Question: cygwin error when i try to install platypus (variant caller)
0
gravatar for reza
2.7 years ago by
reza210
Iran
reza210 wrote:

when i try to install platypus and samtools on cygwin, i get below error:

htslibWrapper.c:243:25: fatal error: htslib/bgzf.h: No such file or directory compilation terminated. error: command 'gcc' failed with exit status 1

Setup failed. Check previous lines for errors

what is htslib/bgzf? if i install mentioned programs on linux, i'll get same errors?

snp software error • 1.2k views
ADD COMMENTlink written 2.7 years ago by reza210

Can you elaborate on how you were installing those tools? What did you download, which commands did you execute?

ADD REPLYlink written 2.7 years ago by WouterDeCoster38k

htslib can be downloaded here. See INSTALL file for build instructions.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by genomax65k

i installed htslib using below commands:

./configure

make

make install

and then tried to install platypus and now i getting following error

htslibWrapper.c:1:0: warning: -fPIC ignored for target (all code is position independent) /* Generated by Cython 0.21.1 */ ^ gcc -shared -Wl,--enable-auto-image-base -L. build/temp.cygwin-2.5.2-x86_64-2.7/htslibWrapper.o -L/usr/lib/python2.7

/config -L/usr/lib -lhts -lpython2.7 -o build/lib.cygwin-2.5.2-x86_64-2.7/htslibWrapper.dll

/usr/lib/gcc/x86_64-pc-cygwin/5.4.0/../../../../x86_64-pc-cygwin/bin/ld: cannot find -lhts collect2: error: ld returned 1 exit status

error: command 'gcc' failed with exit status 1

Setup failed. Check previous lines for errors

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by reza210
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