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[JOSS Review] - Documentation #48

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vinisalazar opened this issue Nov 1, 2023 · 4 comments
Closed

[JOSS Review] - Documentation #48

vinisalazar opened this issue Nov 1, 2023 · 4 comments

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@vinisalazar
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vinisalazar commented Nov 1, 2023

Hi,

attached are some suggestions for the documentation based on my review:

conda create -n dnaapler_env dnaapler

  • Include -c bioconda, like in the command specified in Line 95 of the same file. This should prevent many first-time users from running into a "package not found" error, as it is unlikely they will have read the Beginner Conda Installation section of the docs. You may also link this section here.

You will need to install BLAST v2.10 or higher separately.

  • Specify that this is only required if installing with pip (would Prodigal be required too if the user wants to use the Pyrodigal commands?)

3. Install miniconda and follow the prompts.

  • This list numbering is rendering incorrectly in the readthedocs page.

I will update this issue if I find anything else.

cc openjournals/joss-reviews#5968

@gbouras13
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gbouras13 commented Nov 6, 2023

re openjournals/joss-reviews#5968

Hi @vinisalazar ,

Thanks for these. Also linking to #51 regarding your third point as they will be dealt with together.

Your first point has been fixed in the README.md to make it easier for beginners to follow - namely, by making an empty conda env and then installing dnaapler (I did not get good results trying to do it all in one line, therefore a beginner will have a harder time!).

The second point also has been fixed.

To clarify, prodigal is not required in dnaapler at all. This is because pyrodigal is a self contained Python package that reimplements and provides python bindings to Prodigal and therefore does not require it as a dependency. pyrodigal will always be installed with a pip install of dnaapler.

Regarding your third point, install.md is overhauled after #51 - the correct numbering will be used.

George

@mkerin
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mkerin commented Nov 8, 2023

This is a quick comment to say that I think there is an unfinished sentence on line 54 of docs/example.md here

In the results in the output directory, you will see that the `C333_reorientation_summary.tsv` file shows that `dnaapler` has identified the C333 genome to begin with coordinate

I also think that, other than this typo, the new docs/example.md section is excellent.

@gbouras13
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Hi @mkerin,

Thanks for picking this up - I've made a fix now in the commit references above.

George

@vinisalazar
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LGTM @gbouras13.

I will close this issue for now but @mkerin or @gbouras13 please reopen it if you deem it necessary.

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