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