Comments (3)
Try version 1.2.
Outlook for Android
On Mon, Jul 25, 2016 at 11:21 AM +0800, "Lachlan Musicman" [email protected] wrote:
Every attempt to ./INSTALL fails with this error:
g++ -L/config/binaries/htslib/1.3.1/ -Wl,-rpath /config/binaries/htslib/1.3.1//lib 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
/usr/bin/ld: cannot find -lhts
collect2: error: ld returned 1 exit status
make[1]: *** [pindel] Error 1
make[1]: Leaving directory `/config/source/pindel/src'
make: *** [pindel] Error 2INSTALL failed
Possible reasons:
- 'cannot cd to [path]
->the htslib path provided was incorrect- 'cannot find -lbam'
->htslib was not properly compiled/made, in that case, go to the htslib directory and follow the htslib installation instructions
and run 'make'.
Things I have tried:
- first attempt used our samtools installation (/config/binaries/samtools/1.3.1/) failed with above
- installed htslib from .tgz on the github site, failed with same error
- installed htslib from git clone, switched to 1.3.1, failed with the same error
- installed htslib from git clone, back on head, failed with the same error
- edited Makefile.local to put an "=" between rpath and the lib path, removed the extraneous /. Failed with the same error.
Running
ld --verbose -L/config/binaries/htslib/1.3.1/lib/ -lhts
on the command line gets me the error
attempt to open /config/binaries/htslib/1.3.1/lib//libhts.so succeeded
-lhts (/config/binaries/htslib/1.3.1/lib//libhts.so)
(lots of "found libs" msgs removed)
ld: warning: cannot find entry symbol _start; not setting start address
Is there something obvious I'm doing wrong?
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#46
from pindel.
The makefile was broken a while back. Apply the following:
elif [ -d $(HTSLIB)/lib ]; then \
- echo "HTSLIB_LDFLAGS=-L$(HTSLIB) -Wl,-rpath $(HTSLIB)/lib" >> $@; \
+ echo "HTSLIB_LDFLAGS=-L$(HTSLIB)/lib -Wl,-rpath,$(HTSLIB)/lib" >> $@; \
else \
- echo "HTSLIB_LDFLAGS=-L$(HTSLIB) -Wl,-rpath $(HTSLIB)" >> $@; \
+ echo "HTSLIB_LDFLAGS=-L$(HTSLIB) -Wl,-rpath,$(HTSLIB)" >> $@; \
Not sure why $(realpath …)
was previously removed…
from pindel.
You can try the procedure listed in the Dockerfile shown below.
https://github.com/genome/pindel/pull/45/files
from pindel.
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