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[REVIEW]: LTRpred: de novo annotation of intact retrotransposons #2170

Closed whedon closed 4 years ago

whedon commented 4 years ago

Submitting author: @HajkD (Hajk-Georg Drost) Repository: https://github.com/HajkD/LTRpred Version: v1.1.0 Editor: @lpantano Reviewers: @dcassol, @mdozmorov Archive: 10.5281/zenodo.3895754

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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) by leaving comments 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

@dcassol, 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.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @lpantano know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @dcassol

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @mdozmorov

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @dcassol it looks like you're currently assigned to review this paper :tada:.

:star: Important :star:

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whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

lpantano commented 4 years ago

@whedon add @mdozmorov as reviewer

whedon commented 4 years ago

OK, @mdozmorov is now a reviewer

arfon commented 4 years ago

:wave: @dcassol, @mdozmorov - just a friendly check-in to see how things are going with your reviews?

mdozmorov commented 4 years ago

The package has installation problems, the issues have been opened https://github.com/HajkD/LTRpred/issues/14, https://github.com/HajkD/LTRpred/issues/13. The review will continue when the package will be possible to test

HajkD commented 4 years ago

Dear all,

with the most recent Dockerfile on GitHub it is now possible to run all examples shown in the manuscript. As well as playing with all LTRpred functions.

https://github.com/HajkD/LTRpred/blob/master/Dockerfile

This Dockerfile can be used to create a ltrpred Docker container as follows:

# assuming the Dockerfile is in the current working directory
docker build -t ltrpred .
# running ltrpred container
docker run --rm -ti ltrpred
# open R
:/app# R

Now in the R prompt:

# all tools are installed and the example LTRpred::LTRpred(...) run etc can be used
LTRpred::LTRpred(genome.file = system.file("Hsapiens_ChrY.fa", package = "LTRpred"))

What is missing and I would like to add is the ability to copy a local genome fasta file to the running ltrpred docker image. In addition, I think it could be nice and useful for users to be able to communicate with the ltrpred docker image via RStudio. For this purpose, I am implementing an interface between the ltrpred docker image and RStudio.

The core functionality of LTRpred, however, can now be used.

I hope this helps to make it easier to interact with this package.

I will try to have the final interfaces (ltrpred docker/RStudio and local file copy to ltrpred docker) running in the next few days.

Many thanks!

HajkD commented 4 years ago

P.S. I will also push the final docker image to Docker Hub so that users can easily retrieve LTRpred.

HajkD commented 4 years ago

Dear all,

Please accept my apologies for being silent for a while, but I wanted to make sure that this time I can deliver a complete and interactive ltrpred container toolkit rather than a Dockerfile prototype.

As a result, I developed two types of ltrpred containers which are available at Docker Hub:

1) Running the LTRpred pipeline through the R command line prompt: https://hub.docker.com/repository/docker/drostlab/ltrpred/. 2) Running the LTRpred pipeline through an RStudio Server interface: https://hub.docker.com/repository/docker/drostlab/ltrpred_rstudio.

I now documented in detail how to install, interact, and run both types of docker images here: https://hajkd.github.io/LTRpred/articles/Introduction.html#ltrpred-docker-container

A minimal example to get you started right away is the following:

# retrieve docker image from dockerhub
docker pull drostlab/ltrpred
# run ltrpred container
docker run --rm -ti drostlab/ltrpred
# start R prompt within ltrpred container
~:/app# R

Within the ltrpred container R prompt run the ltrpred example:

LTRpred::LTRpred(genome.file = system.file("Hsapiens_ChrY.fa", package = "LTRpred"))

The RStudio variant can be found here: https://hajkd.github.io/LTRpred/articles/Introduction.html#download-ltrpred_rstudio-container-for-use-with-rstudio-server

It took me a while to find the best way to allow users to run ltrpred through a RStudio Server interface, but I think the solution presented here should make it as easy as possible to use the ltrpred pipeline with RStudio.

I would like to express my gratitude for this brilliant suggestion and I am sure that future users will appreciate having access to a pipeline environment where all tool dependencies are preinstalled.

