Issues installing Pindel from git

Issues installing Pindel from git


I’m currently attempting to install Pindel on my ubuntu machine (16.04 server), but have been having issues with running the ./INSTALL file.

The ./INSTALL file takes the path to htslib as an argument, so I also installed htslib from git with

git clone
sudo make install

which compiled without any errors in the output. But when I run the pindel install file as

./INSTALL ../htslib/

I get the following error message:

path is now: /mnt/raid/Resources/Software/htslib/ make -C src pindel

make[1]: Entering directory '/mnt/raid/Resources/Software/pindel/src'

g++  -L/mnt/raid/Resources/Software/samtools-1.3.1/ -Wl,-rpath

/mnt/raid/Resources/Software/samtools-1.3.1/ pindel.o reader.o

reporter.o searcher.o parameter.o refreader.o control_state.o

search_deletions_nt.o search_inversions.o search_inversions_nt.o

bam2depth.o search_tandem_duplications.o

search_tandem_duplications_nt.o output_sorter.o farend_searcher.o

search_variant.o searchshortinsertions.o searchdeletions.o

output_file_data.o bddata.o shifted_vector.o read_buffer.o

line_reader.o ifstream_line_reader.o gz_line_reader.o

pindel_read_reader.o user_defined_settings.o fn_parameters.o   logstream.o search_MEI_util.o search_MEI.o assembly.o genotyping.o -O3

-fopenmp -lhts -lm -lz -o pindel reader.o: In function `ks_shuffle_uint32_t(unsigned long, unsigned int*)':

/mnt/raid/Resources/Software/pindel/src/reader.cpp:67: undefined

reference to `hts_drand48()' collect2: error: ld returned 1 exit

status Makefile:36: recipe for target 'pindel' failed make[1]: ***

[pindel] Error 1 make[1]: Leaving directory

'/mnt/raid/Resources/Software/pindel/src' Makefile:12: recipe for

target 'pindel' failed make: *** [pindel] Error 2

mv: cannot stat 'src/pindel': No such file or directory mv: cannot

stat 'src/pindel2vcf': No such file or directory mv: cannot stat

'src/sam2pindel': No such file or directory mv: cannot stat

'src/pindel2vcf4tcga': No such file or directory

Pindel successfully compiled. The pindel executable can be found in this directory.

You can test pindel with the example files in the demo directory; example commands are given in the RUNME in that directory.

For help and background information, see the pindel wiki and its FAQ on as well as the FAQ file in the Pindel root directory (the same directory as this INSTALL script is located) or contact us on

I can’t find references to this error online, would anyone be able to offer advice?

software error



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