Mercurial > repos > ebi-gxa > score_genes_aucell

view get_test_data.sh @ 6:a33eb7d3b053 draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 54818daabaf1251642a267e5766f13741cb7faeb
author ebi-gxa
date Sun, 15 Sep 2024 09:56:28 +0000
parents c700f0381e84
children
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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