Mercurial > repos > ebi-gxa > fastq_trim_poly_at
diff get_test_data.sh @ 0:dcc82e999439 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
author | ebi-gxa |
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date | Tue, 15 Feb 2022 07:54:15 +0000 |
parents | |
children | ebca4912eabe |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_test_data.sh Tue Feb 15 07:54:15 2022 +0000 @@ -0,0 +1,43 @@ +#!/usr/bin/env bash + +BASE_LINK="https://raw.githubusercontent.com/nunofonseca/fastq_utils/master/tests" + +BAR11_FILE="barcode_test_1.fastq.gz" +BAR12_FILE="barcode_test_2.fastq.gz" +BAR21_FILE="barcode_test2_1.fastq.gz" +BAR22_FILE="barcode_test2_2.fastq.gz" +INTER_FILE="inter.fastq.gz" +A1_FILE="a_1.fastq.gz" +POLYAT_FILE="poly_at.fastq.gz" +POLYAT3_FILE="poly_at_len3.fastq.gz" + +BAR11_LINK=$BASE_LINK"/"$BAR11_FILE +BAR12_LINK=$BASE_LINK"/"$BAR12_FILE +BAR21_LINK=$BASE_LINK"/"$BAR21_FILE +BAR22_LINK=$BASE_LINK"/"$BAR22_FILE +INTER_LINK=$BASE_LINK"/"$INTER_FILE +A1_LINK=$BASE_LINK"/"$A1_FILE +POLYAT_LINK=$BASE_LINK"/"$POLYAT_FILE +POLYAT3_LINK=$BASE_LINK"/"$POLYAT3_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 $BAR11_LINK $BAR11_FILE +get_data $BAR12_LINK $BAR12_FILE +get_data $BAR21_LINK $BAR21_FILE +get_data $BAR22_LINK $BAR22_FILE +get_data $INTER_LINK $INTER_FILE +get_data $A1_LINK $A1_FILE +get_data $POLYAT_LINK $POLYAT_FILE +get_data $POLYAT3_LINK $POLYAT3_FILE