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[REVIEW]: GUESSmyLT: Software to guess the RNA-Seq library type of paired and single end read files #1344

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whedon opened this issue Mar 22, 2019 · 57 comments

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commented Mar 22, 2019

Submitting author: @Juke34 (Jacques Dainat)
Repository: https://github.com/NBISweden/GUESSmyLT
Version: v1.0
Editor: @lpantano
Reviewer: @mistrm82
Archive: 10.5281/zenodo.3268394

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/48dd8e1d72e65ce23f3a0216d0b035e7"><img src="http://joss.theoj.org/papers/48dd8e1d72e65ce23f3a0216d0b035e7/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/48dd8e1d72e65ce23f3a0216d0b035e7/status.svg)](http://joss.theoj.org/papers/48dd8e1d72e65ce23f3a0216d0b035e7)

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

@mistrm82, 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 @lpantano know.

Please try and complete your review in the next two weeks

Review checklist for @mistrm82

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: v1.0
  • Authorship: Has the submitting author (@Juke34) 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)?
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commented Mar 22, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @mistrm82 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
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commented Mar 22, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Mar 22, 2019

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commented Mar 22, 2019

Thanks @mistrm82 to take time to review this paper!

@Juke34, please, go over the items that the reviewer will need to check and make sure all are good to go.

I think @mistrm82 will start reviewing the paper around Next Thursday.

Cheers

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commented Mar 22, 2019

Everything sounds ok except we didn't have any Community guidelines. Now is done. I have re-flagged this last version as v1.0. I took the opportunity to add acknowledgements in the paper too, and move all the paper related files into the paper dedicated folder. So, I guess we should compile the pdf again...

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commented Mar 22, 2019

@whedon generate pdf

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commented Mar 22, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Mar 22, 2019

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commented Apr 9, 2019

Apologies for the delay, I should have this complete by tomorrow

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commented Apr 10, 2019

@Juke34 I am having some problems installing (created an issue) so I have not been able to assess the "Functionality" section

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commented Apr 11, 2019

I think this is a great tool with functionality that meets a need for researchers doing NGS analysis. The problems I encountered is that installation is quite involved. I created a conda environment with the prerequisites (biopython, pysam, bcbio-gff) which was not too much of an issue. However, when trying to run some commands I encountered errors due to the lack of other required programs (i.e busco, trinity). Working on a cluster environment, the installation of these tools is not always straightforward. Is there any way to have these extra programs be installed as dependencies when you run the setup.py install? This would make it easier. Since I couldn't do these installations I was unable to fully test out functionality.

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commented Apr 18, 2019

Hi @Juke34, Do you think you can address @mistrm82 comment to get a better way to get the tool installed?

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commented Apr 19, 2019

Yes I think we can make a bioconda package.

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commented May 12, 2019

👋 @Juke34 — How are you getting along? Can you give us a status update on this submission?

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commented May 12, 2019

I started to work on it but I have to do some test before to release it. I'm currently busy by teachings. I hope it could be done by the end of may.

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commented Jun 8, 2019

Hi @Juke34 — Can you give us an update? If you're not close to done, please let me know of a time period to set a reminder for you.

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commented Jun 9, 2019

Thank you for your patience. Here are the updates: We have slightly modified the installation. We have created a PyPi package (https://pypi.org/project/guessmylt/), allowing installation using pip. So, using pip install GUESSmyLT will install most of the dependencies. Still Bowtie2, BUSCO and Trinity (depending of the user need Trinity is not mandatory) has to be installed aside.

Working on conda to package the whole, I have seen differences in the BUSCO results between osx and linux, and Trinity does not work on osx. So I have created a Bioconda recipe that should be compiled on linux (bioconda/bioconda-recipes#15786). Each package added to Bioconda also has a corresponding Docker BioContainer automatically created and uploaded to Quay.io. Once the container available, the reproducibility problem (different result between mac and linux) would be solved. The thing is, my Bioconda package is currently stuck at the check step because the bioconda-utils is encountered some issues (bioconda/bioconda-utils#567) that have to be resolved first.

May the simplification with pip install GUESSmyLT enough for publication?

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commented Jun 9, 2019

@mistrm82 — Let us know your assessment and response to the author's reply, above.

