Mercurial > repos > ebi-gxa > pyscenic_ctx
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 |
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date | Tue, 20 Aug 2024 12:48:31 +0000 |
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-1:000000000000 | 0:931cd3661690 |
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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 |