ImportError: No module named variantcaller

[stre...@cardiff.ac.uk]

I have been trying to install Platypus and I get the finished building Platypus message but I get an error when I try to use it. I have put the errors I get below. I'm sorry if this is silly question but I'm still learning this sort of thing.

v57-0a0e386f:Platypus_0.7.9.1 alexstretton$ ./buildPlatypus.sh

Building Platypus

running build

running build_py

copying vcf.py -> build/lib

running build

running build_py

copying extendedoptparse.py -> build/lib

running build

running build_py

copying window.py -> build/lib

running build

running build_py

copying variantutils.py -> build/lib

running build

running build_py

copying platypusexceptions.py -> build/lib

running build

running build_py

running build

running build_py

copying filez.py -> build/lib

running build

running build_py

copying runner.py -> build/lib

running build

running build_ext

building 'ctabix' extension

cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch x86_64 -arch i386 -pipe -Itabix -Ipysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c ctabix.c -o build/temp.macosx-10.9-intel-2.7/ctabix.o

In file included from ctabix.c:16:

/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/Python.h:33:10: fatal error: 

      'stdio.h' file not found

#include <stdio.h>

         ^

1 error generated.

error: command 'cc' failed with exit status 1

Finished building Platypus

v57-0a0e386f:Platypus_0.7.9.1 alexstretton$ python Platypus.py callVariant --bamFiles=13M03098_align_sorted.bam --refFile=/Users/alexstretton/Documents/NGS/bwa-0.7.5a/ucsc.hg19.fasta --output=13M03098_1.vcf --filterDuplicates=0 --minFlank=0

Traceback (most recent call last):

  File "Platypus.py", line 9, in <module>

    import runner

  File "/Users/alexstretton/Documents/NGS/Platypus_0.7.9.1/runner.py", line 9, in <module>

    import variantcaller

ImportError: No module named variantcaller

 

Thanks

Alex

[Andy Rimmer]

Hi Alex,

What operating system are you running?

Kind regards,
Andy

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?

[Christine Lee]

Hi Andy I'm having a similar issue as Alex. I'm running Platypus as part of Fast-GBS. My operating system is ubuntu 14.04 LTS

Search the variants with platypus

Traceback (most recent call last):

    File "Platypus.py", line 9, in <module>

        import runner

ImportError: No module named runner

        !!!There is a problem at the Platypus step

[Christine Lee]

It appears to be an issue with the script? Similar issue with Ansible found on the internet: http://docs.ansible.com/ansible/latest/dev_guide/developing_api.html#python-api-2-0 .....Likely need to change script to work with Python 2.0  ? But I'm not sure how to do this...