Mercurial > repos > ebi-gxa > decoupler_pathway_inference

comparison get_test_data.sh @ 0:77d680b36e23 draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
author ebi-gxa
date Fri, 15 Mar 2024 12:17:49 +0000
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-1:000000000000 0:77d680b36e23
1 #!/usr/bin/env bash
2
3 BASENAME_FILE='mito_counted_anndata.h5ad'
4
5 MTX_LINK='https://zenodo.org/record/7053673/files/Mito-counted_AnnData'
6
7 # convenience for getting data
8 function get_data {
9 local link=$1
10 local fname=$2
11
12 if [ ! -f $fname ]; then
13 echo "$fname not available locally, downloading.."
14 wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link
15 fi
16 }
17
18 # get matrix data
19 mkdir -p test-data
20 pushd test-data
21 get_data $MTX_LINK $BASENAME_FILE
22
23
24 # Download input anndata for decoupler-pathway_inference
25 BASENAME_FILE='pbmc3k_processed.h5ad'
26
27 MTX_LINK='https://zenodo.org/records/3752813/files/pbmc3k_processed.h5ad'
28
29 get_data $MTX_LINK $BASENAME_FILE
30
31 # Download output anndata for decoupler-pathway_inference
32 BASENAME_FILE='test.h5ad'
33
34 MTX_LINK='https://zenodo.org/records/10401958/files/test.h5ad'
35
36 get_data $MTX_LINK $BASENAME_FILE
37