Pindel does not compile with samtools from git

[jvhaarst]

I am trying to install Pindel, using the following steps:

First compile samtools:

mkdir /mnt/nexenta/haars001/projects/yeast_evolution/ && cd $_
git clone https://github.com/samtools/samtools.git && git clone https://github.com/samtools/htslib.git && cd samtools && make && ./samtools --version && cd -

Which nicely returns samtools 0.2.0-rc6.

Then try to install Pindel:

git clone https://github.com/genome/pindel && cd pindel && ./INSTALL /mnt/nexenta/haars001/projects/yeast_evolution/samtools/

With that I get a lot of errors (see below), as khash.h can't be found, although it is there (in htslib) :

jvh@assembly:/mnt/nexenta/haars001/projects/yeast_evolution$ find . -name khash.h
./htslib/htslib/khash.h

If I use the latest samtools (0.1.19) from Sourceforge, Pindel compiles fine.

---

Compilation errors :

jvh@assembly:/mnt/nexenta/haars001/projects/yeast_evolution$ git clone https://github.com/genome/pindel && cd pindel && ./INSTALL /mnt/nexenta/haars001/projects/yeast_evolution/samtools/
Cloning into 'pindel'...
remote: Reusing existing pack: 3760, done.
remote: Total 3760 (delta 0), reused 0 (delta 0)
Receiving objects: 100% (3760/3760), 81.82 MiB | 777 KiB/s, done.
Resolving deltas: 100% (2830/2830), done.
Checking out files: 100% (161/161), done.
path is now: /mnt/nexenta/haars001/projects/yeast_evolution/samtools/
WARNING: Created default Makefile.local; please review it.
make: *** No rule to make target `Makefile.local', needed by `pindel'.  Stop.
If this is the first time you're running this install script please wait a moment as we create the Makefile.local
make -C src pindel
make[1]: Entering directory `/mnt/nexenta/haars001/projects/yeast_evolution/pindel/src'
In file included from control_state.h:29:0,
                 from genotyping.h:21,
                 from genotyping.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from assembly.h:21,
                 from assembly.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from search_MEI.cpp:15:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from search_MEI_util.h:26:0,
                 from search_MEI_util.cpp:21:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from fn_parameters.cpp:10:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from user_defined_settings.cpp:9:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from pindel_read_reader.h:13:0,
                 from pindel_read_reader.cpp:9:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from ifstream_line_reader.cpp:3:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from read_buffer.h:13:0,
                 from read_buffer.cpp:8:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from bddata.h:14,
                 from bddata.cpp:3:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from searchdeletions.cpp:22:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from searchshortinsertions.cpp:22:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from search_variant.cpp:29:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from farend_searcher.cpp:23:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from output_sorter.cpp:27:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reporter.h:27:0,
                 from search_tandem_duplications_nt.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reporter.h:27:0,
                 from search_tandem_duplications.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from bam2depth.cpp:11:0:
/mnt/nexenta/haars001/projects/yeast_evolution/samtools/bam.h:54:25: fatal error: htslib/bgzf.h: No such file or directory
compilation terminated.
In file included from reporter.h:27:0,
                 from search_inversions_nt.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reporter.h:27:0,
                 from search_inversions.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reporter.h:27:0,
                 from search_deletions_nt.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from control_state.cpp:22:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from refreader.cpp:26:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from searcher.cpp:22:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reporter.cpp:32:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reader.cpp:29:0:
/mnt/nexenta/haars001/projects/yeast_evolution/samtools/bam.h:54:25: fatal error: htslib/bgzf.h: No such file or directory
compilation terminated.
In file included from pindel.cpp:35:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from genotyping.h:21,
                 from genotyping.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from assembly.h:21,
                 from assembly.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from search_MEI.cpp:15:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from search_MEI_util.h:26:0,
                 from search_MEI_util.cpp:21:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from fn_parameters.cpp:10:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from user_defined_settings.cpp:9:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from pindel_read_reader.h:13:0,
                 from pindel_read_reader.cpp:9:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from ifstream_line_reader.cpp:3:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from read_buffer.h:13:0,
                 from read_buffer.cpp:8:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from bddata.h:14,
                 from bddata.cpp:3:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from searchdeletions.cpp:22:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from searchshortinsertions.cpp:22:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from search_variant.cpp:29:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from farend_searcher.cpp:23:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from output_sorter.cpp:27:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reporter.h:27:0,
                 from search_tandem_duplications_nt.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reporter.h:27:0,
                 from search_tandem_duplications.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from bam2depth.cpp:11:0:
/mnt/nexenta/haars001/projects/yeast_evolution/samtools/bam.h:54:25: fatal error: htslib/bgzf.h: No such file or directory
compilation terminated.
In file included from reporter.h:27:0,
                 from search_inversions_nt.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reporter.h:27:0,
                 from search_inversions.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reporter.h:27:0,
                 from search_deletions_nt.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from control_state.cpp:22:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from refreader.cpp:26:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from searcher.cpp:22:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reporter.cpp:32:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reader.cpp:29:0:
/mnt/nexenta/haars001/projects/yeast_evolution/samtools/bam.h:54:25: fatal error: htslib/bgzf.h: No such file or directory
