Mercurial > repos > ebi-gxa > decoupler_pathway_inference

annotate get_test_data.sh @ 2:82b7cd3e1bbd draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit b01245159f9cb67101497bb974b2c13bcee019b7
author ebi-gxa
date Tue, 16 Apr 2024 11:49:19 +0000
parents 77d680b36e23
children
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77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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1 #!/usr/bin/env bash
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3 BASENAME_FILE='mito_counted_anndata.h5ad'
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5 MTX_LINK='https://zenodo.org/record/7053673/files/Mito-counted_AnnData'
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7 # convenience for getting data
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8 function get_data {
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9 local link=$1
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10 local fname=$2
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12 if [ ! -f $fname ]; then
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13 echo "$fname not available locally, downloading.."
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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14 wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link
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15 fi
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16 }
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18 # get matrix data
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19 mkdir -p test-data
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20 pushd test-data
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21 get_data $MTX_LINK $BASENAME_FILE
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24 # Download input anndata for decoupler-pathway_inference
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25 BASENAME_FILE='pbmc3k_processed.h5ad'
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27 MTX_LINK='https://zenodo.org/records/3752813/files/pbmc3k_processed.h5ad'
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29 get_data $MTX_LINK $BASENAME_FILE
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31 # Download output anndata for decoupler-pathway_inference
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32 BASENAME_FILE='test.h5ad'
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34 MTX_LINK='https://zenodo.org/records/10401958/files/test.h5ad'
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36 get_data $MTX_LINK $BASENAME_FILE
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