Mercurial > repos > ebi-gxa > seurat_select_integration_features

comparison get_test_data.sh @ 0:699c0ca328f2 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
author ebi-gxa
date Sat, 02 Mar 2024 10:40:57 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:699c0ca328f2
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
19 H5AD_SC182_LINK='https://drive.google.com/uc?export=download&id=16PUJ2KAkXT8F1UkfqU-9LWoOJUkUG1rp'
20 SCE_LINK='https://drive.google.com/uc?export=download&id=1UKdyf3M01uAt7oBg93JfmRvNVB_jlUKe'
21
22 # Seurat v4 exclusives
23 IFNB_BASE_FILE='ifnb_'
24
25 IFNB_CTRL_INT_LINK='https://drive.google.com/uc?export=download&id=15E_MLz-UclJYInNaA7YKLhLo5W-qlykL'
26 IFNB_STIM_INT_LINK='https://drive.google.com/uc?export=download&id=14iKgCJGPk16dEmpJJF-Gp_lBDcOdo-54'
27
28 ## Classify and UMAP mapping
29 CLASSIFY_QUERY_LINK='https://oc.ebi.ac.uk/s/MlEDILFYRrvkS6E/download'
30 CLASSIFY_RESULTS_ANCHORS_OBJECT_LINK='https://drive.google.com/uc?export=download&id=1Xtv4K_CxIU1cJ8RjJ7NTvzLQkLvc8a3i'
31 # UMAP_RESULT_OBJECT_LINK='https://oc.ebi.ac.uk/s/k4MdM07y9DAnurp/download'
32 UMAP_RESULT_OBJECT_LINK='https://oc.ebi.ac.uk/s/D1z4z2ef1e3dyc3/download'
33
34
35 function get_data {
36 local link=$1
37 local fname=$2
38
39 if [ ! -f $fname ]; then
40 echo "$fname not available locally, downloading.."
41 wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link
42 fi
43 }
44
45 # get matrix data
46 mkdir -p test-data
47 pushd test-data
48 get_data $MTX_LINK mtx.zip
49 unzip mtx.zip
50 rm -f mtx.zip
51
52 get_data $RDS_LINK $BASENAME_FILE".rds"
53 get_data $NORM_LINK $BASENAME_FILE"-normalised.rds"
54 get_data $FVG_LINK $BASENAME_FILE"-fvg.rds"
55 get_data $SCALED_LINK $BASENAME_FILE"-scaled.rds"
56 get_data $PCA_LINK $BASENAME_FILE"-pca.rds"
57 get_data $NEIGHBOURS_LINK $BASENAME_FILE"-neighbours.rds"
58 get_data $CLUSTERS_LINK $BASENAME_FILE"-clusters.rds"
59 get_data $TSNE_LINK $BASENAME_FILE"-tsne.rds"
60 get_data $MARKERS_LINK $BASENAME_FILE"-markers.csv.zip"
61
62 unzip $BASENAME_FILE"-markers.csv.zip"
63 rm -f $BASENAME_FILE"-markers.csv.zip"
64
65 get_data $LOOM_LINK $BASENAME_FILE"_loom.h5"
66 get_data $SCE_LINK $BASENAME_FILE"_sce.rds"
67 get_data $H5AD_LINK $BASENAME_FILE".h5ad"
68
69 get_data $H5AD_SC182_LINK $BASENAME_FILE"_sc182.h5ad"
70
71 get_data $IFNB_CTRL_INT_LINK $IFNB_BASE_FILE"ctrl_norm_fvg.rds"
72 get_data $IFNB_STIM_INT_LINK $IFNB_BASE_FILE"stim_norm_fvg.rds"
73
74 get_data $CLASSIFY_QUERY_LINK "Classify_query.rds"
75 get_data $CLASSIFY_RESULTS_ANCHORS_OBJECT_LINK "Classify_anchors.rds"
76 get_data $UMAP_RESULT_OBJECT_LINK "UMAP_result_integrated.rds"
77