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biohackrxiv / bhxiv-gen-pdf

Generate a PDF for BioHackrXiv.org
GNU General Public License v3.0
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Run via docker doesn't work? #13

Closed bblodfon closed 3 years ago

bblodfon commented 3 years ago

I run the two commands as specified here after cloning the repo, and I got back:

Unknown option --citeproc.
Try pandoc --help for more information.
Failed to generate paper.pdf!

My pandoc includes it though (I think!):

pandoc --version
pandoc 2.12
Compiled with pandoc-types 1.22, texmath 0.12.1.1, skylighting 0.10.4,
citeproc 0.3.0.8, ipynb 0.1.0.1

Any idea what might be causing this?

inutano commented 3 years ago

You meant the two commands below, right?

$ docker build -t biohackrxiv/gen-pdf:local -f docker/Dockerfile .
$ docker run --rm -it -v $(pwd):/work -w /work biohackrxiv/gen-pdf:local gen-pdf /work/example/logic

This will use the Dockerfile here and it specifies to install the pandoc 2.2, though it's a bit old one. Your local pandoc version is not relevant since the process will be completed inside the container.

If you don't edit the Dockerfile, correctly build the image, and run it, you should get this:

$ docker run --rm -it -v $(pwd):/work -w /work biohackrxiv/gen-pdf:local pandoc --version
pandoc 2.2.1
Compiled with pandoc-types 1.17.5.1, texmath 0.11.1, skylighting 0.7.5
Default user data directory: /root/.pandoc
Copyright (C) 2006-2018 John MacFarlane
Web:  http://pandoc.org
This is free software; see the source for copying conditions.
There is no warranty, not even for merchantability or fitness
for a particular purpose.

I've confirmed that I successfully built the container and run the command without error. Could you provide the commands you actually typed?

bblodfon commented 3 years ago

Hi @inutano , thanks for looking at this. I've run exactly the two commands you provided. I did so today as well. Removed all docker images associated with the biohackrxiv/gen-pdf and recreated a new image from scratch. The docker run command resulted in the same error as I displayed in the first message (Unknown option --citeproc.). I ran the other command as well and got the same thing: 

john:~$ docker run --rm -it -v $(pwd):/work -w /work biohackrxiv/gen-pdf:local pandoc --version
pandoc 2.2.1
Compiled with pandoc-types 1.17.5.1, texmath 0.11.1, skylighting 0.7.5
Default user data directory: /root/.pandoc
Copyright (C) 2006-2018 John MacFarlane
Web:  http://pandoc.org
This is free software; see the source for copying conditions.
There is no warranty, not even for merchantability or fitness
for a particular purpose.
bblodfon commented 3 years ago

Updated pandoc looks like this now:

docker run --rm -it -v $(pwd):/work -w /work biohackrxiv/gen-pdf:local pandoc --version
pandoc 2.16.1
Compiled with pandoc-types 1.22.1, texmath 0.12.3.2, skylighting 0.12.1,
citeproc 0.6, ipynb 0.1.0.2
User data directory: /root/.local/share/pandoc
Copyright (C) 2006-2021 John MacFarlane. Web:  https://pandoc.org
This is free software; see the source for copying conditions. There is no
warranty, not even for merchantability or fitness for a particular purpose.
bblodfon commented 3 years ago

PR #17 solved this