Mercurial > repos > ufz > genomad_end_to_end
diff test-data/README.test_db @ 0:955e33326e20 draft
planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/longorf/ commit 483ade5362574a59ddc87e3788334bcbff253805
| author | ufz |
|---|---|
| date | Tue, 18 Jun 2024 14:28:44 +0000 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/README.test_db Tue Jun 18 14:28:44 2024 +0000 @@ -0,0 +1,13 @@ +creating of a smaller reference database: https://github.com/apcamargo/genomad/issues/104#issuecomment-2170949010 + +- Download reference db v1.7 +- store in dir genomad_db in test-data +- 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 +- join -1 2 -2 1 genomad_db/genomad_db.lookup markers | cut -d" " -f 2 | sort -u -n > sorted_markers +- cd genomad_db +- `mmseqs createsubdb ~/projects/tools-iuc/tools/genomad/test-data/sorted_markers genomad_db genomad_microdb` +- mv genomad_microdb.index genomad_db.index +- mv genomad_microdb.dbtype genomad_db.dbtype +- mv genomad_microdb genomad_db +- genomad_microdb* +