Issues installing Pindel from git

Question

[jsneaththompson]

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 [e-mail]

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

[GenoMax]

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.

[Edmond]

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

[GenoMax]

Install using conda. Instructions for installing conda (LINK).

Then do: https://anaconda.org/bioconda/pindel

[Edmond]

A different way to install pindel is via git. https://github.com/xjtu-omics/pindel from this repo. IT works ! and you doesn't need conda

Answer 1

[jsneaththompson]

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.

[ATpoint]

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