annotate get_test_data.sh @ 0:31a8c822882f draft default tip

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
author ebi-gxa
date Sun, 15 Sep 2024 10:13:34 +0000
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31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
ebi-gxa
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1 #!/usr/bin/env bash
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
ebi-gxa
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2 TF_DATA_LINK='https://raw.githubusercontent.com/aertslab/scenic-nf/master/example/allTFs_hg38.txt'
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
ebi-gxa
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3 MOTIF2TF_LINK='https://raw.githubusercontent.com/aertslab/scenic-nf/master/example/motifs.tbl'
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
ebi-gxa
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4 RANKING_LINK='https://zenodo.org/records/13328724/files/genome-ranking_v2.feather'
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
ebi-gxa
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5 LOOM_INPUT_LINK='https://raw.githubusercontent.com/aertslab/scenic-nf/master/example/expr_mat.loom'
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
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31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
ebi-gxa
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7 REGULONS_LINK='https://zenodo.org/records/13328724/files/regulons.tsv'
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
ebi-gxa
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8 TF2TARGETS_LINK='https://zenodo.org/records/13328724/files/tf2targets.tsv'
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
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9
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
ebi-gxa
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10 function get_data {
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
ebi-gxa
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11 local link=$1
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
ebi-gxa
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12 local fname=$2
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
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31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
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14 if [ ! -f $fname ]; then
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
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15 echo "$fname not available locally, downloading.."
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
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16 wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
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17 fi
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
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18 }
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
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31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
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20 # get matrix data
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
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21 mkdir -p test-data
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
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22 pushd test-data
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
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23 get_data $TF_DATA_LINK "allTFs_hg38.txt"
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
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24 get_data $MOTIF2TF_LINK "motifs.tbl"
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
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25 get_data $RANKING_LINK "genome-ranking_v2.feather"
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
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26 get_data $LOOM_INPUT_LINK "expr_mat.loom"
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
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27 get_data $REGULONS_LINK regulons.tsv
31a8c822882f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4
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28 get_data $TF2TARGETS_LINK tf2targets.tsv