This page was last updated on Wednesday, 17-Sep-2014 15:10:59 CDT

Installation notes for khmer version 0.5

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Prerequisites

• git
• python development environment
  
  1. $ sudo apt-get install python-dev
• python easy-install
  
  1. $ sudo apt-get install python-setuptools
• If you get this error:

  The required version of setuptools (>=3.4.1) is not available,
  and can't be installed while this script is running. Please
  install a more recent version first, using
  'easy_install -U setuptools'.

  Then do as it says
  1. $ sudo easy_install -U setuptools

Installation

1. $ ver=""
2. $ cd /usr/local/bin
3. $ git clone git://github.com/ged-lab/screed.git
4. $ git clone git://github.com/ged-lab/khmer.git
5. $ sudo easy_install screed
6. $ cd khmer
7. $ make clean all
8. $ sudo easy_install nose
9. $ make test
   …

   Ran 369 tests in 13.290s
   
   OK

10. $ sudo easy_install /usr/local/bin/khmer

    Processing khmer
    Writing /usr/local/bin/khmer/setup.cfg
    Running setup.py -q bdist_egg --dist-dir /usr/local/bin/khmer/egg-dist-tmp-_0R7Oc
    warning: no previously-included files matching '*.orig' found anywhere in distribution
    make: Nothing to be done for `PIC'.
    #gcc -shared -Wl,-soname -Wl,libbz2.so.1.0 -o libbz2.so.1.0.6 blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o
    #gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2-shared bzip2.c libbz2.so.1.0.6
    #rm -f libbz2.so.1.0
    #ln -s libbz2.so.1.0.6 libbz2.so.1.0
    Adding khmer 1.2-rc1-66-g1292fa7-dirty to easy-install.pth file
    Installing filter-abund-single.py script to /usr/local/bin
    Installing abundance-dist.py script to /usr/local/bin
    Installing split-paired-reads.py script to /usr/local/bin
    Installing count-median.py script to /usr/local/bin
    Installing extract-partitions.py script to /usr/local/bin
    Installing find-knots.py script to /usr/local/bin
    Installing extract-paired-reads.py script to /usr/local/bin
    Installing load-into-counting.py script to /usr/local/bin
    Installing sample-reads-randomly.py script to /usr/local/bin
    Installing filter-abund.py script to /usr/local/bin
    Installing load-graph.py script to /usr/local/bin
    Installing extract-long-sequences.py script to /usr/local/bin
    Installing fastq-to-fasta.py script to /usr/local/bin
    Installing interleave-reads.py script to /usr/local/bin
    Installing make-initial-stoptags.py script to /usr/local/bin
    Installing abundance-dist-single.py script to /usr/local/bin
    Installing filter-stoptags.py script to /usr/local/bin
    Installing annotate-partitions.py script to /usr/local/bin
    Installing merge-partitions.py script to /usr/local/bin
    Installing partition-graph.py script to /usr/local/bin
    Installing do-partition.py script to /usr/local/bin
    Installing normalize-by-median.py script to /usr/local/bin
    Installing count-overlap.py script to /usr/local/bin
    
    Installed /usr/local/lib/python2.7/dist-packages/khmer-1.2_rc1_66_g1292fa7_dirty-py2.7-linux-x86_64.egg
    Processing dependencies for khmer==1.2-rc1-66-g1292fa7-dirty
    Finished processing dependencies for khmer==1.2-rc1-66-g1292fa7-dirty

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