Variantcaller import error

[Austin Diamond]

I have installed and built Platypus 0_7_4 and got a "Finished building Platypus" on a Ubuntu 12.04 platform.

When I try to run (even the command python Platypus.py callVariants --help) I get the following:

Traceback (most recent call last):
  File "Platypus.py", line 7, in <module>
    import runner
  File "/home/austin/ngs/Platypus_0.7.4/runner.py", line 10, in <module>
    import variantcaller
ImportError: No module named variantcaller

Can you tell me what I need to do now?

I should add that I have very little experience with Linux so it is more than possible I have made a very basic error!


Thank you

Austin

[Andy Rimmer]

Hi Austin,

It looks like something went wrong with the build (despite the 'Finished...' message). Can you remove the directory, unpack it again
from the .tgz file, run the build script and send me the output?

Also can you tell me which Python version you are using?

Kind regards,
Andy

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[Austin Diamond]

Andy

Thanks for your prompt reply.

Python version is 2.7.3

Output:
austin@EMGS-HP-Z400:~/ngs$ tar -xvzf Platypus-latest.tgz
Platypus_0.7.4/
Platypus_0.7.4/extendedoptparse.py
Platypus_0.7.4/setup.py
Platypus_0.7.4/tandem.c
Platypus_0.7.4/align.c
Platypus_0.7.4/align.h
Platypus_0.7.4/variantFilter.c
Platypus_0.7.4/window.py
Platypus_0.7.4/platypusexceptions.py
Platypus_0.7.4/pysam_util.h
Platypus_0.7.4/fastafile.c
Platypus_0.7.4/tabix/
Platypus_0.7.4/tabix/tabix.h
Platypus_0.7.4/tabix/bgzf.h
Platypus_0.7.4/tabix/pysam.h
Platypus_0.7.4/tabix/kseq.h
Platypus_0.7.4/tabix/bgzip.c.pysam.c
Platypus_0.7.4/tabix/bam_endian.h
Platypus_0.7.4/tabix/bgzf.c.pysam.c
Platypus_0.7.4/tabix/knetfile.h
Platypus_0.7.4/tabix/index.c.pysam.c
Platypus_0.7.4/tabix/bedidx.c.pysam.c
Platypus_0.7.4/tabix/ksort.h
Platypus_0.7.4/tabix/kstring.h
Platypus_0.7.4/tabix/knetfile.c.pysam.c
Platypus_0.7.4/tabix/khash.h
Platypus_0.7.4/tabix/kstring.c.pysam.c
Platypus_0.7.4/Platypus.py
Platypus_0.7.4/cerrormodel.c
Platypus_0.7.4/tabix_util.c
Platypus_0.7.4/cpopulation.c
Platypus_0.7.4/runner.py
Platypus_0.7.4/variantutils.py
Platypus_0.7.4/filez.py
Platypus_0.7.4/LICENSE
Platypus_0.7.4/calign.c
Platypus_0.7.4/variant.c
Platypus_0.7.4/chaplotype.c
Platypus_0.7.4/platypusutils.c
Platypus_0.7.4/README.txt
Platypus_0.7.4/variantcaller.c
Platypus_0.7.4/cwindow.c
Platypus_0.7.4/ctabix.c
Platypus_0.7.4/samtoolsWrapper.c
Platypus_0.7.4/assembler.c
Platypus_0.7.4/samtools/
Platypus_0.7.4/samtools/sam_view.c
Platypus_0.7.4/samtools/bedidx.c
Platypus_0.7.4/samtools/sam_header.c
Platypus_0.7.4/samtools/bam_maqcns.h
Platypus_0.7.4/samtools/sam.h
Platypus_0.7.4/samtools/bam.h
Platypus_0.7.4/samtools/bgzf.h
Platypus_0.7.4/samtools/bam_md.c
Platypus_0.7.4/samtools/glf.c
Platypus_0.7.4/samtools/COPYING
Platypus_0.7.4/samtools/glf.h
