Mercurial > repos > ebi-gxa > fastq_quality_trimmer

view get_test_data.sh @ 0:27e997d5c273 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
parents
children
line wrap: on
line source

#!/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