I am very well aware that the ltrpred pipeline depends on a large number of other tools, but the new functionality and analyses that can be performed thanks to the integration of all these tools are very useful for transposable element research and the type of annotation and analysis output generated by ltrpred was urgently needed.

I now very much look forward to hearing your feedback regarding the pipeline and further ways to improve it.

Your help and efforts are very much appreciated!

Many thanks,

Hajk

mdozmorov commented 4 years ago

The software LTRpred software for annotation of retrotransposons within genomic sequences is fully functional. The author should be applauded for the amount of effort to make the software accessible to users. Besides the original purpose, the GitHub repository contains good examples of complex Docker files that automate the installation of dependencies and enable the use of the software both in the command line and via the RStudio interface. The documentation is up-to-date. The manuscript accurately describes the functionality of LTRpred. @whedon accept

lpantano commented 4 years ago

@dcassol , how is your reviewing coming? Could you give us some update?

dcassol commented 4 years ago

@lpantano Yes, by the end of the week I can give you feedback. Thanks!

lpantano commented 4 years ago

@dcassol, just asking for an update on this, thanks.

dcassol commented 4 years ago

I made small comments here: HajkD/LTRpred#17 @lpantano How can I make comments on the article? Find a typo.

lpantano commented 4 years ago

you can open an issue there as well since the source of the paper is in their repo: https://github.com/HajkD/LTRpred/blob/master/paper.md

dcassol commented 4 years ago

LTRpred pipeline focuses on the annotation of retrotransposons and retrieving structurally intact elements within any sequence of genomes. The software fulfills all the required checkboxes for the review. In particular, I am impressed with the availability of the Docker container for the package which makes the installation and running process much more easer, special for users with less programming skills. The author also provides the possibility of deploying the software both in the command line and via the RStudio interface. Also, the paper is well written and the code is clear, easy to use, and properly documented.

lpantano commented 4 years ago

Hi @HajkD, let me know when the issues are addressed and closed so I can move forward with the acceptance :)

HajkD commented 4 years ago

Dear Lorena,

Thank you so much for handling the editorial process of the LTRpred manuscript despite the ongoing Covid19 pandemic. I very much appreciate your efforts to keep the review process as smoothly as possible.

I now addressed all remaining suggestions raised by Dani and would wait for her approval and closure of the last issue.

Dear Mikhail and Dani,

I am truly grateful for all your excellent suggestions and for catching all shortcomings of the LTRpred functionality.

I am convinced that your efforts have vastly increased the accessibility of LTRpred to a much wider life science audience and it taught me to always go the extra mile from now on and build a container for all my tools.

I hope that the review process didn't disrupt your daily adjustments to the Covid19 pandemic too much and I will always be grateful to all of you for your continued service to the academic cycle.

With the warmest wishes, Hajk

HajkD commented 4 years ago

Dear Lorena,

all issues all closed now.

Thank you very much for arranging the next steps of the submission process.

Best wishes, Hajk

lpantano commented 4 years ago

@whedon check references

lpantano commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

PDF failed to compile for issue #2170 with the following error:

lpantano commented 4 years ago

perfect! meanwhile we solve this technical issues, @HajkD can you confirm the current version of your tool?

HajkD commented 4 years ago

Brilliant! Thank you very much!

I can confirm that the current version of LTRpred is v1.1.0.

arfon commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

HajkD commented 4 years ago

Dear @arfon

Thank you for generating the article proof. I can confirm that the text and formatting are correct and as they are supposed to be. Just a very quick question: Would it be possible to rotate Figure 1? Is there a way I can control the figure rotation in the Markdown file? I was trying a few LateX tricks, but they didn't work. This isn't absolutely necessary, but would make the manuscript as flawless as possible.

Your help with this is truly appreciated!

Many thanks, Hajk

arfon commented 4 years ago

Hrmm, I'm not sure sorry @HajkD. I don't think it's possible to rotate with Markdown/Pandoc. Perhaps it has something to do with the figure being a PDF? Could you try converting it to a PNG and see if that preserves the correct rotation?

