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

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

Hi,

I am trying to instal samtools on MacBook Pro using this:
tar -xjvf samtools.tar.bz2
cd samtools-1.7
make
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?
thanks

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

Join Date: Jul 2008
Posts: 146
Default

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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