Joss-reviews: [REVIEW]: reper - Genome-wide identification, classification and quantification of repetitive elements without an assembled genome

[whedon]

Submitting author: @nterhoeven (Niklas Terhoeven)
Repository: https://github.com/nterhoeven/reper
Version: v1.0.0
Editor: @mgymrek
Reviewer: @jsgalan
Archive: 10.5281/zenodo.1167969

Status

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@jsgalan, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @mgymrek know.

### Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Version: Does the release version given match the GitHub release (v1.0.0)?
• [x] Authorship: Has the submitting author (@nterhoeven) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• [x] Authors: Does the paper.md file include a list of authors with their affiliations?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @jsgalan it looks like you're currently assigned as the reviewer for this paper :tada:.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

https://github.com/openjournals/joss-papers/blob/joss.00527/joss.00527/10.21105.joss.00527.pdf

[jsgalan]

I still have major problems with the docker installation.

I am blaming mostly the osx High Sierra docker for Mac for the inconvenience.

Any other reviewer using osx High Sierra and Docker could help?

Best

[nterhoeven]

Hi @jsgalan that's a pity.

As it seems, there are other poeple who have problems with Docker after upgrading to High Sierra. For some reinstalling docker seems to work. I am not a Mac expert, but maybe it is worth a try.

If docker is not working for you, you can take a look at singularity. This is a similar tool. Take a look at the reper wiki for instructions to run reper with singularity.

Message me if you have any questions.

[nterhoeven]

Hi @jsgalan,

I opened an issue about your problem here: https://github.com/nterhoeven/reper/issues/9

[jsgalan]

Hi @nterhoeven i have been trying with Singularity, i got a few steps farther than with Docker, still somehow the VM crashed and wasnt able to restart it, I will try it today again.

[nterhoeven]

good. Feel free to open issues if you have any problems

[jsgalan]

Hi I am done with the review.

Where should i submit the review?

Best

[jsgalan]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the reviewer of this submission
@whedon assign @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Open the review issue
@whedon start review

🚧 🚧 🚧 Experimental Whedon features 🚧 🚧 🚧

# Compile the paper
@whedon generate pdf

[jsgalan]

@whedon start review

[whedon]

I'm sorry @jsgalan, I'm afraid I can't do that. That's something only editors are allowed to do.

[arfon]

Where should i submit the review?

@jsgalan - sorry for not being clear - this review issue _is the review_. Please leave comments in this thread for @nterhoeven to respond to.

[nterhoeven]

Hi @jsgalan, I just wanted to ask, if you have any news regarding uploading your review comments. I would like to read them :-)

[jsgalan]

Hi @nterhoeven

The paper and implementation are excellent. A few corrections are needed:

• (kmer counts based on jelly sh (Marçais and Kingsford 2011)) <-- check parenthesis use here
• To create exemplar sequences of each repeat in the genome, the assembled repeats ar clustered using cd-hit ((W. Li and Godzik 2006),(Fu et al. 2012)). <-- should read "repeats are clustered"

Hope this finishes the review process

Best

[mgymrek]

Thanks @jsgalan!
@nterhoeven after you make these minor changes update the thread and then we should be ready to go.

[nterhoeven]

Hi @jsgalan and @mgymrek,

thanks for the comments :-) I created an updated version of the paper.md file.

How are we going to proceed? I believe I have to create a new release and provide you with a DOI for it. Is this correct?

[mgymrek]

Thanks @nterhoeven. @arfon we're ready to accept this. @arfon will be able to help with the next steps.

[arfon]

@nterhoeven - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

[nterhoeven]

Hi @arfon,
I created a new release (v1.1.0). Here is the new DOI: 10.5281/zenodo.1167969

[arfon]

@whedon set 10.5281/zenodo.1167969 as archive

[whedon]

OK. 10.5281/zenodo.1167969 is the archive.

[arfon]

@jsgalan - many thanks for your review here and to @mgymrek for editing this submission ✨

@nterhoeven - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00527 ⚡️ 🚀 💥

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippet:

[![DOI](http://joss.theoj.org/papers/10.21105/joss.00527/status.svg)](https://doi.org/10.21105/joss.00527)

This is how it will look in your documentation:

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[nterhoeven]

Great :smile: Thanks a lot @arfon @mgymrek @jsgalan