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tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
GNU General Public License v2.0
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symbolic links #203

Closed dwilkin799 closed 5 years ago

dwilkin799 commented 6 years ago

Dear Pr Seemann, I managed to get the latest version of nullarbor working on an Ubuntu 18 VM, which I run through VirtualBox. Just thought I would raise one potential issue here. I notice that you have favoured the use of symbolic links over copying files in nullarbor 2 - good idea to save on disk usage. However, some virtual machines (it may be VirtualBox specific, I haven't checked) do not allow you to create symbolic links on shared drives.... and I favour the use of shared data drives when using a VM in order to keep the VM image file small. I managed to get around this on my system simply by replacing the use of 'ln' with 'cp', but I can't find them all - specifically if you do not call "--trim", I'm not sure where the symbolic links to the reads files are created.

This was the main problem I encountered getting it installed, and I did each of the dependencies individually as local installs with shortcuts in usr/bin... so I was expecting more issues - so fantastic work on the update of nullarbor! this is a massive improvement over nullarbor1.

tseemann commented 6 years ago

Yes i have had a few msgs about symlink problems. I didn't anticipate that so many people were using CIFS volumes or shared Windows/Mac drives, especially given Nullarbor takes a long time to run.

I am thinking of switching it back to copying files.

Also thank you for the positive feedback. I'm impressed you did manual install!

If you are using Windows 10 you can use the "Linux subsystem" (which is Ubuntu).

Also, in a VM you should use Conda or Brew to install all the software for you?

tseemann commented 5 years ago

@dwilkin799 you can now use nullarbor.pl --link-cmd 'cp' or make LINK="cp"