[REVIEW]: chloroExtractor: extraction and assembly of the chloroplast genome from whole genome shotgun data #464

whedon · 2017-11-17T08:32:11Z

Submitting author: @greatfireball (Frank Förster)
Repository: https://github.com/chloroExtractorTeam/chloroExtractor
Version: v1.0.0
Editor: @pjotrp
Reviewer: @jdeligt
Archive: 10.5281/zenodo.1148955

Status

Status badge code:

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Markdown: [![status](http://joss.theoj.org/papers/eaceb6ac6723a3ea5749f7f50d4a4ad4/status.svg)](http://joss.theoj.org/papers/eaceb6ac6723a3ea5749f7f50d4a4ad4)

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

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

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

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

Conflict of interest

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

I confirm that I read and will adhere to the JOSS 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 (@greatfireball) 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)?

The text was updated successfully, but these errors were encountered:

pjotrp · 2017-11-17T08:39:38Z

Thanks @jdeligt for being willing to review this submission! Make sure to accept the invite to the 'openjournals/joss-reviews' repository to be able to tick above boxes and read the reviewer instructions http://joss.theoj.org/about. @greatfireball it is very helpful if you can go through above checklist first and make sure the important points are implemented. Please reply here if you think it all hunky dory!

jdeligt · 2017-11-17T11:28:12Z

I'll wait with further review until @greatfireball has gone through the checklist.
Found one small issue in the paper.md that has been raised on their repo:
chloroExtractorTeam/chloroExtractor#80

jdeligt · 2017-11-17T13:18:21Z

And please check the docker image and example usage, currently it fails:
chloroExtractorTeam/chloroExtractor#81

jdeligt · 2017-11-17T15:07:33Z

As well as the binary download:

[17-11-17 15:57:06] [fcg] Unable to open file 'ass/assembly_graph.fastg'
[17-11-17 15:57:06] [PipeWrap] fcg exited:256
[17-11-17 15:57:06] [PipeWrap] at /Users/jdeligt/code/chloroExtractor/bin/../lib/PipeWrap.pm line 153

jdeligt · 2017-12-05T15:41:39Z

Dependencies do not contain version numbers

pjotrp · 2017-12-06T06:28:15Z

Dear @greatfireball please fix/comment before we continue.

greatfireball · 2017-12-18T23:27:41Z

Hey @pjotrp and @jdeligt sorry for the delay. Think we could close those issues above by chloroExtractorTeam/chloroExtractor#83 and chloroExtractorTeam/chloroExtractor#81. @jdeligt mentioned another issue, but we need some more information to reproduce his finding. Nevertheless, the his major concerns should be solved. Please let us know, how we can help you to continue the review process. Thanks again for your time, your help, and your review.

Best,
Frank

pjotrp · 2017-12-19T06:05:08Z

@whedon commands

whedon · 2017-12-19T06:05:11Z

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

pjotrp · 2017-12-19T06:05:31Z

@whedon generate pdf

whedon · 2017-12-19T06:05:34Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2017-12-19T06:05:38Z

PDF failed to compile for issue #464 with the following error: 

 /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-453fa9fb981d/lib/whedon/author.rb:32:in `block in build_affiliation_string': Problem with affiliations for Markus J Ankenbrand, perhaps the affiliations index need quoting? (RuntimeError)
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-453fa9fb981d/lib/whedon/author.rb:31:in `each'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-453fa9fb981d/lib/whedon/author.rb:31:in `build_affiliation_string'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-453fa9fb981d/lib/whedon/author.rb:11:in `initialize'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-453fa9fb981d/lib/whedon.rb:97:in `new'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-453fa9fb981d/lib/whedon.rb:97:in `block in parse_authors'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-453fa9fb981d/lib/whedon.rb:95:in `each'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-453fa9fb981d/lib/whedon.rb:95:in `parse_authors'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-453fa9fb981d/lib/whedon.rb:76:in `initialize'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-453fa9fb981d/lib/whedon/processor.rb:26:in `new'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-453fa9fb981d/lib/whedon/processor.rb:26:in `set_paper'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-453fa9fb981d/bin/whedon:37:in `prepare'
	from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:in `run'
	from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in `invoke_command'
	from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:in `dispatch'
	from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/base.rb:466:in `start'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-453fa9fb981d/bin/whedon:99:in `<top (required)>'
	from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in `load'
	from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in `<main>'

pjotrp · 2017-12-19T06:07:09Z

@greatfireball while @jdeligt wraps up the review you can generate and check the PDF using above command. It should come out clean.

arfon · 2017-12-19T11:43:36Z

@whedon generate pdf

whedon · 2017-12-19T11:43:39Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2017-12-19T11:44:05Z

https://github.com/openjournals/joss-papers/blob/joss.00464/joss.00464/10.21105.joss.00464.pdf

greatfireball · 2017-12-19T11:48:49Z

Thanks for generating the PDF @arfon

arfon · 2017-12-19T11:58:02Z

Thanks for generating the PDF @arfon

No problem. You raised an interesting bug in our processing system with your paper :-)

greatfireball · 2017-12-19T12:04:59Z

Always a pleasure :)

greatfireball · 2018-01-06T21:45:56Z

Happy new year to both of you @pjotrp and @jdeligt, hope you had a wonderful holiday season. We updated our paper.md and added some more citations. We are still waiting for the more detailed description of the issue @jdeligt found. Please let us know if we can help you finishing the review process.

jdeligt · 2018-01-10T10:39:35Z

Thanks for the reminder and updating the documentation and contribution sections. The latest & greatest binary is running now, if it produces errors I will raise a well documented issue, if not I will tick the last box and the review will be concluded.

jdeligt · 2018-01-10T11:28:31Z

Apart from a minor issue with relative paths chloroExtractorTeam/chloroExtractor#88 no further problems were encountered and this issue can be worked around by the average user. Seen how the previous issues were handled I am confident that this will be resolved and should not impede publication.

