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[PRE REVIEW]: ORIS: An interactive software tool for prediction of replication origin in prokaryotic genomes #1585

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whedon opened this issue Jul 20, 2019 · 14 comments

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commented Jul 20, 2019

Submitting author: @urmi-21 (Urminder Singh)
Repository: https://github.com/urmi-21/ORIS
Version: v1.0
Editor: Pending
Reviewer: Pending

Author instructions

Thanks for submitting your paper to JOSS @urmi-21. Currently, there isn't an JOSS editor assigned to your paper.

@urmi-21 if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

@whedon whedon added the pre-review label Jul 20, 2019

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commented Jul 20, 2019

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

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

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

What happens now?

This submission is currently in a pre-review state which means we are waiting for an editor to be assigned and for them to find some reviewers for your submission. This may take anything between a few hours to a couple of weeks. Thanks for your patience 😸

You can help the editor by looking at this list of potential reviewers to identify individuals who might be able to review your submission (please start at the bottom of the list). Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here.

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commented Jul 20, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jul 20, 2019

PDF failed to compile for issue #1585 with the following error:

Can't find any papers to compile :-(

@whedon whedon added Java TeX labels Jul 20, 2019

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commented Jul 20, 2019

@whedon generate pdf

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commented Jul 20, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jul 20, 2019

PDF failed to compile for issue #1585 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1585/paper/paper.md): did not find expected key while parsing a block mapping at line 2 column 1 (Psych::SyntaxError) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse_stream'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:325:in parse' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:252:in load'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:473:in block in load_file' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in open'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in load_file' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon.rb:95:in load_yaml'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon.rb:78:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon/processor.rb:36:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/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-5a9319b684e6/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 `

'

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commented Jul 20, 2019

👋 @csoneson - you've been requested as the editor - are you willing to edit this submission?

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commented Jul 20, 2019

👋 @urmi-21 - A fix for the paper compilation issues might be in urmi-21/ORIS#2 Please merge this and see if it fixes the problem, by adding a comment here that says @whedon generate pdf - feel free to iterate

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commented Jul 20, 2019

@whedon generate pdf

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commented Jul 20, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jul 20, 2019

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commented Jul 20, 2019

@danielskatz Thanks for the suggesting the fix in paper.md. The compiled pdf looks good to me.

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commented Jul 20, 2019

While we are in the process of assigning an editor, you might suggestion some possible reviewers, either from this list (please start at the bottom of the list) or elsewhere, who might be able to review your submission. Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here.

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commented Jul 20, 2019

I would like to suggest the following reviewers: @holtgrewe @jdeligt
I hope my submission is appropriate for them to review.

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