Question: Platypus install - build problems
0
gravatar for csjlee08
20 months ago by
csjlee0810
csjlee0810 wrote:

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

ADD COMMENTlink modified 20 months ago by Pierre Lindenbaum122k • written 20 months ago by csjlee0810

/usr/bin/ld: cannot find -lhts

libhts is missing:

have you done everything below ?

https://github.com/andyrimmer/Platypus

Platypus requires HTSlib 1.2.1 or greater. HTSlib can be downloaded from the HTSlib Web site.

To build and install HTSlib, cd into HTSlib source and type make install. This will install HTSlib under /usr/local/ (see note below). To install HTSlib in any other directory use make install prefix=/path/to/dir.

NOTE: HTSlib should be installed in a standard location (e.g. /usr/local/). If not installed in a standard location, you will need to set your library paths:

...

ADD REPLYlink written 20 months ago by Pierre Lindenbaum122k

I installed Platypus and HTSlib to the path: /media/greg/Overflow/fastgbs/fastgbsfiles

This is the recommended action:

export C_INCLUDE_PATH=/path/to/dir/include
export LIBRARY_PATH=/path/to/dir/lib (only for making)
export LD_LIBRARY_PATH=/path/to/dir/lib

Therefore I tried first, and then re-run:

export C_INCLUDE_PATH=/media/greg/Overflow/fastgbs/fastgbsfiles/htslib-1.6/include
export LIBRARY_PATH=/media/greg/Overflow/fastgbs/fastgbsfiles/htslib-1.6/lib 
export LD_LIBRARY_PATH=/media/greg/Overflow/fastgbs/fastgbsfiles/htslib-1.6/lib

Still have same error.

ADD REPLYlink modified 20 months ago by Pierre Lindenbaum122k • written 20 months ago by csjlee0810

what is the output of

find ${LD_LIBRARY_PATH} -name "*.so"

?

ADD REPLYlink written 20 months ago by Pierre Lindenbaum122k

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

ADD REPLYlink written 20 months ago by csjlee0810
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
ADD REPLYlink modified 20 months ago by genomax70k • written 20 months ago by csjlee0810

: No such file or directory

your LD_LIBRARY_PATH is wrong.

ADD REPLYlink written 20 months ago by Pierre Lindenbaum122k

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

ADD REPLYlink written 20 months ago by csjlee0810
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