diff get_test_data.sh @ 0:f408bd51bb59 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_test_data.sh	Tue Aug 20 12:48:20 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
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