Mercurial > repos > ebi-gxa > fastq_pair

diff get_test_data.sh @ 0:6e13890afaef draft default tip

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
author ebi-gxa
date Thu, 17 Mar 2022 01:46:15 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_test_data.sh	Thu Mar 17 01:46:15 2022 +0000
@@ -0,0 +1,31 @@
+#!/usr/bin/env bash
+
+BASE_LINK="https://raw.githubusercontent.com/linsalrob/fastq-pair/master/test"
+
+LEFT_FILE="left.fastq"
+RIGHT_FILE="right.fastq"
+LEFTGZ_FILE="left.fastq.gz"
+RIGHTGZ_FILE="right.fastq.gz"
+
+LEFT_LINK=$BASE_LINK"/"$LEFT_FILE
+RIGHT_LINK=$BASE_LINK"/"$RIGHT_FILE
+LEFTGZ_LINK=$BASE_LINK"/"$LEFTGZ_FILE
+RIGHTGZ_LINK=$BASE_LINK"/"$RIGHTGZ_FILE
+
+function get_data {
+  local link=$1
+  local fname=$2
+
+  if [ ! -f $fname ]; then
+    echo "$fname not available locally, downloading.."
+    wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link
+  fi
+}
+
+# Get test data
+pushd test-data
+
+get_data $LEFT_LINK $LEFT_FILE
+get_data $RIGHT_LINK $RIGHT_FILE
+get_data $LEFTGZ_LINK $LEFTGZ_FILE
+get_data $RIGHTGZ_LINK $RIGHTGZ_FILE