Platypus_0.7.4/samtools/kprobaln.h
Platypus_0.7.4/samtools/sample.c
Platypus_0.7.4/samtools/kseq.h
Platypus_0.7.4/samtools/bam_endian.h
Platypus_0.7.4/samtools/bam.c
Platypus_0.7.4/samtools/faidx.c
Platypus_0.7.4/samtools/sam.c
Platypus_0.7.4/samtools/knetfile.h
Platypus_0.7.4/samtools/sample.h
Platypus_0.7.4/samtools/kprobaln.c
Platypus_0.7.4/samtools/bgzip.c
Platypus_0.7.4/samtools/bam_aux.c
Platypus_0.7.4/samtools/razf.c
Platypus_0.7.4/samtools/ksort.h
Platypus_0.7.4/samtools/kstring.h
Platypus_0.7.4/samtools/kstring.c
Platypus_0.7.4/samtools/bam_rmdupse.c
Platypus_0.7.4/samtools/kaln.c
Platypus_0.7.4/samtools/kaln.h
Platypus_0.7.4/samtools/bam_cat.c
Platypus_0.7.4/samtools/bgzf.c
Platypus_0.7.4/samtools/faidx.h
Platypus_0.7.4/samtools/bam_import.c
Platypus_0.7.4/samtools/bam_color.c
Platypus_0.7.4/samtools/errmod.c
Platypus_0.7.4/samtools/sam_header.h
Platypus_0.7.4/samtools/klist.h
Platypus_0.7.4/samtools/knetfile.c
Platypus_0.7.4/samtools/bam_reheader.c
Platypus_0.7.4/samtools/khash.h
Platypus_0.7.4/samtools/razf.h
Platypus_0.7.4/samtools/bam_maqcns.c
Platypus_0.7.4/samtools/bam_index.c
Platypus_0.7.4/samtools/errmod.h
Platypus_0.7.4/src/
Platypus_0.7.4/src/pysam/
Platypus_0.7.4/src/pysam/COPYING
Platypus_0.7.4/src/pysam/tabix_util.c
Platypus_0.7.4/src/pysam/ctabix.c
Platypus_0.7.4/src/pysam/TabProxies.c
Platypus_0.7.4/src/variantFilter.pyx
Platypus_0.7.4/src/assembler.pyx
Platypus_0.7.4/src/cpopulation.pyx
Platypus_0.7.4/src/TabProxies.pyx
Platypus_0.7.4/src/TabProxies.pxd
Platypus_0.7.4/src/platypusutils.pyx
Platypus_0.7.4/src/samtoolsWrapper.pyx
Platypus_0.7.4/src/cgenotype.pyx
Platypus_0.7.4/src/chaplotype.pyx
Platypus_0.7.4/src/ctabix.pxd
Platypus_0.7.4/src/calign.pyx
Platypus_0.7.4/src/vcfutils.pyx
Platypus_0.7.4/src/variantcaller.pyx
Platypus_0.7.4/src/cerrormodel.pyx
Platypus_0.7.4/src/variant.pyx
Platypus_0.7.4/src/cwindow.pyx
Platypus_0.7.4/src/fastafile.pyx
Platypus_0.7.4/src/ctabix.pyx
Platypus_0.7.4/pysam_util.c
Platypus_0.7.4/cgenotype.c
Platypus_0.7.4/TabProxies.c
Platypus_0.7.4/pyvcf/
Platypus_0.7.4/pyvcf/filez.pyc
Platypus_0.7.4/pyvcf/vcf-diff.py
Platypus_0.7.4/pyvcf/test.vcf
Platypus_0.7.4/pyvcf/axt2variants.py
Platypus_0.7.4/pyvcf/vcf.py
Platypus_0.7.4/pyvcf/vcf-add-hr.py
Platypus_0.7.4/pyvcf/vcf-mendelian.py
Platypus_0.7.4/pyvcf/filez.py
Platypus_0.7.4/pyvcf/vcf-extract.py
Platypus_0.7.4/pyvcf/vcf.pyc
Platypus_0.7.4/pyvcf/vcf-add-ac.py
Platypus_0.7.4/pyvcf/vcf-add-labels.py
Platypus_0.7.4/pyvcf/vcf-indel-polarize.py
Platypus_0.7.4/pyvcf/bam-naive-caller.py
Platypus_0.7.4/pyvcf/vcf-compare.py
Platypus_0.7.4/pyvcf/__init__.pyc
Platypus_0.7.4/pyvcf/vcf-concordance.py
Platypus_0.7.4/pyvcf/__init__.py
Platypus_0.7.4/vcfutils.c
Platypus_0.7.4/buildPlatypus.sh
Platypus_0.7.4/tandem.h
austin@EMGS-HP-Z400:~/ngs$ cd Platypus_0.7.4
austin@EMGS-HP-Z400:~/ngs/Platypus_0.7.4$ ./buildPlatypus.sh
Building Platypus
