Question: Issues installing Pindel from git
0
gravatar for jsneaththompson
10 months ago by
jsneaththompson50 wrote:

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?

pindel software error • 703 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by jsneaththompson50
1

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.

ADD REPLYlink modified 10 months ago • written 10 months ago by genomax55k
2
gravatar for jsneaththompson
10 months ago by
jsneaththompson50 wrote:

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.

ADD COMMENTlink written 10 months ago by jsneaththompson50

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

ADD REPLYlink written 10 months ago by ATpoint7.5k
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