Mercurial > repos > ebi-gxa > seurat_integration
comparison get_test_data.sh @ 0:dd6db951c33a draft default tip
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
author | ebi-gxa |
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date | Sat, 02 Mar 2024 10:42:39 +0000 |
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-1:000000000000 | 0:dd6db951c33a |
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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 |