BTW, you can experiment with paper compilation either here (which creates some notification noise for all parties) or using our preview service at http://whedon.theoj.org

HajkD commented 4 years ago

Brilliant! Thank you very much! I will try this option and will come back to all of you soon.

HajkD commented 4 years ago

Dear @arfon

The trick worked like a charm!

Thank you so much for your help with this!

I added the PNG figure change to the Markdown file. The manuscript is perfect now.

Many thanks, Hajk

lpantano commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

lpantano commented 4 years ago

@whedon check references

lpantano commented 4 years ago

@HajkD, can you make a Zenodo archive and send me the link. The title and the authors should match the paper information. I think you can sync Zenodo with the releases and it will create one archive link for each release. Thanks!

HajkD commented 4 years ago

Dear @lpantano

I just created a LTRpred release for the GitHub repo and created a Zenodo archive.

The corresponding link is as follows:

https://doi.org/10.5281/zenodo.3895754

Thank you very much for arranging the next steps!

With very best wishes, Hajk

lpantano commented 4 years ago

thank you. But I think we need an archive without tar the content. It should look like this: https://zenodo.org/record/3755304

HajkD commented 4 years ago

Dear Lorena,

Thank you very much for making me aware of this.

In my last JOSS paper I also submitted a *.tar.gz file, since this is the source format for R packages:

https://zenodo.org/record/1286221#.XunyeZ4zahc

Would it be possible to check wether there is a way to use *.tar.gz files in JOSS, because the Zenodo policy states:

Note: File addition, removal or modification are not allowed after an upload has been published. This is because a Digital Object Identifier (DOI) is registered with DataCite for each upload.

Thank you very much for your help with this and I apologise if I have caused any additional work.

With very best wishes, Hajk

lpantano commented 4 years ago

@whedon set 10.5281/zenodo.3895754 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3895754 is the archive.

lpantano commented 4 years ago

@whedon accept

whedon commented 4 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 4 years ago

PDF failed to compile for issue #2170 with the following error:

E, [2020-06-18 16:35:28#1452] ERROR -- : Failed to parse BibTeX on value "," (COMMA) [#, "@", #, {:title=>["Transposon age and non-CG methylation"], :author=>["Wang, Zhengming and Baulcombe, David"], :abstract=>["Silencing of transposable elements (TEs) is established by small RNA-directed DNA methylation (RdDM). Maintenance of silencing is then based on a combination of RdDM and RNA-independent mechanisms involving DNA methyltransferase MET1 and chromodomain DNA methyltransferases (CMTs). Involvement of RdDM, according to this model should decrease with TE age but here we show a different pattern in tomato and Arabidopsis. In these species the CMTs silence long terminal repeat (LTR) transposons in the distal chromatin that are younger than those affected by RdDM. To account for these findings we propose that, after establishment of primary RdDM as in the original model, there is an RNA-independent maintenance phase involving CMTs followed by secondary RdDM. This progression of epigenetic silencing in the gene-rich distal chromatin is likely to influence the transcriptome either in cis or in trans depending on whether the mechanisms are RNA-dependent or -independent."], :journal=>["Nature Communications"], :volume=>["In press."]}, ",", "number", "="] bibtex.y:138:in on_error': Failed to parse BibTeX on value "," (COMMA) [#<BibTeX::Bibliography data=[16]>, "@", #<BibTeX::Entry >, {:title=>["Transposon age and non-CG methylation"], :author=>["Wang, Zhengming and Baulcombe, David"], :abstract=>["Silencing of transposable elements (TEs) is established by small RNA-directed DNA methylation (RdDM). Maintenance of silencing is then based on a combination of RdDM and RNA-independent mechanisms involving DNA methyltransferase MET1 and chromodomain DNA methyltransferases (CMTs). Involvement of RdDM, according to this model should decrease with TE age but here we show a different pattern in tomato and Arabidopsis. In these species the CMTs silence long terminal repeat (LTR) transposons in the distal chromatin that are younger than those affected by RdDM. To account for these findings we propose that, after establishment of primary RdDM as in the original model, there is an RNA-independent maintenance phase involving CMTs followed by secondary RdDM. This progression of epigenetic silencing in the gene-rich distal chromatin is likely to influence the transcriptome either in cis or in trans depending on whether the mechanisms are RNA-dependent or -independent."], :journal=>["Nature Communications"], :volume=>["In press."]}, ",", "number", "="] (BibTeX::ParseError) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/racc/parser.rb:259:in_racc_do_parse_c' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/racc/parser.rb:259:in do_parse' from bibtex.y:111:inparse' from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.1.4/lib/bibtex/bibliography.rb:67:in parse' from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.1.4/lib/bibtex/bibliography.rb:50:inopen' from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.1.4/lib/bibtex/utilities.rb:25:in open' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-2081a6a6226c/lib/whedon/bibtex_parser.rb:36:ingenerate_citations' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-2081a6a6226c/lib/whedon/compilers.rb:245:in crossref_from_markdown' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-2081a6a6226c/lib/whedon/compilers.rb:21:ingenerate_crossref' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-2081a6a6226c/lib/whedon/processor.rb:95:in compile' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-2081a6a6226c/bin/whedon:79:incompile' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:ininvoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:instart' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-2081a6a6226c/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:inload' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

