Mercurial > repos > ebi-gxa > fastq_pair
comparison get_test_data.sh @ 0:6e13890afaef draft default tip
"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 |
| parents | |
| children |
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| -1:000000000000 | 0:6e13890afaef |
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| 1 #!/usr/bin/env bash | |
| 2 | |
| 3 BASE_LINK="https://raw.githubusercontent.com/linsalrob/fastq-pair/master/test" | |
| 4 | |
| 5 LEFT_FILE="left.fastq" | |
| 6 RIGHT_FILE="right.fastq" | |
| 7 LEFTGZ_FILE="left.fastq.gz" | |
| 8 RIGHTGZ_FILE="right.fastq.gz" | |
| 9 | |
| 10 LEFT_LINK=$BASE_LINK"/"$LEFT_FILE | |
| 11 RIGHT_LINK=$BASE_LINK"/"$RIGHT_FILE | |
| 12 LEFTGZ_LINK=$BASE_LINK"/"$LEFTGZ_FILE | |
| 13 RIGHTGZ_LINK=$BASE_LINK"/"$RIGHTGZ_FILE | |
| 14 | |
| 15 function get_data { | |
| 16 local link=$1 | |
| 17 local fname=$2 | |
| 18 | |
| 19 if [ ! -f $fname ]; then | |
| 20 echo "$fname not available locally, downloading.." | |
| 21 wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link | |
| 22 fi | |
| 23 } | |
| 24 | |
| 25 # Get test data | |
| 26 pushd test-data | |
| 27 | |
| 28 get_data $LEFT_LINK $LEFT_FILE | |
| 29 get_data $RIGHT_LINK $RIGHT_FILE | |
| 30 get_data $LEFTGZ_LINK $LEFTGZ_FILE | |
| 31 get_data $RIGHTGZ_LINK $RIGHTGZ_FILE |