fqtools
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Does not build per instructions, missing sam.h file.
Following the instructions on the main page:
git clone https://github.com/alastair-droop/fqtools
cd fqtools/
git clone https://github.com/samtools/htslib
cd htslib/
autoheader
autoconf
./configure
make
make install
cd ..
make
Fails at the last step with:
In file included from src/fqprocess_view.c:14:0: src/fqheader.h:22:10: fatal error: sam.h: No such file or directory #include <sam.h>
I do not find a sam.h definition in htslib. I do however find a sam.h definition with in the separate samtools project. However if I modify for the Makefile to use that location as well I receive an error about too many parameters:
In file included from ../samtools-1.10/sam.h:29:0, from src/fqheader.h:22, from src/fqfile.c:14: src/fqfile.c: In function ‘fqfile_open_read_file_bam’: ../samtools-1.10/bam.h:209:22: error: too many arguments to function ‘samtools_sam_open’ #define sam_open samtools_sam_open
Could this be because samtools htslib etc. are now separately maintained projects?
I had the same issue, but I found sam.h
file inside ./htslib/htslib
folder.
Inside src/fqheader.h
, I changed the include statement from
#include <sam.h>
to
#include "htslib/sam.h"
then I could run make
successfully.
I followed above advice from bug1303 and managed to build fqtools
, however running fqtool brings me an error:
fqtools: error while loading shared libraries: libhts.so.3: cannot open shared object file: No such file or directory
libhts.so & libhts.so.3 I added to LD_LIBRARY_PATH:
>echo $LD_LIBRARY_PATH: /usr/local/lib/libhts.so:/usr/local/lib/libhts.so.3
what could be the problem? thanks.
Hi @vokuryshev
Try to add the folder rather than the file:
export LD_LIBRARY_PATH=/usr/local/lib
This fixed it for me.