bam2wig compilation

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katharina
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bam2wig compilation

Post by katharina »

Originally posted in the old forum by jfk on 10.03.2014 - 16:40
Dear all,
while trying to compile I am running into some issues with samtools. I cloned samtools from github. Samtools run fine, but while trying to compile bam2wig from AUGUSTUS auxprogs it is missing folders/libraries, e.g. below. Did I clone the wrong samtools? In https://github.com/samtools/htslib, I as well cannot find a bgzf.h?

Code: Select all

jfk@undecan:$ make
gcc -g -Wall -O2 -I/home/software/src/samtool/samtools/ -I. -c bam2wig.c -o bam2wig.o -I/home/software/src/samtool/samtools/ -I.
In file included from /home/software/src/samtool/samtools/sam.h:5:0,
                 from bam2wig.c:18:
/home/software/src/samtool/samtools/bam.h:54:25: fatal error: htslib/bgzf.h: No such file or directory
compilation terminated.
make: *** [bam2wig.o] Error 1
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katharina
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Re: bam2wig compilation

Post by katharina »

by jfk on 11.03.2014 - 15:56
Rephrase
Which samtools do you use to compile bam2wig? Can anyone supply me with a working source?
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Re: bam2wig compilation

Post by katharina »

by katharina on 18.03.2014 - 14:24
I use samtools Version: 0.1.7 (r510) (available from http://samtools.sourceforge.net/)
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