middle_x <- tpaf[1, shift_tstart] + tpaf[.N, pad_tend] / 2
 
-
-
 all_contig_names <- c(tpaf[, unique(tname)])
 all_colours <- viridis(
     length(all_contig_names) + palette_space + 1
@@ -189,6 +205,7 @@ names(all_colours) <- c(
 )
 
 # Plot the ideogram with ribbons connecting the two sets of contigs
+message("Plotting")
 gp <- ggplot() +
     theme_void(base_family = "Lato", base_size = 12) +
     scale_fill_manual(
@@ -246,6 +263,7 @@ gp <- ggplot() +
         vjust = 0.5
     )
 
+message("Writing the plot to file")
 ggsave(plot_file,
     gp,
     width = plot_width,
@@ -255,6 +273,7 @@ ggsave(plot_file,
 )
 
 # Print session info to stderr
+message("\nsessionInfo():\n")
 sink(stderr())
 sessionInfo()
 sink()

tools/plot_ragtag_paf/plot_ragtag_paf.xml

@@ -14,9 +14,9 @@
     <command detect_errors="exit_code"><![CDATA[
 
     ## Suppress R warnings about container
-    mv /etc/R/Rprofile.site /etc/R/Rprofile.site.old &&
-    echo "options(bspm.sudo = TRUE)" > /etc/R/Rprofile.site &&
-    cat /etc/R/Rprofile.site.old >> /etc/R/Rprofile.site &&
+    sed -i 
+    '/options(bspm.version.check=FALSE)/i options(bspm.sudo = TRUE)' 
+    /etc/R/Rprofile.site &&
 
     ## Print the plot config to stderr
     sed -e 's/^[ \t]*//' -e '/^$/d' '${plot_config}' > config.yaml &&
@@ -40,8 +40,6 @@
             palette_space: '${plot_params.palette_space}'
             plot_height: '${plot_params.plot_height}'
             plot_width: '${plot_params.plot_width}'
-            q_y: '${plot_params.q_y}'
-            t_y: '${plot_params.t_y}'
         </configfile>
     </configfiles>
     <inputs>
@@ -54,8 +52,6 @@
             <param type="integer" name="fontsize" label="Fontsize (pt)" value="12"/>
             <param type="integer" name="palette_space" label="Number of unused colours in the colour palette between the query contig colour and the colour of the first reference contig." help="Try a higher value if the query contigs look too similar to the reference contigs." value="4"/>
             <param type="float" min="0" max="1" name="gap_size" label="Total length of gaps between contigs relative to the total assembly length." help="Try a higher value if the contigs look too close together." value="0.1"/>
-            <param type="integer" name="t_y" label="Position of reference contigs on the y-axis" value="1"/>
-            <param type="integer" name="q_y" label="Position of query contigs on the y-axis" value="2"/>
         </section>
     </inputs>
     <outputs>