Pindel build fails every time on htslib

[lachlansimpson]

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 2

INSTALL failed
Possible reasons:

1. 'cannot cd to [path]
   ->the htslib path provided was incorrect
2. '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?

[liangkaiye]

Try version 1.2.

Outlook for Android

On Mon, Jul 25, 2016 at 11:21 AM +0800, "Lachlan Musicman" notifications@github.com 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 2

INSTALL failed
Possible reasons:

1. 'cannot cd to [path]
   ->the htslib path provided was incorrect
2. '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

[jmarshall]

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…

[sleongmgi]

You can try the procedure listed in the Dockerfile shown below.

https://github.com/genome/pindel/pull/45/files