comparison get_test_data.sh @ 0:931cd3661690 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
author ebi-gxa
date Tue, 20 Aug 2024 12:48:31 +0000
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comparison
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-1:000000000000 0:931cd3661690
1 #!/usr/bin/env bash
2 TF_DATA_LINK='https://raw.githubusercontent.com/aertslab/scenic-nf/master/example/allTFs_hg38.txt'
3 MOTIF2TF_LINK='https://raw.githubusercontent.com/aertslab/scenic-nf/master/example/motifs.tbl'
4 RANKING_LINK='https://zenodo.org/records/13328724/files/genome-ranking_v2.feather'
5 LOOM_INPUT_LINK='https://raw.githubusercontent.com/aertslab/scenic-nf/master/example/expr_mat.loom'
6
7 REGULONS_LINK='https://zenodo.org/records/13328724/files/regulons.tsv'
8 TF2TARGETS_LINK='https://zenodo.org/records/13328724/files/tf2targets.tsv'
9
10 function get_data {
11 local link=$1
12 local fname=$2
13
14 if [ ! -f $fname ]; then
15 echo "$fname not available locally, downloading.."
16 wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link
17 fi
18 }
19
20 # get matrix data
21 mkdir -p test-data
22 pushd test-data
23 get_data $TF_DATA_LINK "allTFs_hg38.txt"
24 get_data $MOTIF2TF_LINK "motifs.tbl"
25 get_data $RANKING_LINK "genome-ranking_v2.feather"
26 get_data $LOOM_INPUT_LINK "expr_mat.loom"
27 get_data $REGULONS_LINK regulons.tsv
28 get_data $TF2TARGETS_LINK tf2targets.tsv