lpantano commented 4 years ago

Only thing to double-check whether the archive is valid being an tar file by the board of editors.

lpantano commented 4 years ago

oh oh @HajkD, did you change something? it rendered well a couple of days before. Let us know if you don't know how to fix this.

arfon commented 4 years ago

oh oh @HajkD, did you change something? it rendered well a couple of days before. Let us know if you don't know how to fix this.

@lpantano this looks to be a bug on our side. Investigating...

Only thing to double-check whether the archive is valid being an tar file by the board of editors.

Also, this is fine I think.

arfon commented 4 years ago

@HajkD - this PR should fix the issue with your paper: https://github.com/HajkD/LTRpred/pull/19

HajkD commented 4 years ago

@arfon - brilliant! Thanks so much! I just merged your pull request.

arfon commented 4 years ago

@whedon accept

whedon commented 4 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 4 years ago 
Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1093/nar/gkv1272 may be missing for title: The Dfam database of repetitive DNA families
- https://doi.org/10.1093/nar/gkr367 may be missing for title: HMMER web server: interactive sequence similarity searching
- https://doi.org/10.1093/bioinformatics/btq461 may be missing for title: Search and clustering orders of magnitude faster than BLAST
- https://doi.org/10.1109/tcbb.2013.68 may be missing for title: GenomeTools: a comprehensive software library for efficient processing of structured genome annotations
- https://doi.org/10.1093/nar/gkp759 may be missing for title: Fine-grained annotation and classification of de novo predicted LTR retrotransposons
- https://doi.org/10.1186/1471-2105-9-18 may be missing for title: LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons
- https://doi.org/10.1371/journal.pcbi.1003118 may be missing for title: Software for computing and annotating genomic ranges
- https://doi.org/10.1038/nrg.2016.139 may be missing for title: Regulatory activities of transposable elements: from conflicts to benefits
- https://doi.org/10.1101/517508 may be missing for title: Environmental and epigenetic regulation of Rider retrotransposons in tomato
- https://doi.org/10.1093/gbe/evz255 may be missing for title: Becoming a Selfish Clan: Recombination Associated to Reverse-Transcription in LTR Retrotransposons
- https://doi.org/10.1038/s41477-018-0320-9 may be missing for title: Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants
- https://doi.org/10.1093/bioinformatics/btw821 may be missing for title: Biomartr: genomic data retrieval with R
- https://doi.org/10.1038/s41467-020-14995-6 may be missing for title: Transposon age and non-CG methylation
- https://doi.org/10.1186/gb-2012-13-8-r77 may be missing for title: ggbio: an R package for extending the grammar of graphics for genomic data
- https://doi.org/10.1038/s41467-017-01374-x may be missing for title: High-frequency recombination between members of an LTR retrotransposon family during transposition bursts

INVALID DOIs

- None