shell-genomics

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I've noticed there are some inconsistencies in the instructions for Windows users across the course around the usage of GitBash/PuTTY.

On the setup page, Git Bash is now the first 'recommended' software and PuTTY is down as 'alternative' but then going through the course the Windows-specific steps are written for PuTTY (e.g. the PSCP section in 05-writing-scripts, & this is also an issue in the Cloud section of the genomics course but that's in a separate repository).

Obviously, one of the advantages of Git Bash is that they will mainly be able to follow the UNIX instructions but this doesn't seem to be explained anywhere and will lead to confusion when they try and follow the Windows specific steps if not covered by the instructors.

I'm not sure where the maintainers stand r.e. the recommendations of Git Bash / PuTTY on this course. I personally prefer Git Bash but I feel that as long as the instructions are updated to avoid confusion the PuTTY specific instructions should stay for those that are required to use PuTTY.

Not suggesting any particular direction. In my experience PuTTY has been helpful because it does not require installation (unlike Gitbash or Windows Linux subsystem). This can be useful since sometimes learners have not done pre-installation instructions or lack permissions on their machines. Users are quickly on the remote instance anyway so the subsequent use of Linux shell is handled well there.

This is Tommy and I am serving as the chair of the genomic curriculum advisor committee. The Committee met and discussed it.

PuTTY seems to be a good backup if Git Bash won't install, concern in this issue is that there is some back and forth for the instructions. For consistency, it is better to stick with Git Bash but PuTTY as extra instruction/alternative.

As @JasonJWilliamsNY said, we are not suggesting any particular direction, we are just sharing our experience.

Thanks, all the maintainers for your hard work!

+1 to this issue. The problem still stands: section 05 talks about "the same suite of tools as the PuTTY program we have been using to connect", but this is wrong, as most people will have installed gitbash and will be confused by this statement. And as an instructor, I'm not a Windows user and don't know how to do that with git bash (does it have scp? if so that makes it easy).