On Sun, 26 Aug 2018, Michael Bunnemeyer wrote:
I am unable to use Samtools at present. Each time I try, there is an error stating: "HTSlib development files not found”. This occurs despite the fact that HTSlib- development/INSTALL directory is on the same hard drive. Now several other commands are not found. I have attached two files illustrating the problem.
It looks like you're trying to build the samtools tar file, is that correct? The release tar file includes a copy of htslib, so you shouldn't need it separately.
It's likely that the problem is caused by the space in the path to the location where you unpacked samtools (/Volumes/Seagate 6TB/samtools-1.9). Samtools' build scripts are unlikely to work with spaces in path names. If you can rename that volume to something without a space in it you may find the build works better.
It also looks like you downloaded htslib as a zip file from GitHub. If samtools doesn't find a copy of htslib in its own directory (as supplied with the tar file) it will look in `../htslib`. Try renaming your copy of htslib from 'htslib-develop' to 'htslib' to see if that fixes the problem.
Finally, you should read (rather than try to run) the INSTALL file for information on how to build the package.
Rob Davies [email protected] The Sanger Institute http://www.sanger.ac.uk/ Hinxton, Cambs., Tel. +44 (1223) 834244 CB10 1SA, U.K. Fax. +44 (1223) 494919 --The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
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