Closed whedon closed 4 years ago
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Attempting PDF compilation. Reticulating splines etc...
@luizirber, @peterwc - this is where the review happens. Instructions are available above, don't hesitate to ping me if you have questions!
@lskatz - please have a look at the checklists above and make sure that your submission has all required components. Otherwise, please add them already now to simplify the review.
A couple of comments about your paper that would be good if you could address:
Thank you @luizirber and @peterwc for reviewing!
Thank you @csoneson! I edited the figure legends so that they have titles. I also took the text that I thought was in the figure legend and placed them into the actual legend. I will ask the bot to regenerate the pdf to make sure the formatting works. I can also remove some text from the introduction in a future edit.
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #1762 with the following error:
/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-efe915e61673/lib/whedon.rb:135:in check_fields': Paper YAML header is missing expected fields: tags, authors, affiliations (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-efe915e61673/lib/whedon.rb:87:in
initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-efe915e61673/lib/whedon/processor.rb:36:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-efe915e61673/lib/whedon/processor.rb:36:in
set_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-efe915e61673/bin/whedon:55:in prepare' 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:in invoke_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:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-efe915e61673/bin/whedon:116:in
<top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #1762 with the following error:
Error producing PDF. ! Argument of \caption@ydblarg has an extra }.
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #1762 with the following error:
Error producing PDF. ! Argument of \caption@ydblarg has an extra }.
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
I will leave it there for now and will attempt to shorten the introduction after receiving reviewer feedback.
Hi @luizirber, @peterwc - just checking in on how the reviews are progressing. Do you think you can have comments for @lskatz within the next week or so? Don't hesitate to let me know if you have questions. Thanks!
Working on it this week. I apologize for the delay. Expecting a Friday completion.
Thanks, Peter
On Thu, Oct 10, 2019 at 10:58 AM Charlotte Soneson notifications@github.com wrote:
Hi @luizirber https://github.com/luizirber, @peterwc https://github.com/peterwc - just checking in on how the reviews are progressing. Do you think you can have comments for @lskatz https://github.com/lskatz within the next week or so? Don't hesitate to let me know if you have questions. Thanks!
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Overall this is all very good, thanks @lskatz! Here's some review points:
The install instructions and requirements could have a bit more information, I
had to dig a bit to find proper Perl package names (for use with cpanm
) and
links to quicktree
and mash
.
Also adding that mashtree is available on bioconda!
This is what I ended up doing to install using an Ubuntu docker image and the "Installation from Git" section:
git clone https://github.com/lskatz/mashtree.git
cd mashtree
docker run -it -v $PWD:/mashtree ubuntu:latest /bin/bash
Inside docker (travis config was more useful here): https://github.com/lskatz/mashtree/blob/e9697e7496b5c6a85ae69832189ea8350cacfdfb/.travis.yml
apt update
apt install -y build-essential cpanminus libexpat1-dev wget sqlite3 libsqlite3-dev
cd /mashtree
cpanm -n BioPerl Bio::Sketch::Mash DBD::SQLite DBI Graph::Dijkstra
wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar
tar xf mash-Linux64-v2.2.tar
mv mash-Linux64-v2.2/mash /usr/bin/mash
wget https://github.com/khowe/quicktree/archive/v2.5.zip
tar xf v2.5.tar.gz
cd quicktree-2.5
make
mv quicktree /usr/bin
cd ..
perl Makefile.PL
make test
(see above)
This is missing for using it as a library in Perl, but since the primary form of interaction is through the CLI I think it is OK.
I didn't see it in the README, but you can also create a CONTRIBUTING file (GitHub recognizes it and render the content when a new issue or PR is opened): https://github.blog/2012-09-17-contributing-guidelines/
Most of them are missing DOIs, can you please add them?
Thank you @luizirber ! I am working on addressing these helpful comments. For the references comment, are you asking for me to add DOIs to the references in the paper itself or in the git repo (I can do either or both, just making sure).
@lskatz put the DOIs in the paper.bib file in your repo, when the paper is regenerated by whedon they will be picked up.
Thank you for your comments @luizirber ! I did the following:
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
@csoneson I will continue with my review but I realized that I may be in a gray area for this review. I apologize for not bringing it up sooner. I am a bioinformatics researcher at the CDC, but I work in a different division than @lskatz. I have not been on any papers with him, but I do know him personally. After reading through the ethics guidelines I decided it would be best to ask for waiver before submitting my review. I am impartial and will provide a complete and thorough review if I am granted a waiver.
I will ping the other potential reviewers, @csoneson. I don't anticipate anyone else will have @peterwc's concerns. What is the process for adding them as reviewers?
I also want to point out that yes @peterwc works at CDC, and I work at CDC, but we are in totally different centers and do not work with each other. His center has about 1500 people in it currently, and mine has about 2800 people in it.
@peterwc - thanks a lot for your disclosure. After consideration, and in light of your personal connection with @lskatz, I would actually prefer to try to recruit a different reviewer for this submission; but I would like to thank you for engaging with JOSS and I hope we can get back to you for another review in the future!
@ondovb - would you be interested in reviewing this submission for the Journal of Open Source Software?
"Mashtree: a rapid comparison of whole genome sequence files" GitHub repository: https://github.com/lskatz/mashtree
@csoneson Thank you and please keep me in mind for other opportunities to review. I am still available for this one if things change.
