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Old 02-01-2018, 09:09 AM   #1
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Location: Belfast

Join Date: Feb 2018
Posts: 1
Default Samtools MAC install error


I am trying to instal samtools on MacBook Pro using this:
tar -xjvf samtools.tar.bz2
cd samtools-1.7
sudo make prefix=/usr/local/bin install

The following error message came up:
cram/cram_io.c:61:10: fatal error: 'lzma.h' file not found
#include <lzma.h>
1 error generated.
make[1]: *** [cram/cram_io.o] Error 1
make: *** [htslib-1.7/libhts.a] Error 2
jcsmr-027583ml:samtools-1.7 u1035854$ sudo make prefix=/usr/local/bin install

And after the last line it asked for a password. Which password?
What should I do?

Last edited by Panova; 02-01-2018 at 09:12 AM.
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Old 02-02-2018, 08:58 AM   #2
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Location: Cambridge, UK

Join Date: Jul 2008
Posts: 146

Try running ./configure;make first. Does that work? (Check the output carefully from configure too to see if it works only by dint of removing lzma support entirely!)

If it doesn't, you'll need to install to the lzma dev package; possibly xz-utils-dev or similar? I don't know what it's called on MacOS, but I think the htslib README/INSTALL file explains it all.
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