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commented Jun 10, 2019

HI @Juke34 and @labarba I will take a look over the next few days and will respond to the new updates. thanks!

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commented Jun 10, 2019

@Juke34 The problem with your package is not related to the bioconda-utils PR mentioned.

  • You are currently installing files to site-packages/example_run which should go to site-packages/GUESSmlLT or be omitted from distributed package.
  • The package currently fails in testing. If you look at the build logs, you will find at the bottom during the tests in an isolated minimal container an exception raised by gitpython indicating that git is missing. It's likely due to a missing run dependency on git itself.
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commented Jun 13, 2019

Thanks to @epruesse and @HadrienG I have been able to create a bioconda recipe. GUESSmyLT should be available for osx and linux through bioconda once the PR bioconda/bioconda-recipes#15786 will be accepted.

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commented Jun 20, 2019

I have added the right tag to get this merged, if not I could ping the bioconda team. Thanks for the effort.

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commented Jun 24, 2019

Thanks @Juke34 for both the PyPi package (https://pypi.org/project/guessmylt/) and the bioconda recipe. The problem I had previously was the inability to get Busco and so I think I will hold off on testing the PyPi package and wait for the PR merge from bioconda

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commented Jun 26, 2019

@whedon generate pdf

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commented Jun 26, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jun 26, 2019

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commented Jul 3, 2019

@whedon check references

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commented Jul 3, 2019

Attempting to check references...
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commented Jul 3, 2019


OK DOIs

- 10.1093/bioinformatics/bts356 is OK
- 10.1038/nmeth.4197 is OK
- 10.1038/nmeth.1923 is OK
- doi: 10.1093/molbev/msx319  is OK
- 10.1038/nbt.1883 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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commented Jul 3, 2019

@whedon generate pdf

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commented Jul 3, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jul 3, 2019

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commented Jul 3, 2019

@Juke34, We are almost there. Can you generate a Zenodo archive pointing to your github current version and making sure title and authors match the Zenodo link? Thanks

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commented Jul 3, 2019

@whedon set v1.0 as version

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commented Jul 3, 2019

OK. v1.0 is the version.

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commented Jul 4, 2019

Here is the doi: 10.5281/zenodo.3268394

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commented Jul 5, 2019

@whedon set 10.5281/zenodo.3268394 as archive

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commented Jul 5, 2019

OK. 10.5281/zenodo.3268394 is the archive.

@lpantano lpantano added the accepted label Jul 5, 2019

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commented Jul 5, 2019

Thanks for the hard work to the authors and reviewers. @openjournals/joss-eics this is accepted now.

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commented Jul 5, 2019

I'm confused by the author list: are commas missing, or something? It looks like some authors have a single-letter last name. Are first and last names being displayed in the wrong order?

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commented Jul 7, 2019

My mistake sorry. It should be now fixed.

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commented Jul 7, 2019

@whedon generate pdf

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commented Jul 7, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jul 7, 2019

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commented Jul 7, 2019

@whedon accept

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commented Jul 7, 2019

Attempting dry run of processing paper acceptance...
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commented Jul 7, 2019


OK DOIs

- 10.1093/bioinformatics/bts356 is OK
- 10.1038/nmeth.4197 is OK
- 10.1038/nmeth.1923 is OK
- doi: 10.1093/molbev/msx319  is OK
- 10.1038/nbt.1883 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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commented Jul 7, 2019

Check final proof 👉 openjournals/joss-papers#820

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#820, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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commented Jul 7, 2019

@whedon accept deposit=true

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commented Jul 7, 2019

Doing it live! Attempting automated processing of paper acceptance...
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commented Jul 7, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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commented Jul 7, 2019

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#821
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01344
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

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commented Jul 7, 2019

Congratulations, @Juke34, your JOSS paper is published! 🚀

Big thanks to our editor: @lpantano, and the reviewer: @mistrm82 🙏

@labarba labarba closed this Jul 7, 2019

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commented Jul 7, 2019

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

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

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01344/status.svg)](https://doi.org/10.21105/joss.01344)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01344">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01344/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01344/status.svg
   :target: https://doi.org/10.21105/joss.01344

This is how it will look in your documentation:

DOI

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