Mercurial > repos > ebi-gxa > seurat_run_pca

comparison get_test_data.sh @ 5:9547ebb03f6f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
author ebi-gxa
date Fri, 04 Mar 2022 07:29:26 +0000
parents
children 8ded486b0014
comparison
equal deleted inserted replaced
4:3fd59cdcb477 5:9547ebb03f6f
1 #!/usr/bin/env bash
2
3 BASENAME_FILE='E-MTAB-6077-3k_features_90_cells'
4
5 MTX_LINK='https://drive.google.com/uc?export=download&id=1-1ejn7scP80xsbrG0FtWzsozjg0hhc23'
6 RDS_LINK='https://drive.google.com/uc?export=download&id=1KW_GX6xznSUpWRWUykpNaSbAhyClf7_n'
7 NORM_LINK='https://drive.google.com/uc?export=download&id=1mvo3ENkBvEAOyWG6ejApzQTPDLX5yBKU'
8 FVG_LINK='https://drive.google.com/uc?export=download&id=13Fhruuj-vEEo1WM138ahtAYqfHc7LsaZ'
9 SCALED_LINK='https://drive.google.com/uc?export=download&id=18TK8us235LWNajarWDBAtASUXMYAxvw0'
10 PCA_LINK='https://drive.google.com/uc?export=download&id=1gf3BTB4dygDsom1TzjsBfgZnZepcoG5c'
11 NEIGHBOURS_LINK='https://drive.google.com/uc?export=download&id=1N2lHoKRBZ7pmAYGfghLWB9KUrLA5WoNX'
12 CLUSTERS_LINK='https://drive.google.com/uc?export=download&id=1HWxZWHbNUNo4z__9PhhL_CJOLzec_ETa'
13 TSNE_LINK='https://drive.google.com/uc?export=download&id=1qsvMr_GkCSp1dyTJt1BZ6cElJwFFX2zO'
14 MARKERS_LINK='https://drive.google.com/uc?export=download&id=18OmWNc7mF-4pzH6DQkPp1eKunN4BfvxD'
15
16 LOOM_LINK='https://drive.google.com/uc?export=download&id=1qNk5cg8hJG3Nv1ljTKmUEnxTOf11EEZX'
17 H5AD_LINK='https://drive.google.com/uc?export=download&id=1YpE0H_t_dkh17P-WBhPijKvRiGP0BlBz'
18 SCE_LINK='https://drive.google.com/uc?export=download&id=1UKdyf3M01uAt7oBg93JfmRvNVB_jlUKe'
19
20 function get_data {
21 local link=$1
22 local fname=$2
23
24 if [ ! -f $fname ]; then
25 echo "$fname not available locally, downloading.."
26 wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link
27 fi
28 }
29
30 # get matrix data
31 pushd test-data
32 get_data $MTX_LINK mtx.zip
33 unzip mtx.zip
34 rm -f mtx.zip
35
36 get_data $RDS_LINK $BASENAME_FILE".rds"
37 get_data $NORM_LINK $BASENAME_FILE"-normalised.rds"
38 get_data $FVG_LINK $BASENAME_FILE"-fvg.rds"
39 get_data $SCALED_LINK $BASENAME_FILE"-scaled.rds"
40 get_data $PCA_LINK $BASENAME_FILE"-pca.rds"
41 get_data $NEIGHBOURS_LINK $BASENAME_FILE"-neighbours.rds"
42 get_data $CLUSTERS_LINK $BASENAME_FILE"-clusters.rds"
43 get_data $TSNE_LINK $BASENAME_FILE"-tsne.rds"
44 get_data $MARKERS_LINK $BASENAME_FILE"-markers.csv.zip"
45
46 unzip $BASENAME_FILE"-markers.csv.zip"
47 rm -f $BASENAME_FILE"-markers.csv.zip"
48
49 get_data $LOOM_LINK $BASENAME_FILE"_loom.h5"
50 get_data $SCE_LINK $BASENAME_FILE"_sce.rds"
51 get_data $H5AD_LINK $BASENAME_FILE".h5ad"