Hi @csoneson if no one responds, can I suggest these other reviewers? I picked them from the JOSS list of potential reviewers.
I'd be happy to conduct a review if needed. 👍
Me too, just send me a note
@whedon remove @peterwc as reviewer
OK, @peterwc is no longer a reviewer
@standage, @greatfireball - that's great, thank you for agreeing to review, it would be great to get your input! I'll add you both as reviewers here, and also add a checklist for each of you in the first post above.
@whedon add @standage as reviewer
OK, @standage is now a reviewer
@whedon add @greatfireball as reviewer
OK, @greatfireball is now a reviewer
* All instructions you suggested have been incorporated. They were very helpful, thank you! However, I switched some details so that it could be installed outside of Docker. Docker at my institution and at many other places is a security risk and so I feel like installation in a home directory is more universal.
Sounds great! I did in docker to avoid having to install a lot of extra packages in my system, but doing a home directory installation is the best path (since many people won't have admin rights to their system).
1. Thank you for the community guidelines suggestion. I added guidelines per your suggestion. 1. I added DOIs and will double check whether @whedon generates the PDF without error momentarily.
This all looks good. Thanks @lskatz!
@csoneson, checklist complete for me.
Thank you @luizirber! And thank you to my new reviewers! I am looking forward to your feedback!
---
title: 'Review of Mashtree: a rapid comparison of whole genome sequence files'
author: Daniel Standage
date: 2019-10-31
---
The authors describe Mashtree, a utility for constructing trees from sequence reads or assemblies using Min-hash sketch distances. Mashtree leverages Mash to compute distances rapidly and efficiently, and QuickTree to build a neighbor-joining tree from the resulting distance matrix. Mashtree supports two modes of operation: a "fast" mode based on a fixed minimum k-mer abundance filter, and an "accurate" mode where the filter is inferred empirically from the k-mer abundance distribution. Mashtree also implements two resampling methods for estimating the confidence of the trees it constructs.
Mashtree provides several features bioinformatics and genomics practitioners will find convenient, including the following.
I have added several comments below for the authors' consideration, but in any case I endorse this submission for publication in JOSS.
TL;DR Conda and from-source installation modes seem to work well. 👍
Mashtree's documentation describes multiple modes of installation/execution, including Bioconda, Docker, CPAN, and from the source code distribution. Installing from Bioconda on my OS X system was painless, although I was skeptical whether this reflected the latest version. Accordingly, I also installed from source (latest master
on Githuub) on a fresh Ubuntu VM. This process was also fairly straightforward, although I do have a couple comments.
export PERL5LIB=$PERL5LIB:$HOME/lib/perl5
for configuring a Perl environment in your home directory. I'm not sure whether I missed a step, but initially Mashtree couldn't find the requisite libraries I had just installed. After tinkering for a bit, I was able to finally able to get it to work by adding $HOME/perl5/lib/perl5
to the PERL5LIB
variable. Although not necessary for this review, I suggest that the authors try the installation procedures verbatim on a fresh Linux VM and update the documentation if/as needed.perl5/
instance somewhere (and setting PERL5LIB
appropriately) would work, although I'm not 100% certain I could go back later to track down and remove all library installation artifacts. I also suspect that installing Mashtree in a dedicated Conda environment (to handle all prerequisites) and then running Mashtree directly from a git clone of the latest source would also work. NOTE: This isn't a critique of Mashtree, nor even a firm suggestion to the authors necessarily. I just wanted to point out a potential use case for their consideration.TL;DR CI GOOD 👍, MOAR PR!
The Mashtree repository includes an automated test suite, which is executed frequently in a Contintuous Integration (CI) environment. Potential users of Mashtree can be confident that bugs will be identified early and often, and hopefully most will be addressed before stable releases are published.
Pull requests and CI have been used to review 3rd-party (and possibly internal/collaborator) contributions. I'd suggest that the corresponding author consider using pull requests more routinely—i.e., for all non-trivial updates to the repository. Even for projects where I am the sole active contributor, I have found value in providing a summary and description of each update, linking to relevant issue threads as necessary, and waiting to merge the pull request until the CI build passes.
@csoneson, this completes my review of Mashtree.
@lskatz, if you have any comments or questions, feel free to keep the conversation going here or on the Mashtree issue tracker—just @ me! 😎
@csoneson, this completes my review of Mashtree.
@standage - thanks for this!
Thank you @standage for that wonderful review! To address one concern, I think that the issue might have been that I did not have a complete cpanm
command, when I should have had -l ~
in there. In other words, it should fix where the libraries should install to, $HOME/lib/perl5. So now one of the lines in INSTALL.md now reads as
cpanm -l ~ --notest BioPerl Bio::Sketch::Mash DBD::SQLite DBI Graph::Dijkstra
Fixed in 71f7470
@greatfireball - did you have a chance to look at this submission?
Submitting author: @lskatz (Lee Katz) Repository: https://github.com/lskatz/mashtree Version: v1.0 Editor: @csoneson Reviewers: @luizirber, @standage Archive: 10.5281/zenodo.3568386
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@luizirber & @peterwc, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
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✨ Please try and complete your review in the next two weeks ✨
Review checklist for @luizirber
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
Review checklist for @standage
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper