New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[REVIEW]: reper - Genome-wide identification, classification and quantification of repetitive elements without an assembled genome #527

Closed
whedon opened this Issue Jan 8, 2018 · 26 comments

Comments

Projects
None yet
5 participants
@whedon
Collaborator

whedon commented Jan 8, 2018

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

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/f0d16a43d8b031695f151ea25e0d47b0"><img src="http://joss.theoj.org/papers/f0d16a43d8b031695f151ea25e0d47b0/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/f0d16a43d8b031695f151ea25e0d47b0/status.svg)](http://joss.theoj.org/papers/f0d16a43d8b031695f151ea25e0d47b0)

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

Code of Conduct

General checks

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

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • 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

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

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

This comment has been minimized.

Show comment
Hide comment
@whedon

whedon Jan 8, 2018

Collaborator

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 🎉.

⭐️ Important ⭐️

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:

watching

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

notifications

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

@whedon commands
Collaborator

whedon commented Jan 8, 2018

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 🎉.

⭐️ Important ⭐️

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:

watching

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

notifications

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

@whedon commands
@whedon

This comment has been minimized.

Show comment
Hide comment
@whedon

whedon Jan 8, 2018

Collaborator
Attempting PDF compilation. Reticulating splines etc...
Collaborator

whedon commented Jan 8, 2018

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Show comment
Hide comment
@whedon

whedon Jan 8, 2018

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

whedon commented Jan 8, 2018

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

This comment has been minimized.

Show comment
Hide comment
@jsgalan

jsgalan Jan 11, 2018

Collaborator

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

Collaborator

jsgalan commented Jan 11, 2018

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

This comment has been minimized.

Show comment
Hide comment
@nterhoeven

nterhoeven Jan 11, 2018

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 commented Jan 11, 2018

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

This comment has been minimized.

Show comment
Hide comment
@nterhoeven

nterhoeven Jan 12, 2018

Hi @jsgalan,

I opened an issue about your problem here: nterhoeven/reper#9

nterhoeven commented Jan 12, 2018

Hi @jsgalan,

I opened an issue about your problem here: nterhoeven/reper#9

@jsgalan

This comment has been minimized.

Show comment
Hide comment
@jsgalan

jsgalan Jan 12, 2018

Collaborator

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.

Collaborator

jsgalan commented Jan 12, 2018

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

This comment has been minimized.

Show comment
Hide comment
@nterhoeven

nterhoeven Jan 12, 2018

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

nterhoeven commented Jan 12, 2018

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

@jsgalan

This comment has been minimized.

Show comment
Hide comment
@jsgalan

jsgalan Jan 22, 2018

Collaborator

Hi I am done with the review.

Where should i submit the review?

Best

Collaborator

jsgalan commented Jan 22, 2018

Hi I am done with the review.

Where should i submit the review?

Best

@jsgalan

This comment has been minimized.

Show comment
Hide comment
@jsgalan

jsgalan Jan 22, 2018

Collaborator

@whedon commands

Collaborator

jsgalan commented Jan 22, 2018

@whedon commands

@whedon

This comment has been minimized.

Show comment
Hide comment
@whedon

whedon Jan 22, 2018

Collaborator

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

Collaborator

whedon commented Jan 22, 2018

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

This comment has been minimized.

Show comment
Hide comment
@jsgalan

jsgalan Jan 22, 2018

Collaborator

@whedon start review

Collaborator

jsgalan commented Jan 22, 2018

@whedon start review

@whedon

This comment has been minimized.

Show comment
Hide comment
@whedon

whedon Jan 22, 2018

Collaborator

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

Collaborator

whedon commented Jan 22, 2018

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

@arfon

This comment has been minimized.

Show comment
Hide comment
@arfon

arfon Jan 22, 2018

Member

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.

Member

arfon commented Jan 22, 2018

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

This comment has been minimized.

Show comment
Hide comment
@nterhoeven

nterhoeven Feb 1, 2018

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

nterhoeven commented Feb 1, 2018

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

@jsgalan

This comment has been minimized.

Show comment
Hide comment
@jsgalan

jsgalan Feb 5, 2018

Collaborator

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

Collaborator

jsgalan commented Feb 5, 2018

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

This comment has been minimized.

Show comment
Hide comment
@mgymrek

mgymrek Feb 5, 2018

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

mgymrek commented Feb 5, 2018

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

@nterhoeven nterhoeven referenced this issue Feb 6, 2018

Merged

Develop #10

@nterhoeven

This comment has been minimized.

Show comment
Hide comment
@nterhoeven

nterhoeven Feb 6, 2018

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?

nterhoeven commented Feb 6, 2018

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

This comment has been minimized.

Show comment
Hide comment
@mgymrek

mgymrek Feb 6, 2018

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

mgymrek commented Feb 6, 2018

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

@arfon

This comment has been minimized.

Show comment
Hide comment
@arfon

arfon Feb 6, 2018

Member

@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.

Member

arfon commented Feb 6, 2018

@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

This comment has been minimized.

Show comment
Hide comment
@nterhoeven

nterhoeven Feb 7, 2018

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

nterhoeven commented Feb 7, 2018

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

@arfon

This comment has been minimized.

Show comment
Hide comment
@arfon

arfon Feb 8, 2018

Member

@whedon set 10.5281/zenodo.1167969 as archive

Member

arfon commented Feb 8, 2018

@whedon set 10.5281/zenodo.1167969 as archive

@whedon

This comment has been minimized.

Show comment
Hide comment
@whedon

whedon Feb 8, 2018

Collaborator

OK. 10.5281/zenodo.1167969 is the archive.

Collaborator

whedon commented Feb 8, 2018

OK. 10.5281/zenodo.1167969 is the archive.

@arfon

This comment has been minimized.

Show comment
Hide comment
@arfon

arfon Feb 8, 2018

Member

@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 ⚡️ 🚀 💥

Member

arfon commented Feb 8, 2018

@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 ⚡️ 🚀 💥

@arfon arfon closed this Feb 8, 2018

@arfon arfon reopened this Feb 8, 2018

@arfon arfon added the accepted label Feb 8, 2018

@arfon arfon closed this Feb 8, 2018

@whedon

This comment has been minimized.

Show comment
Hide comment
@whedon

whedon Feb 8, 2018

Collaborator

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Collaborator

whedon commented Feb 8, 2018

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

@nterhoeven

This comment has been minimized.

Show comment
Hide comment
@nterhoeven

nterhoeven Feb 8, 2018

Great 😄 Thanks a lot @arfon @mgymrek @jsgalan

nterhoeven commented Feb 8, 2018

Great 😄 Thanks a lot @arfon @mgymrek @jsgalan

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment