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blahah / transrate

Understand your transcriptome assembly
http://hibberdlab.com/transrate
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`terminal_columns': undefined method `winsize' for nil:NilClass #216

Open antonkulaga opened 6 years ago

antonkulaga commented 6 years ago

When I install transrate and run transrate command I get misterious

`terminal_columns': undefined method `winsize' for nil:NilClass

here is the docker file content, so you can reproduce it:

FROM ruby:2.2.8

MAINTAINER Anton Kulaga <antonkulaga@gmail.com>

RUN apt-get update && \
 apt-get upgrade -y && \
 apt-get install -y cmake zip wget gcc git build-essential

RUN gem install transrate
RUN transrate --install-deps all

RUN mkdir /data
WORKDIR /data

CMD ["transrate"]
antonkulaga commented 6 years ago

@blahah any updates?

dpryan79 commented 4 years ago

For the bioconda recipe and biocontainer I've needed to disable the chunk of code that checks the console size before printing the banner https://github.com/bioconda/bioconda-recipes/pull/18581/files

This solves the issue, though it'd probably be better to simply not bother with the banner. Interestingly, without patching it runs without printing the transrate banner outside of the docker container but in the CI environment, so it seems like the io-container ruby gem needs something that's just not in minimal docker containers.

blahah commented 4 years ago

@dpryan79 do you think it's the case that we should just disable the banner stuff to maximise compatibility? Happy to push small fixes if I can.

dpryan79 commented 4 years ago

@blahah yeah, that'd be the path of least resistance. Just print a small banner with simple print functions if you really want to.

blahah commented 4 years ago

So much for trying to add a little flare to the day of bioinformaticians :joy:

OK. I'll carve out the banner (everything with colours) and leave it plain. Usability and composability do more social good than fun I suppose.