Mercurial > repos > iuc > ebi_metagenomics_run_downloader

diff download_ebi_metagenomics_run_data @ 0:e2e9fae080ad draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
author: iuc
date: Thu, 01 Dec 2016 15:27:59 -0500
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/download_ebi_metagenomics_run_data	Thu Dec 01 15:27:59 2016 -0500
@@ -0,0 +1,44 @@
+#!/usr/bin/env bash
+set -e
+
+python_script=$1
+run_id=$2
+information_type=$3
+information_to_download=$4
+chunk_type=$5
+output_file=$6
+
+touch $output_file
+
+run_link=$(python $python_script getRunLink $run_id)
+run_link="$run_link/$information_type/$information_to_download"
+
+if [[ $chunk_type == 'multiple_chunks' ]]; then
+    chunk_nb=$(curl "$run_link/chunks")
+
+    if [[ "$chunk_nb" < 1 ]]; then
+        >&2 echo "-----"
+        >&2 echo "ERROR"
+        >&2 echo "-----"
+        >&2 echo "No data are found for this link:"
+        >&2 echo "$run_link/chunks"
+        >&2 echo "-----"
+        exit 6
+    fi
+
+    for i in $(seq "$chunk_nb"); do
+        curl "$run_link/chunks/$i" | gunzip >> $output_file
+    done
+else
+    curl "$run_link" >> $output_file
+fi
+
+if [ ! -s $output_file ]; then
+    >&2 echo "-----"
+    >&2 echo "ERROR"
+    >&2 echo "-----"
+    >&2 echo "The output file is empty probably because the following link is not working:"
+    >&2 echo "$run_link"
+    >&2 echo "-----"
+    exit 6
+fi