diff get-bams.bash @ 31:1429b9638055 draft

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 7fab8f3658c9289e1d229bcde0beff80a0814c4c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get-bams.bash	Wed Mar 26 20:17:43 2025 +0000
@@ -0,0 +1,46 @@
+#!/usr/bin/env bash
+
+set -o errexit
+set -o nounset
+set -o pipefail
+
+##
+## Collect output bam files from STAR
+##
+
+bam_temp_dir=$(mktemp --directory ./egapx_out/bam.XXXXXXXXXX) || {
+    echo "ERROR: failed making temporary directory"
+    exit 1
+}
+
+bam_files_file="$bam_temp_dir/bam-files.txt"
+touch "$bam_files_file" || {
+    echo "ERROR: failed creating temporary file"
+    exit 1
+}
+trap 'rm -f -- "$bam_files_file"' EXIT
+
+find . -type f -name \*Aligned.out.Sorted.bam -print > "$bam_files_file" || {
+    echo "ERROR: failed finding bam files"
+    exit 1
+}
+
+idx=0
+while IFS="" read pathname; do
+    filename=$(basename "$pathname" ".bam")
+
+    dest_path_prefix="$bam_temp_dir/$filename"
+    if [ -e "${dest_path_prefix}.bam" ]; then
+        dest_path_prefix="${dest_path_prefix}.${idx}"
+        idx=$((idx + 1))
+    fi
+    dest_pathname="${dest_path_prefix}.bam"
+
+    cp "$pathname" "$dest_pathname" || {
+        echo "ERROR: failed: cp \"$pathname\" \"$dest_pathname\""
+        exit 1
+    }
+
+done < "$bam_files_file"
+
+exit 0