update pharokka to latest version

[bgruening]

FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
• This PR updates an existing tool or tool collection
• This PR does something else (explain below)

We need some new test database, until then the tests will fail I think.

[bgruening]

@paulzierep do you remember how you have created the test DB?

[gbouras13]

Hi @bgruening @paulzierep ,

The only major parameter that should be added for the update to the new version (v1.7.4) is --fast. It might also be good to add --prefix and --locustag e.g. for users who may want to submit directly to NCBI/ENA etc.

Another suggestion would be to remove the terminate subunit reorientation option (which is available on v1.3.2) in place of --dnaapler, which is used much more commonly now by users, as it does automatic reorientation.

Otherwise, I think it's all ok - the advanced specific parameters aren't necessary I think for this interface.

George

[gbouras13]

@bgruening - I made a small dummy test database for Paul back when he installed v1.3.2. I'll do the same now with the latest version.

George

[bgruening]

@gbouras13 having the test database would be absolutely great! Thanks.

[paulzierep]

@gbouras13 can you also provide the latest DB you would like to be used with this version ? Or will install_databases.py -d using this tool version be the one required ?

[gbouras13]

Hi @paulzierep ,

install_databases.py -d or install_databases.py -o <db_dir> will get the correct database for v1.7.4. You can also find the tarball here if that fails https://zenodo.org/records/8276347 . I'll add a test DB now, sorry for the delay.

George

[gbouras13]

pharokka_test_db_1.7.4.tar.gz

I've attached the tiny test dummy db like I did for the original v1.3.2 release on galaxy - I've tested it and pharokka v1.7.4 with this locally for me, so should be fine for your purposes.

George

[paulzierep]

Here is the updated DM: #6680
@gbouras13 the test dummy db you provided contains a few hidden files, are they needed ?
ls -l ->

.
..
._1Aug2023_data.tsv
1Aug2023_data.tsv
._1Aug2023_genomes.fa.msh
1Aug2023_genomes.fa.msh
all_phrogs.h3m
._aro_index.tsv
aro_index.tsv
._CARD
CARD
._CARD.dbtype
 
...

[gbouras13]

No sure why they are there (maybe from my MacBook) - definitely don't need any hidden files.

George