Hello,
I'm trying to install samtools 1.3 on my ubuntu instance. When I try "make" it get the following error
I have previously installed samtools using "apt-get" pre-compiled binary, but that is such an old version, I would like to get the latest version of samtools 1.3
Could anyone help me figure out how to fix this problem ?
> ubuntu@ubuntu:~/Documents/software/samtools-1.3$ make
Makefile:99: config.mk: No such file or directory
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_index.o bam_index.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_plcmd.o bam_plcmd.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o sam_view.o sam_view.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_cat.o bam_cat.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_md.o bam_md.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_reheader.o bam_reheader.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_sort.o bam_sort.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bedidx.o bedidx.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o kprobaln.o kprobaln.c
kprobaln.c: In function ‘kpa_glocal’:
kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
^
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_rmdup.o bam_rmdup.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_rmdupse.o bam_rmdupse.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_mate.o bam_mate.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_stat.o bam_stat.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_color.o bam_color.c
echo '#define SAMTOOLS_VERSION "1.3"' > version.h
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bamtk.o bamtk.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam2bcf.o bam2bcf.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam2bcf_indel.o bam2bcf_indel.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o errmod.o errmod.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o sample.o sample.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o sam_opts.o sam_opts.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o cut_target.o cut_target.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o phase.o phase.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam2depth.o bam2depth.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o padding.o padding.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bedcov.o bedcov.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bamshuf.o bamshuf.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o faidx.o faidx.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o dict.o dict.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o stats.o stats.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o stats_isize.o stats_isize.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_flags.o bam_flags.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_split.o bam_split.c
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_tview.o bam_tview.c
echo '/* Basic config.h generated by Makefile */' > config.h
echo '#define HAVE_CURSES' >> config.h
echo '#define HAVE_CURSES_H' >> config.h
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_tview_curses.o bam_tview_curses.c
bam_tview_curses.c:41:20: fatal error: curses.h: No such file or directory
compilation terminated.
Makefile:130: recipe for target 'bam_tview_curses.o' failed
make: *** [bam_tview_curses.o] Error 1**
Here are the steps I followed to fix it. Hope this is helpful to others