Mercurial > repos > ebi-gxa > pyscenic_grn

annotate get_test_data.sh @ 1:c1207fb29b08 draft default tip

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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 10:13:26 +0000
parents 95431f03a8fc
children
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95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
parents:
diff changeset
1 #!/usr/bin/env bash
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
parents:
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2 TF_DATA_LINK='https://raw.githubusercontent.com/aertslab/scenic-nf/master/example/allTFs_hg38.txt'
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
parents:
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3 MOTIF2TF_LINK='https://raw.githubusercontent.com/aertslab/scenic-nf/master/example/motifs.tbl'
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
parents:
diff changeset
4 RANKING_LINK='https://zenodo.org/records/13328724/files/genome-ranking_v2.feather'
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
parents:
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5 LOOM_INPUT_LINK='https://raw.githubusercontent.com/aertslab/scenic-nf/master/example/expr_mat.loom'
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
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6
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
parents:
diff changeset
7 REGULONS_LINK='https://zenodo.org/records/13328724/files/regulons.tsv'
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
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8 TF2TARGETS_LINK='https://zenodo.org/records/13328724/files/tf2targets.tsv'
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
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9
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
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10 function get_data {
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
parents:
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11 local link=$1
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
parents:
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12 local fname=$2
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
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95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
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14 if [ ! -f $fname ]; then
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
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15 echo "$fname not available locally, downloading.."
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
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16 wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
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17 fi
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
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18 }
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
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95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
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20 # get matrix data
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
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21 mkdir -p test-data
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
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22 pushd test-data
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
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23 get_data $TF_DATA_LINK "allTFs_hg38.txt"
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
parents:
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24 get_data $MOTIF2TF_LINK "motifs.tbl"
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
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25 get_data $RANKING_LINK "genome-ranking_v2.feather"
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
parents:
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26 get_data $LOOM_INPUT_LINK "expr_mat.loom"
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
parents:
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27 get_data $REGULONS_LINK regulons.tsv
95431f03a8fc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4990a52ac6fd3d97434a24051e5828c86c8a802c
ebi-gxa
parents:
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28 get_data $TF2TARGETS_LINK tf2targets.tsv