Adding updated wonderdump.sh

contrib/wonderdump.sh

@@ -0,0 +1,57 @@
+#!/bin/bash
+
+#
+# Wonderdump is a workaround to download SRA files directly
+# when fastq-dump's internet connection does not work.
+# Which can happen surprisingly frequently.
+#
+# Usage:
+#   wonderdump -X 10000 SRR1553500
+
+# this is a slightly modified version of wonderdump
+# please see http://data.biostarhandbook.com/scripts/README.html for the
+# original version
+
+set -ue
+
+# This is where we will store the file.
+SRA_DIR=./
+
+# Make the directory if it does not exist.
+mkdir -p $SRA_DIR
+
+# All other parameters up to last.
+PARAMS=${@:1:$(($# - 1))}
+
+# The last parameter must be the SRR number.
+SRR=${@:$#}
+
+if [ -z "$SRR" ]
+then
+      echo "*** Please specify an SRR number"
+      exit;
+fi
+
+echo "*** Getting SRR run: $SRR"
+
+# Create the full path to the file.
+SRA_FILE="$SRA_DIR/$SRR.sra"
+TMP_FILE="$SRA_DIR/$SRR.tmp"
+
+# Download only if it does not exist.
+if [ ! -f $SRA_FILE ];
+then
+    CLEAN_SRR=${SRR:0:10}
+    URL="https://sra-pub-run-odp.s3.amazonaws.com/sra/$CLEAN_SRR/$CLEAN_SRR"
+    echo "*** Downloading: $URL"
+    echo "*** Saving to: $SRA_FILE"
+    curl $URL > $TMP_FILE
+
+    # Move to local file only if successful.
+    mv $TMP_FILE $SRA_FILE
+else
+    echo "*** SRA file found: $SRA_FILE"
+fi
+
+# Run the fastq-dump.
+fastq-dump $PARAMS ${SRA_FILE}