Mercurial > repos > ebi-gxa > fastq_quality_trimmer

diff get_test_data.sh @ 0:27e997d5c273 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_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
author ebi-gxa
date Fri, 11 Mar 2022 03:56:00 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_test_data.sh	Fri Mar 11 03:56:00 2022 +0000
@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+
+BASE_LINK="https://raw.githubusercontent.com/agordon/fastx_toolkit/master/galaxy/test-data"
+
+FQ_FILE="fastq_quality_trimmer.fastq"
+
+FQ_LINK=$BASE_LINK"/"$FQ_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 $FQ_LINK $FQ_FILE