This page was last updated on Monday, 24-Aug-2020 14:16:21 CDT

Installation notes for Platypus version 0.8.1

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Prerequisites

• Samtools htslib

Installation

1. $ ver="0.8.1"
2. $ cd /programinstallers/
3. $ wget -N https://www.rdm.ox.ac.uk/resolveuid/599a7efc8ec04059a101c59714353209 -O platypus-latest.tgz
4. $ tar -zxvf platypus-latest.tgz
5. $ sudo mv Platypus_$ver /usr/local/bin/
6. $ cd /usr/local/bin/Platypus_$ver
7. $ ln -s /usr/local/bin/samtools1/include/htslib
8. $ export LIBRARY_PATH='LIBRARY_PATH:/usr/local/bin/samtools1/lib'
9. $ ./buildPlatypus.sh
   …
   Finished building Platypus
10. $ cd ..
11. $ ln -s Platypus_$ver Platypus
12. Add to default PATH for all users
    $ sudo nano /etc/profile
    …
    PATH="$PATH:/usr/local/bin/Platypus
    …
13. $ Platypus.py

    Traceback (most recent call last):
      File "/usr/local/bin/Platypus/Platypus.py", line 9, in 
        import runner
      File "/usr/local/bin/Platypus_0.8.1/runner.py", line 9, in 
        import variantcaller
      File "htslibWrapper.pxd", line 203, in init variantcaller (variantcaller.c:16971)
    ImportError: libhts.so.3: cannot open shared object file: No such file or directory

14. Create a wrapper to include the path to libhts
    $ nano /usr/local/bin/Platypus/Platypus

    #!/bin/bash
    export LD_LIBRARY_PATH='LD_LIBRARY_PATH:/usr/local/bin/samtools1/lib'
    /usr/local/bin/Platypus/Platypus.py $@

15. $ chmod +x /usr/local/bin/Platypus/Platypus
16. Error on cranberry and pickle

    Traceback (most recent call last):
      File "/usr/local/bin/Platypus/Platypus.py", line 9, in 
        import runner
      File "/usr/local/bin/Platypus_0.8.1/runner.py", line 9, in 
        import variantcaller
      File "variant.pxd", line 17, in init variantcaller (variantcaller.c:16975)
      File "variant.pyx", line 1, in init variant (variant.c:10330)
    ImportError: /usr/local/bin/Platypus_0.8.1/cerrormodel.so: undefined symbol: min

    See Issue #52
    which references this change which corrects the issue dc81f46