Mercurial > repos > ebi-gxa > score_genes_aucell
annotate get_test_data.sh @ 0:1e8697931d73 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
author | ebi-gxa |
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date | Thu, 09 Nov 2023 11:36:08 +0000 |
parents | |
children | c700f0381e84 |
rev | line source |
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0
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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changeset
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1 #!/usr/bin/env bash |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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2 |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
diff
changeset
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3 BASENAME_FILE='mito_counted_anndata.h5ad' |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
diff
changeset
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4 |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
diff
changeset
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5 MTX_LINK='https://zenodo.org/record/7053673/files/Mito-counted_AnnData' |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
diff
changeset
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6 |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
diff
changeset
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7 # convenience for getting data |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
diff
changeset
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8 function get_data { |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
diff
changeset
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9 local link=$1 |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
diff
changeset
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10 local fname=$2 |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
diff
changeset
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11 |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
diff
changeset
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12 if [ ! -f $fname ]; then |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
diff
changeset
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13 echo "$fname not available locally, downloading.." |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
diff
changeset
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14 wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
diff
changeset
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15 fi |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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16 } |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
diff
changeset
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17 |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
diff
changeset
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18 # get matrix data |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
diff
changeset
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19 mkdir -p test-data |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
diff
changeset
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20 pushd test-data |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
diff
changeset
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21 get_data $MTX_LINK $BASENAME_FILE |