command 'x86_64-linux-gnu-gcc' failed. Compilation failed

[NVSmirnova]

I cannot install Platypus. There were mistakes with htslib (though I have made all steps from your readme).

I work in docker-container build from Ubuntu 14.04. Inside the container I made commands from the attached file. In brief, I install cython, htslib-1.9, then made $git clone this repository and in /Platypus made $make.

I got this error:

skipping 'cython/htslibWrapper.c' Cython extension (up-to-date) building 'htslibWrapper' extension x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/usr/include/python2.7 -c cython/htslibWrapper.c -o build/temp.linux-x86_64-2.7/cython/htslibWrapper.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function cython/htslibWrapper.c:356:25: fatal error: htslib/bgzf.h: No such file or directory

include "htslib/bgzf.h"

^ compilation terminated. error: command 'x86_64-linux-gnu-gcc' failed with exit status 1 make: *** [platypus] Error 1)

I copied htslib-1.9 folder everywhere (really in every directory like /Platypus; /Platypus/src/; /Platypus/htslib; /Platypus/src/htslib; I changed LD_LIBRARY_PATH="$SOFT/Platypus/src/htslib/lib:$LD_LIBRARY_PATH" \ LIBRARY_PATH="$SOFT/Platypus/src/htslib/lib" \ C_INCLUDE_PATH="$SOFT/Platypus/src/htslib/include"

the first mistake is gone now, but still I have this mistake after $make

building 'htslibWrapper' extension x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/usr/include/python2.7 -c cython/htslibWrapper.c -o build/temp.linux-x86_64-2.7/cython/htslibWrapper.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function In file included from ./htslib/hts.h:35:0, from cython/htslibWrapper.c:357: ./htslib/hts_log.h:52:6: warning: function declaration isn't a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/cython/htslibWrapper.o -L./lib -lhts -o build/lib.linux-x86_64-2.7/htslibWrapper.so /usr/bin/ld: cannot find -lhts collect2: error: ld returned 1 exit status error: command 'x86_64-linux-gnu-gcc' failed with exit status 1 make: *** [platypus] Error 1

commands_inside_docker.txt

[Ehiole]

Try using htslib-1.3. I couldn't get it to work for me with htslib-1.9, there was always some *.so file that it could not find...

[NVSmirnova]

Try using htslib-1.3. I couldn't get it to work for me with htslib-1.9, there was always some *.so file that it could not find...

thanks, I will try it =)