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cygwin error when i try to install platypus (variant caller)

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?

software error snp
• 3,040 views • link
written by reza reza

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

• 1 views • link
written by WouterDeCoster WouterDeCoster

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

• 1 views • link
written by GenoMax GenoMax

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

• 1 views • link
written by reza reza

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