Mercurial > repos > ebi-gxa > seurat_normalise_data

comparison get_test_data.sh @ 6:3f49bc9c9213 draft default tip

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planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
author ebi-gxa
date Sat, 02 Mar 2024 10:42:30 +0000
parents a835b38e389f
children
comparison
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5:a835b38e389f 6:3f49bc9c9213
13 TSNE_LINK='https://drive.google.com/uc?export=download&id=1qsvMr_GkCSp1dyTJt1BZ6cElJwFFX2zO' 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' 14 MARKERS_LINK='https://drive.google.com/uc?export=download&id=18OmWNc7mF-4pzH6DQkPp1eKunN4BfvxD'
15 15
16 LOOM_LINK='https://drive.google.com/uc?export=download&id=1qNk5cg8hJG3Nv1ljTKmUEnxTOf11EEZX' 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' 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'
18 SCE_LINK='https://drive.google.com/uc?export=download&id=1UKdyf3M01uAt7oBg93JfmRvNVB_jlUKe' 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
19 34
20 function get_data { 35 function get_data {
21 local link=$1 36 local link=$1
22 local fname=$2 37 local fname=$2
23 38
26 wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link 41 wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link
27 fi 42 fi
28 } 43 }
29 44
30 # get matrix data 45 # get matrix data
46 mkdir -p test-data
31 pushd test-data 47 pushd test-data
32 get_data $MTX_LINK mtx.zip 48 get_data $MTX_LINK mtx.zip
33 unzip mtx.zip 49 unzip mtx.zip
34 rm -f mtx.zip 50 rm -f mtx.zip
35 51
47 rm -f $BASENAME_FILE"-markers.csv.zip" 63 rm -f $BASENAME_FILE"-markers.csv.zip"
48 64
49 get_data $LOOM_LINK $BASENAME_FILE"_loom.h5" 65 get_data $LOOM_LINK $BASENAME_FILE"_loom.h5"
50 get_data $SCE_LINK $BASENAME_FILE"_sce.rds" 66 get_data $SCE_LINK $BASENAME_FILE"_sce.rds"
51 get_data $H5AD_LINK $BASENAME_FILE".h5ad" 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