annotate get_test_data.sh @ 6:07fc9f4841b3 draft default tip

planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
author ebi-gxa
date Sat, 02 Mar 2024 10:42:01 +0000
parents 3dd20b758756
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
1 #!/usr/bin/env bash
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
2
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
3 BASENAME_FILE='E-MTAB-6077-3k_features_90_cells'
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
4
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
5 MTX_LINK='https://drive.google.com/uc?export=download&id=1-1ejn7scP80xsbrG0FtWzsozjg0hhc23'
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
6 RDS_LINK='https://drive.google.com/uc?export=download&id=1KW_GX6xznSUpWRWUykpNaSbAhyClf7_n'
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
7 NORM_LINK='https://drive.google.com/uc?export=download&id=1mvo3ENkBvEAOyWG6ejApzQTPDLX5yBKU'
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
8 FVG_LINK='https://drive.google.com/uc?export=download&id=13Fhruuj-vEEo1WM138ahtAYqfHc7LsaZ'
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
9 SCALED_LINK='https://drive.google.com/uc?export=download&id=18TK8us235LWNajarWDBAtASUXMYAxvw0'
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
10 PCA_LINK='https://drive.google.com/uc?export=download&id=1gf3BTB4dygDsom1TzjsBfgZnZepcoG5c'
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
11 NEIGHBOURS_LINK='https://drive.google.com/uc?export=download&id=1N2lHoKRBZ7pmAYGfghLWB9KUrLA5WoNX'
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
12 CLUSTERS_LINK='https://drive.google.com/uc?export=download&id=1HWxZWHbNUNo4z__9PhhL_CJOLzec_ETa'
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
13 TSNE_LINK='https://drive.google.com/uc?export=download&id=1qsvMr_GkCSp1dyTJt1BZ6cElJwFFX2zO'
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
14 MARKERS_LINK='https://drive.google.com/uc?export=download&id=18OmWNc7mF-4pzH6DQkPp1eKunN4BfvxD'
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
15
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
16 LOOM_LINK='https://drive.google.com/uc?export=download&id=1qNk5cg8hJG3Nv1ljTKmUEnxTOf11EEZX'
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
17 H5AD_LINK='https://drive.google.com/uc?export=download&id=1YpE0H_t_dkh17P-WBhPijKvRiGP0BlBz'
6
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
18
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
19 H5AD_SC182_LINK='https://drive.google.com/uc?export=download&id=16PUJ2KAkXT8F1UkfqU-9LWoOJUkUG1rp'
5
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
20 SCE_LINK='https://drive.google.com/uc?export=download&id=1UKdyf3M01uAt7oBg93JfmRvNVB_jlUKe'
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
21
6
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
22 # Seurat v4 exclusives
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
23 IFNB_BASE_FILE='ifnb_'
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
24
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
25 IFNB_CTRL_INT_LINK='https://drive.google.com/uc?export=download&id=15E_MLz-UclJYInNaA7YKLhLo5W-qlykL'
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
26 IFNB_STIM_INT_LINK='https://drive.google.com/uc?export=download&id=14iKgCJGPk16dEmpJJF-Gp_lBDcOdo-54'
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
27
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
28 ## Classify and UMAP mapping
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
29 CLASSIFY_QUERY_LINK='https://oc.ebi.ac.uk/s/MlEDILFYRrvkS6E/download'
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
30 CLASSIFY_RESULTS_ANCHORS_OBJECT_LINK='https://drive.google.com/uc?export=download&id=1Xtv4K_CxIU1cJ8RjJ7NTvzLQkLvc8a3i'
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
31 # UMAP_RESULT_OBJECT_LINK='https://oc.ebi.ac.uk/s/k4MdM07y9DAnurp/download'
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
32 UMAP_RESULT_OBJECT_LINK='https://oc.ebi.ac.uk/s/D1z4z2ef1e3dyc3/download'
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
33
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
34
5
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
35 function get_data {
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
36 local link=$1
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
37 local fname=$2
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
38
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
39 if [ ! -f $fname ]; then
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
40 echo "$fname not available locally, downloading.."
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
41 wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
42 fi
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
43 }
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
44
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
45 # get matrix data
6
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
46 mkdir -p test-data
5
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
47 pushd test-data
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
48 get_data $MTX_LINK mtx.zip
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
49 unzip mtx.zip
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
50 rm -f mtx.zip
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
51
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
52 get_data $RDS_LINK $BASENAME_FILE".rds"
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
53 get_data $NORM_LINK $BASENAME_FILE"-normalised.rds"
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
54 get_data $FVG_LINK $BASENAME_FILE"-fvg.rds"
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
55 get_data $SCALED_LINK $BASENAME_FILE"-scaled.rds"
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
56 get_data $PCA_LINK $BASENAME_FILE"-pca.rds"
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
57 get_data $NEIGHBOURS_LINK $BASENAME_FILE"-neighbours.rds"
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
58 get_data $CLUSTERS_LINK $BASENAME_FILE"-clusters.rds"
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
59 get_data $TSNE_LINK $BASENAME_FILE"-tsne.rds"
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
60 get_data $MARKERS_LINK $BASENAME_FILE"-markers.csv.zip"
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
61
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
62 unzip $BASENAME_FILE"-markers.csv.zip"
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
63 rm -f $BASENAME_FILE"-markers.csv.zip"
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
64
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
65 get_data $LOOM_LINK $BASENAME_FILE"_loom.h5"
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
66 get_data $SCE_LINK $BASENAME_FILE"_sce.rds"
3dd20b758756 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
diff changeset
67 get_data $H5AD_LINK $BASENAME_FILE".h5ad"
6
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
68
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
69 get_data $H5AD_SC182_LINK $BASENAME_FILE"_sc182.h5ad"
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
70
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
71 get_data $IFNB_CTRL_INT_LINK $IFNB_BASE_FILE"ctrl_norm_fvg.rds"
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
72 get_data $IFNB_STIM_INT_LINK $IFNB_BASE_FILE"stim_norm_fvg.rds"
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
73
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
74 get_data $CLASSIFY_QUERY_LINK "Classify_query.rds"
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
75 get_data $CLASSIFY_RESULTS_ANCHORS_OBJECT_LINK "Classify_anchors.rds"
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
76 get_data $UMAP_RESULT_OBJECT_LINK "UMAP_result_integrated.rds"
07fc9f4841b3 planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents: 5
diff changeset
77