Entering edit mode
6.4 years ago
csjlee08
▴
10
Hi, I'm trying to utilize Platypus and am having issues with the build step.
greg@Genomics:/media/greg/Overflow/fastgbs/fastgbsfile/Platypus_0.8.1$ ./buildPlatypus.sh
Building Platypus
running build
running build_py
running build
running build_py
running build
running build_py
running build
running build_py
running build
running build_py
running build
running build_py
running build
running build_py
running build
running build_py
running build
running build_ext
building 'htslibWrapper' extension
x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c htslibWrapper.c -o build/temp.linux-x86_64-2.7/htslibWrapper.o -msse2 -msse3 -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC
In file included from htslib/hts.h:35:0,
from htslibWrapper.c:244:
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/htslibWrapper.o -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
Setup failed. Check previous lines for errors
libhts is missing:
have you done everything below ?
https://github.com/andyrimmer/Platypus
I installed Platypus and HTSlib to the path: /media/greg/Overflow/fastgbs/fastgbsfiles
This is the recommended action:
Therefore I tried first, and then re-run:
Still have same error.
what is the output of
?
greg@Genomics:/media/greg/Overflow/fastgbs/fastgbsfile$ find ${LD_LIBRARY_PATH} -name "*.so" find: `/media/Users/greg/Overflow/fastgbs/fastgbsfile/htslib-1.6/lib': No such file or directory
your LD_LIBRARY_PATH is wrong.
New error: Search the variants with platypus Traceback (most recent call last): File "Platypus.py", line 9, in <module> import runner ImportError: No module named runner