This is a test version of Biostars. For the public version, visit https://www.biostars.org.
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 https://github.com/samtools/htslib
make
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 gmt.genome.wustl.edu/packages/pindel as well as the FAQ file in the Pindel root directory (the same directory as this INSTALL script is located) or contact us on kaiye@xjtu.edu.cn

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

software error pindel
• 5,477 views • link
updated by Edmond • Edmond • written by jsneaththompson jsneaththompson

Can you confirm that you have a bin directory in ../htslib and it has three executable files in it? Also try providing full path for the htslib directory instead of the relative one when doing pindel install.

• 0 views • link
written by GenoMax GenoMax

Hello, I am having the same issue after 3.9 years. Can any one help me please ?

• 0 views • link
written by Edmond • Edmond

1 answer

Turned out to be an issue with a recent change to htslib where hts_drand48() was defined for C, but not for C++. The fix should be implemented in htslib soon, or the ksort.h file in htslib can be altered as shown in the link above.

• 0 views • link
written by jsneaththompson jsneaththompson

Thanks for posting the solution. Most people quit once the issue is solved, but forget to update their post in order to help others!

• 0 views • link
written by ATpoint ATpoint

Log in to answer this question.

More posts like this