Mercurial > repos > ebi-gxa > seurat_convert
annotate get_test_data.sh @ 1:834f7d8e5b4c draft default tip
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
author | ebi-gxa |
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date | Sat, 02 Mar 2024 10:42:13 +0000 |
parents | 970696a7ae0b |
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970696a7ae0b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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1 #!/usr/bin/env bash |
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2 |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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3 BASENAME_FILE='E-MTAB-6077-3k_features_90_cells' |
970696a7ae0b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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4 |
970696a7ae0b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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5 MTX_LINK='https://drive.google.com/uc?export=download&id=1-1ejn7scP80xsbrG0FtWzsozjg0hhc23' |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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6 RDS_LINK='https://drive.google.com/uc?export=download&id=1KW_GX6xznSUpWRWUykpNaSbAhyClf7_n' |
970696a7ae0b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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7 NORM_LINK='https://drive.google.com/uc?export=download&id=1mvo3ENkBvEAOyWG6ejApzQTPDLX5yBKU' |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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8 FVG_LINK='https://drive.google.com/uc?export=download&id=13Fhruuj-vEEo1WM138ahtAYqfHc7LsaZ' |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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9 SCALED_LINK='https://drive.google.com/uc?export=download&id=18TK8us235LWNajarWDBAtASUXMYAxvw0' |
970696a7ae0b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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10 PCA_LINK='https://drive.google.com/uc?export=download&id=1gf3BTB4dygDsom1TzjsBfgZnZepcoG5c' |
970696a7ae0b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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11 NEIGHBOURS_LINK='https://drive.google.com/uc?export=download&id=1N2lHoKRBZ7pmAYGfghLWB9KUrLA5WoNX' |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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12 CLUSTERS_LINK='https://drive.google.com/uc?export=download&id=1HWxZWHbNUNo4z__9PhhL_CJOLzec_ETa' |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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13 TSNE_LINK='https://drive.google.com/uc?export=download&id=1qsvMr_GkCSp1dyTJt1BZ6cElJwFFX2zO' |
970696a7ae0b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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14 MARKERS_LINK='https://drive.google.com/uc?export=download&id=18OmWNc7mF-4pzH6DQkPp1eKunN4BfvxD' |
970696a7ae0b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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15 |
970696a7ae0b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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16 LOOM_LINK='https://drive.google.com/uc?export=download&id=1qNk5cg8hJG3Nv1ljTKmUEnxTOf11EEZX' |
970696a7ae0b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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17 H5AD_LINK='https://drive.google.com/uc?export=download&id=1YpE0H_t_dkh17P-WBhPijKvRiGP0BlBz' |
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18 |
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19 H5AD_SC182_LINK='https://drive.google.com/uc?export=download&id=16PUJ2KAkXT8F1UkfqU-9LWoOJUkUG1rp' |
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970696a7ae0b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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20 SCE_LINK='https://drive.google.com/uc?export=download&id=1UKdyf3M01uAt7oBg93JfmRvNVB_jlUKe' |
970696a7ae0b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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21 |
1
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22 # Seurat v4 exclusives |
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23 IFNB_BASE_FILE='ifnb_' |
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24 |
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25 IFNB_CTRL_INT_LINK='https://drive.google.com/uc?export=download&id=15E_MLz-UclJYInNaA7YKLhLo5W-qlykL' |
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26 IFNB_STIM_INT_LINK='https://drive.google.com/uc?export=download&id=14iKgCJGPk16dEmpJJF-Gp_lBDcOdo-54' |
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27 |
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28 ## Classify and UMAP mapping |
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29 CLASSIFY_QUERY_LINK='https://oc.ebi.ac.uk/s/MlEDILFYRrvkS6E/download' |
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30 CLASSIFY_RESULTS_ANCHORS_OBJECT_LINK='https://drive.google.com/uc?export=download&id=1Xtv4K_CxIU1cJ8RjJ7NTvzLQkLvc8a3i' |
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31 # UMAP_RESULT_OBJECT_LINK='https://oc.ebi.ac.uk/s/k4MdM07y9DAnurp/download' |
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32 UMAP_RESULT_OBJECT_LINK='https://oc.ebi.ac.uk/s/D1z4z2ef1e3dyc3/download' |
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33 |
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34 |
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970696a7ae0b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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35 function get_data { |
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36 local link=$1 |
970696a7ae0b
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37 local fname=$2 |
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38 |
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39 if [ ! -f $fname ]; then |
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40 echo "$fname not available locally, downloading.." |
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41 wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link |
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42 fi |
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43 } |
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44 |
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45 # get matrix data |
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46 mkdir -p test-data |
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47 pushd test-data |
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48 get_data $MTX_LINK mtx.zip |
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49 unzip mtx.zip |
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50 rm -f mtx.zip |
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51 |
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52 get_data $RDS_LINK $BASENAME_FILE".rds" |
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53 get_data $NORM_LINK $BASENAME_FILE"-normalised.rds" |
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54 get_data $FVG_LINK $BASENAME_FILE"-fvg.rds" |
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55 get_data $SCALED_LINK $BASENAME_FILE"-scaled.rds" |
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56 get_data $PCA_LINK $BASENAME_FILE"-pca.rds" |
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57 get_data $NEIGHBOURS_LINK $BASENAME_FILE"-neighbours.rds" |
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58 get_data $CLUSTERS_LINK $BASENAME_FILE"-clusters.rds" |
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59 get_data $TSNE_LINK $BASENAME_FILE"-tsne.rds" |
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60 get_data $MARKERS_LINK $BASENAME_FILE"-markers.csv.zip" |
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61 |
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62 unzip $BASENAME_FILE"-markers.csv.zip" |
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63 rm -f $BASENAME_FILE"-markers.csv.zip" |
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64 |
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65 get_data $LOOM_LINK $BASENAME_FILE"_loom.h5" |
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66 get_data $SCE_LINK $BASENAME_FILE"_sce.rds" |
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67 get_data $H5AD_LINK $BASENAME_FILE".h5ad" |
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68 |
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69 get_data $H5AD_SC182_LINK $BASENAME_FILE"_sc182.h5ad" |
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70 |
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71 get_data $IFNB_CTRL_INT_LINK $IFNB_BASE_FILE"ctrl_norm_fvg.rds" |
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72 get_data $IFNB_STIM_INT_LINK $IFNB_BASE_FILE"stim_norm_fvg.rds" |
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73 |
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74 get_data $CLASSIFY_QUERY_LINK "Classify_query.rds" |
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75 get_data $CLASSIFY_RESULTS_ANCHORS_OBJECT_LINK "Classify_anchors.rds" |
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76 get_data $UMAP_RESULT_OBJECT_LINK "UMAP_result_integrated.rds" |
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77 |