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/pyvcf
copying pyvcf/vcf-mendelian.py -> build/lib.linux-x86_64-2.7/pyvcf
copying pyvcf/__init__.py -> build/lib.linux-x86_64-2.7/pyvcf
copying pyvcf/vcf-concordance.py -> build/lib.linux-x86_64-2.7/pyvcf
copying pyvcf/vcf-add-ac.py -> build/lib.linux-x86_64-2.7/pyvcf
copying pyvcf/vcf-add-hr.py -> build/lib.linux-x86_64-2.7/pyvcf
copying pyvcf/vcf-diff.py -> build/lib.linux-x86_64-2.7/pyvcf
copying pyvcf/filez.py -> build/lib.linux-x86_64-2.7/pyvcf
copying pyvcf/vcf-add-labels.py -> build/lib.linux-x86_64-2.7/pyvcf
copying pyvcf/axt2variants.py -> build/lib.linux-x86_64-2.7/pyvcf
copying pyvcf/bam-naive-caller.py -> build/lib.linux-x86_64-2.7/pyvcf
copying pyvcf/vcf-indel-polarize.py -> build/lib.linux-x86_64-2.7/pyvcf
copying pyvcf/vcf-extract.py -> build/lib.linux-x86_64-2.7/pyvcf
copying pyvcf/vcf.py -> build/lib.linux-x86_64-2.7/pyvcf
copying pyvcf/vcf-compare.py -> build/lib.linux-x86_64-2.7/pyvcf
running build
running build_py
copying extendedoptparse.py -> build/lib.linux-x86_64-2.7
running build
running build_py
copying window.py -> build/lib.linux-x86_64-2.7
running build
running build_py
copying variantutils.py -> build/lib.linux-x86_64-2.7
running build
running build_py
copying platypusexceptions.py -> build/lib.linux-x86_64-2.7
running build
running build_py
running build
running build_py
copying filez.py -> build/lib.linux-x86_64-2.7
running build
running build_py
copying runner.py -> build/lib.linux-x86_64-2.7
running build
running build_ext
building 'ctabix' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/tabix
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Itabix -Ipysam -I/usr/include/python2.7 -c ctabix.c -o build/temp.linux-x86_64-2.7/ctabix.o
ctabix.c:16:20: fatal error: Python.h: No such file or directory
compilation terminated.
error: command 'gcc' failed with exit status 1


Finished building Platypus

*********************************************************************************************************************

Cheers

Austin

[Andy Rimmer]

Ok, it looks like you don't have the Python header files. I think these are present by default on most distributions, but
if you don't have them then you'll need to install them:

sudo apt-get install python-dev

If you don't have sudo rights then you'll need to ask your administrator to do that. I think that should fix the problem. Let me
know.

I'll also fix the build script so that it doesn't pretend to succeed when it clearly fails.

Kind regards,
Andy

To view this discussion on the web, visit https://groups.google.com/d/msgid/platypus-users/39bddf5f-1c03-44f9-9143-7986d8fd3a3e%40googlegroups.com.

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[Austin Diamond]

Andy

That is exactly right.  Everything now running correctly.

Thanks very much for your help.


Austin