As such I'm closing this review and would recommend publication.

jdeligt · 2018-01-10T11:28:40Z

@whedon close review

jdeligt · 2018-01-10T11:31:59Z

@pjotrp Whedon seems disinclined/unable to close the review process, can you work your editorial powers and move the paper along?

pjotrp · 2018-01-11T09:52:27Z

@arfon we are ready to R&R

arfon · 2018-01-16T01:06:05Z

@greatfireball - 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.

greatfireball · 2018-01-16T07:19:35Z

Of course I can :) I did a copy of the current repository and pushed it to Zenodo. Its DOI is and the current version number was bumped to v1.0.1

@jdeligt, @pjotrp, and @arfon thanks for your efforts!

greatfireball · 2018-01-16T07:37:30Z

I would like to add the guy who did solve the Mac-issues with our container to the acknowledge section of the paper. Would be nice, if that would be possible. I will then create another version for zenodo. So sry @arfon for the delay. Just give me an hour.

greatfireball · 2018-01-16T10:27:55Z

The new DOI is and the current version is 1.0.2

Thanks again!

arfon · 2018-01-16T10:43:01Z

I would like to add the guy who did solve the Mac-issues with our container to the acknowledge section of the paper. Would be nice, if that would be possible. I will then create another version for zenodo. So sry @arfon for the delay. Just give me an hour.

That sounds like a nice idea. Did you add this already @greatfireball?

greatfireball · 2018-01-16T11:27:59Z

Yeah... Version v1.0.2 contains @DanielAmsel in the acknowledgements section

arfon · 2018-01-16T12:37:18Z

@whedon set 10.5281/zenodo.1148955 as archive

whedon · 2018-01-16T12:37:21Z

OK. 10.5281/zenodo.1148955 is the archive.

arfon · 2018-01-16T12:43:30Z

@jdeligt - many thanks for your review here and to @pjotrp for editing this submission ✨

@greatfireball - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00464 ⚡️ 🚀 💥

whedon · 2018-01-16T12:43:33Z

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

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whedon assigned pjotrp Nov 17, 2017

whedon added the review label Nov 17, 2017

whedon mentioned this issue Nov 17, 2017

[PRE REVIEW]: chloroExtractor: extraction and assembly of the chloroplast genome from whole genome shotgun data #420

Closed

pjotrp assigned pjotrp and unassigned pjotrp Nov 17, 2017

openjournals deleted a comment from whedon Nov 17, 2017

iimog mentioned this issue Dec 6, 2017

Requirements do not contain version numbers chloroExtractorTeam/chloroExtractor#83

Closed

openjournals deleted a comment from whedon Jan 10, 2018

arfon added the accepted label Jan 16, 2018

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whedon added published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. labels Mar 2, 2020

This was referenced Oct 19, 2023

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[PRE REVIEW]: Dnaapler: A tool to reorient circular microbial genomes #5748

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editorialbot mentioned this issue Nov 21, 2023

[PRE REVIEW]: Finding and removing introns from RNA-Seq de novo assemblies with IntronSeeker #6081

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[REVIEW]: chloroExtractor: extraction and assembly of the chloroplast genome from whole genome shotgun data #464

[REVIEW]: chloroExtractor: extraction and assembly of the chloroplast genome from whole genome shotgun data #464

Comments

whedon commented Nov 17, 2017 • edited

Status

Reviewer instructions & questions

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

pjotrp commented Nov 17, 2017

jdeligt commented Nov 17, 2017

jdeligt commented Nov 17, 2017

jdeligt commented Nov 17, 2017

jdeligt commented Dec 5, 2017

pjotrp commented Dec 6, 2017

greatfireball commented Dec 18, 2017

pjotrp commented Dec 19, 2017

whedon commented Dec 19, 2017

pjotrp commented Dec 19, 2017

whedon commented Dec 19, 2017

whedon commented Dec 19, 2017

pjotrp commented Dec 19, 2017

arfon commented Dec 19, 2017

whedon commented Dec 19, 2017

whedon commented Dec 19, 2017

greatfireball commented Dec 19, 2017

arfon commented Dec 19, 2017

greatfireball commented Dec 19, 2017

greatfireball commented Jan 6, 2018

jdeligt commented Jan 10, 2018

jdeligt commented Jan 10, 2018

jdeligt commented Jan 10, 2018

jdeligt commented Jan 10, 2018

pjotrp commented Jan 11, 2018

arfon commented Jan 16, 2018

greatfireball commented Jan 16, 2018 • edited

greatfireball commented Jan 16, 2018

greatfireball commented Jan 16, 2018

arfon commented Jan 16, 2018

greatfireball commented Jan 16, 2018

arfon commented Jan 16, 2018

whedon commented Jan 16, 2018

arfon commented Jan 16, 2018

whedon commented Jan 16, 2018

whedon commented Nov 17, 2017 •

edited

greatfireball commented Jan 16, 2018 •

edited