cannot install with htslib support

lidaof commented 3 years ago

Hi there,

I am trying to install v3.1.2 to our Ubuntu 16.04 system, get an error below:

g++ -std=c++11 -DHAVE_CONFIG_H -I.   -I/opt/apps/htslib/1.3.1/htslib  -O3 -MT htslib_wrapper_deprecated.o -MD -MP -MF .deps/htslib_wrapper_deprecated.Tpo -c -o htslib_wrapper_deprecated.o htslib_wrapper_deprecated.cpp
In file included from htslib_wrapper_deprecated.cpp:25:0:
htslib_wrapper_deprecated.hpp:31:24: fatal error: htslib/sam.h: No such file or directory

while the file sam.h is there:

$ ls /opt/apps/htslib/1.3.1/htslib
bgzf.h  cram.h  faidx.h  hfile.h  hts_defs.h  hts.h  kbitset.h  kfunc.h  khash.h  khash_str2int.h  klist.h  knetfile.h  kseq.h  ksort.h  kstring.h  regidx.h  sam.h  synced_bcf_reader.h  tbx.h  vcf.h  vcf_sweep.h  vcfutils.h

can anyone suggest how to fix this? thanks in advance.

lidaof commented 3 years ago

my bad....change -I/opt/apps/htslib/1.3.1/ fix this...sorry!

andrewdavidsmith commented 3 years ago

Just about to suggest that. Thanks for trying preseq!

On Feb 13, 2021, at 4:00 PM, Daofeng Li notifications@github.com wrote:

my bad....change -I/opt/apps/htslib/1.3.1/ fix this...sorry!

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lidaof commented 3 years ago

thanks @andrewdavidsmith !

One minor issue is that I am pretty sure I downloaded 3.1.2, after install it shows 3.1.1 :)

$ preseq 
preseq:  a program for analyzing library complexity
Version: 3.1.1

Usage:   preseq <command> [OPTIONS]

<command>: c_curve    generate complexity curve for a library
           lc_extrap  predict the yield for future experiments
           gc_extrap  predict genome coverage low input
                      sequencing experiments
           bound_pop  lower bound on population size
           pop_size   estimate number of unique species

smithlabcode / preseq

cannot install with htslib support #53