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planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/ commit dddf8b42771f66318f3325607bbd7aa33a3716b5
author ufz
date Mon, 07 Oct 2024 11:51:02 +0000
parents 955e33326e20
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955e33326e20 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/longorf/ commit 483ade5362574a59ddc87e3788334bcbff253805
ufz
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1 creating of a smaller reference database: https://github.com/apcamargo/genomad/issues/104#issuecomment-2170949010
955e33326e20 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/longorf/ commit 483ade5362574a59ddc87e3788334bcbff253805
ufz
parents:
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955e33326e20 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/longorf/ commit 483ade5362574a59ddc87e3788334bcbff253805
ufz
parents:
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3 - Download reference db v1.7
955e33326e20 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/longorf/ commit 483ade5362574a59ddc87e3788334bcbff253805
ufz
parents:
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4 - store in dir genomad_db in test-data
955e33326e20 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/longorf/ commit 483ade5362574a59ddc87e3788334bcbff253805
ufz
parents:
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5 - run test and get ids with `awk -v FS="\t" 'NR>1 && $9!="NA" {print $9}' output/sequence_annotate/sequence_genes.tsv | sort -u > markers
955e33326e20 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/longorf/ commit 483ade5362574a59ddc87e3788334bcbff253805
ufz
parents:
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6 - join -1 2 -2 1 genomad_db/genomad_db.lookup markers | cut -d" " -f 2 | sort -u -n > sorted_markers
955e33326e20 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/longorf/ commit 483ade5362574a59ddc87e3788334bcbff253805
ufz
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7 - cd genomad_db
955e33326e20 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/longorf/ commit 483ade5362574a59ddc87e3788334bcbff253805
ufz
parents:
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8 - `mmseqs createsubdb ~/projects/tools-iuc/tools/genomad/test-data/sorted_markers genomad_db genomad_microdb`
955e33326e20 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/longorf/ commit 483ade5362574a59ddc87e3788334bcbff253805
ufz
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9 - mv genomad_microdb.index genomad_db.index
955e33326e20 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/longorf/ commit 483ade5362574a59ddc87e3788334bcbff253805
ufz
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10 - mv genomad_microdb.dbtype genomad_db.dbtype
955e33326e20 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/longorf/ commit 483ade5362574a59ddc87e3788334bcbff253805
ufz
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11 - mv genomad_microdb genomad_db
955e33326e20 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/longorf/ commit 483ade5362574a59ddc87e3788334bcbff253805
ufz
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12 - genomad_microdb*
955e33326e20 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/longorf/ commit 483ade5362574a59ddc87e3788334bcbff253805
ufz
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