Mercurial > repos > ebi-gxa > fastq_quality_trimmer
comparison get_test_data.sh @ 0:27e997d5c273 draft default tip
"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 |
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date | Fri, 11 Mar 2022 03:56:00 +0000 |
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-1:000000000000 | 0:27e997d5c273 |
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1 #!/usr/bin/env bash | |
2 | |
3 BASE_LINK="https://raw.githubusercontent.com/agordon/fastx_toolkit/master/galaxy/test-data" | |
4 | |
5 FQ_FILE="fastq_quality_trimmer.fastq" | |
6 | |
7 FQ_LINK=$BASE_LINK"/"$FQ_FILE | |
8 | |
9 function get_data { | |
10 local link=$1 | |
11 local fname=$2 | |
12 | |
13 if [ ! -f $fname ]; then | |
14 echo "$fname not available locally, downloading.." | |
15 wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link | |
16 fi | |
17 } | |
18 | |
19 # Get test data | |
20 pushd test-data | |
21 | |
22 get_data $FQ_LINK $FQ_FILE |