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
I get the following error message:
path is now: /mnt/raid/Resources/Software/htslib/ make -C src pindel make: 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: *** [pindel] Error 1 make: 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 email@example.com
I can't find references to this error online, would anyone be able to offer advice?