Mercurial > repos > ebi-gxa > fastq_filter_n

comparison get_test_data.sh @ 0:df87d29fac7f 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_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
author ebi-gxa
date Tue, 15 Feb 2022 16:38:56 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:df87d29fac7f
1 #!/usr/bin/env bash
2
3 BASE_LINK="https://raw.githubusercontent.com/nunofonseca/fastq_utils/master/tests"
4
5 BAR11_FILE="barcode_test_1.fastq.gz"
6 BAR12_FILE="barcode_test_2.fastq.gz"
7 BAR21_FILE="barcode_test2_1.fastq.gz"
8 BAR22_FILE="barcode_test2_2.fastq.gz"
9 INTER_FILE="inter.fastq.gz"
10 A1_FILE="a_1.fastq.gz"
11 POLYAT_FILE="poly_at.fastq.gz"
12 POLYAT3_FILE="poly_at_len3.fastq.gz"
13 TEST212_FILE="test_21_2.fastq.gz"
14
15 BAR11_LINK=$BASE_LINK"/"$BAR11_FILE
16 BAR12_LINK=$BASE_LINK"/"$BAR12_FILE
17 BAR21_LINK=$BASE_LINK"/"$BAR21_FILE
18 BAR22_LINK=$BASE_LINK"/"$BAR22_FILE
19 INTER_LINK=$BASE_LINK"/"$INTER_FILE
20 A1_LINK=$BASE_LINK"/"$A1_FILE
21 POLYAT_LINK=$BASE_LINK"/"$POLYAT_FILE
22 POLYAT3_LINK=$BASE_LINK"/"$POLYAT3_FILE
23 TEST212_LINK=$BASE_LINK"/"$TEST212_FILE
24
25 function get_data {
26 local link=$1
27 local fname=$2
28
29 if [ ! -f $fname ]; then
30 echo "$fname not available locally, downloading.."
31 wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link
32 fi
33 }
34
35 # Get test data
36 pushd test-data
37
38 get_data $BAR11_LINK $BAR11_FILE
39 get_data $BAR12_LINK $BAR12_FILE
40 get_data $BAR21_LINK $BAR21_FILE
41 get_data $BAR22_LINK $BAR22_FILE
42 get_data $INTER_LINK $INTER_FILE
43 get_data $A1_LINK $A1_FILE
44 get_data $POLYAT_LINK $POLYAT_FILE
45 get_data $TEST212_LINK $TEST212_FILE
46 get_data $POLYAT3_LINK $POLYAT3_FILE
47 get_data $TEST212_LINK $TEST212_FILE
48 get_data $POLYAT3_LINK $POLYAT3_FILE