MacOS: mv: rename BWT_Index/bwt_index to ./bwt_index: Is a directory

[tseemann]

Because MacOS uses a case-insensitive file system, the following fails:

mv: rename BWT_Index/bwt_index to ./bwt_index: Is a directory

Can you call bwt_index MapCaller-index perhaps?

Or have a make install command which uses a PREFIX ?= /usr/local/bin setting and copies to $(PREFIX)/ but I can still do make install PREFIX=$HOME/bin for example.

[hsinnan75]

I don't understand what you mean by "MacOS fails the command." I don't own a Mac PC. I'll try to get one and try on it. BWT_index is modified from BWA. You may use BWT index instead to build reference indexes and use them to run MapCaller.

[tseemann]

On MacOS, the filesystem does not treat upper-case and lower-case differently. On MacOS, sinNAN is the same as sinnan. So you can't put bwt_index in the same folder where the folder BWT_index is, becase they have the same name in MacOS.

One solution is to arrange your code like this:

src
 ↳ MapCaller
 ↳ BWT_index

I think it would be cleaner to have a bin folder and copy the binaries into that, instead of the root folder

bin/
src/
 ↳ MapCaller/
 ↳ BWT_index/
test/

[hsinnan75]

Thanks for the explanation. I've followed your suggestion to rearrange the folder structure.

[tseemann]

I would also put all the MapCaller code in it's own folder

src/
 ↳ MapCaller/
 ↳ BWT_index/
 ↳ htslib/

but not very important.

[tseemann]

Don't forget to tag a new release git tag v0.9.9.7 && git push --tags

[pvanheus]

I made a conda recipe for 0.9.9.6 that works around this problem, so there is now a mapcaller package for MacOS and Linux in bioconda. When you release 0.9.9.7 the package will need to be reworked.

[hsinnan75]

Thank you both for your help.