Mercurial > repos > ufz > genomad_end_to_end

annotate test-data/README.test_db @ 0:955e33326e20 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
955e33326e20 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/longorf/ commit 483ade5362574a59ddc87e3788334bcbff253805
ufz
parents:
diff changeset
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:
diff changeset
2
955e33326e20 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/longorf/ commit 483ade5362574a59ddc87e3788334bcbff253805
ufz
parents:
diff changeset
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:
diff changeset
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:
diff changeset
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:
diff changeset
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
parents:
diff changeset
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:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
12 - genomad_microdb*
955e33326e20 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/longorf/ commit 483ade5362574a59ddc87e3788334bcbff253805
ufz
parents:
diff changeset
13