view get_test_data.sh @ 9:8a9c173645d2 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
author ebi-gxa
date Sun, 27 Oct 2024 20:39:27 +0000
parents c700f0381e84
children
line wrap: on
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#!/usr/bin/env bash

BASENAME_FILE='mito_counted_anndata.h5ad'

MTX_LINK='https://zenodo.org/record/7053673/files/Mito-counted_AnnData'

# convenience for getting data
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 $MTX_LINK $BASENAME_FILE


# Download input anndata for decoupler-pathway_inference
BASENAME_FILE='pbmc3k_processed.h5ad'

MTX_LINK='https://zenodo.org/records/3752813/files/pbmc3k_processed.h5ad'

get_data $MTX_LINK $BASENAME_FILE

# Download output anndata for decoupler-pathway_inference
BASENAME_FILE='test.h5ad'

MTX_LINK='https://zenodo.org/records/10401958/files/test.h5ad'

get_data $MTX_LINK $BASENAME_FILE