compilation terminated.
In file included from pindel.cpp:35:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
make[1]: Leaving directory `/mnt/nexenta/haars001/projects/yeast_evolution/pindel/src'
make[1]: Entering directory `/mnt/nexenta/haars001/projects/yeast_evolution/pindel/src'
In file included from control_state.h:29:0,
                 from genotyping.h:21,
                 from genotyping.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from assembly.h:21,
                 from assembly.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from search_MEI.cpp:15:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from search_MEI_util.h:26:0,
                 from search_MEI_util.cpp:21:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from fn_parameters.cpp:10:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from user_defined_settings.cpp:9:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from pindel_read_reader.h:13:0,
                 from pindel_read_reader.cpp:9:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from ifstream_line_reader.cpp:3:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from read_buffer.h:13:0,
                 from read_buffer.cpp:8:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from bddata.h:14,
                 from bddata.cpp:3:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from searchdeletions.cpp:22:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from searchshortinsertions.cpp:22:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from search_variant.cpp:29:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from farend_searcher.cpp:23:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from output_sorter.cpp:27:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reporter.h:27:0,
                 from search_tandem_duplications_nt.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reporter.h:27:0,
                 from search_tandem_duplications.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from bam2depth.cpp:11:0:
/mnt/nexenta/haars001/projects/yeast_evolution/samtools/bam.h:54:25: fatal error: htslib/bgzf.h: No such file or directory
compilation terminated.
In file included from reporter.h:27:0,
                 from search_inversions_nt.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reporter.h:27:0,
                 from search_inversions.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reporter.h:27:0,
                 from search_deletions_nt.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from control_state.cpp:22:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from refreader.cpp:26:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from searcher.cpp:22:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reporter.cpp:32:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reader.cpp:29:0:
/mnt/nexenta/haars001/projects/yeast_evolution/samtools/bam.h:54:25: fatal error: htslib/bgzf.h: No such file or directory
compilation terminated.
In file included from pindel.cpp:35:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from genotyping.h:21,
                 from genotyping.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from assembly.h:21,
                 from assembly.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from search_MEI.cpp:15:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from search_MEI_util.h:26:0,
                 from search_MEI_util.cpp:21:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from fn_parameters.cpp:10:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from user_defined_settings.cpp:9:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from pindel_read_reader.h:13:0,
                 from pindel_read_reader.cpp:9:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from ifstream_line_reader.cpp:3:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from read_buffer.h:13:0,
                 from read_buffer.cpp:8:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from bddata.h:14,
                 from bddata.cpp:3:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from searchdeletions.cpp:22:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from searchshortinsertions.cpp:22:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from search_variant.cpp:29:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from farend_searcher.cpp:23:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from output_sorter.cpp:27:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reporter.h:27:0,
                 from search_tandem_duplications_nt.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reporter.h:27:0,
                 from search_tandem_duplications.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from bam2depth.cpp:11:0:
/mnt/nexenta/haars001/projects/yeast_evolution/samtools/bam.h:54:25: fatal error: htslib/bgzf.h: No such file or directory
compilation terminated.
In file included from reporter.h:27:0,
                 from search_inversions_nt.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reporter.h:27:0,
                 from search_inversions.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reporter.h:27:0,
                 from search_deletions_nt.cpp:23:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from control_state.h:29:0,
                 from control_state.cpp:22:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from refreader.cpp:26:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from searcher.cpp:22:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reporter.cpp:32:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
In file included from reader.cpp:29:0:
/mnt/nexenta/haars001/projects/yeast_evolution/samtools/bam.h:54:25: fatal error: htslib/bgzf.h: No such file or directory
compilation terminated.
In file included from pindel.cpp:35:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
g++  -Wall -g -c -O3 -fopenmp -I/mnt/nexenta/haars001/projects/yeast_evolution/samtools/ pindel.cpp -o pindel.o
In file included from pindel.cpp:35:0:
pindel.h:34:19: fatal error: khash.h: No such file or directory
compilation terminated.
make[1]: *** [pindel.o] Error 1
make[1]: Leaving directory `/mnt/nexenta/haars001/projects/yeast_evolution/pindel/src'
make: *** [pindel] Error 2

INSTALL failed
Possible reasons:
1. 'cannot cd to [path]
->the samtools path provided was incorrect
(so '../samtools/' was used instead of '/home/user/samtools/')

2. 'cannot find -lbam'
->samtools was not properly installed, in that case go to the samtools directory
and run 'make'.

For futher help, see the pindel wiki and its FAQ on https://trac.nbic.nl/pindel/wiki/PindelFaq
Or contact us on kye@genome.wustl.edu

[sauloal]

in my case, the path to samtools has to be the full path to the directory containing khash.h

[liangkaiye]

please use samtools 0.18 and earlier.

On Thu, May 29, 2014 at 7:20 AM, Saulo notifications@github.com wrote:

in my case, the path to samtools has to be the full path to the directory
containing khash.h

—
Reply to this email directly or view it on GitHub
#3 (comment).