Mercurial > repos > ebi-gxa > pyscenic_ctx
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_test_data.sh Tue Aug 20 12:48:31 2024 +0000 @@ -0,0 +1,28 @@ +#!/usr/bin/env bash +TF_DATA_LINK='https://raw.githubusercontent.com/aertslab/scenic-nf/master/example/allTFs_hg38.txt' +MOTIF2TF_LINK='https://raw.githubusercontent.com/aertslab/scenic-nf/master/example/motifs.tbl' +RANKING_LINK='https://zenodo.org/records/13328724/files/genome-ranking_v2.feather' +LOOM_INPUT_LINK='https://raw.githubusercontent.com/aertslab/scenic-nf/master/example/expr_mat.loom' + +REGULONS_LINK='https://zenodo.org/records/13328724/files/regulons.tsv' +TF2TARGETS_LINK='https://zenodo.org/records/13328724/files/tf2targets.tsv' + +function get_data { + local link=$1 + local fname=$2 + + if [ ! -f $fname ]; then + echo "$fname not available locally, downloading.." + wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link + fi +} + +# get matrix data +mkdir -p test-data +pushd test-data +get_data $TF_DATA_LINK "allTFs_hg38.txt" +get_data $MOTIF2TF_LINK "motifs.tbl" +get_data $RANKING_LINK "genome-ranking_v2.feather" +get_data $LOOM_INPUT_LINK "expr_mat.loom" +get_data $REGULONS_LINK regulons.tsv +get_data $TF2TARGETS_LINK tf2targets.tsv \ No newline at end of file