Carrot root and DNA VCRU Bioinformatics USDA ARS Vegetable Crops Research Unit

This page was last updated on Tuesday, 07-Mar-2017 11:47:02 CST

Installation notes for sprai version 0.9.9.23

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Prerequisites

Installation

  1. $ ver="0.9.9.23"
  2. $ cd /programinstallers/
  3. $ wget -N http://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-$ver.tar.gz
  4. $ tar -zxvf sprai-$ver.tar.gz
  5. $ cd sprai-$ver
  6. $ ./waf configure 
    Setting top to                           : /programinstallers/sprai-0.9.9.23 
Setting out to                           : /programinstallers/sprai-0.9.9.23/build 
Checking for 'gcc' (c compiler)          : /usr/bin/gcc 
Checking for minimum perl version        : 5.18.2 
perl module Statistics::Descriptive      : ok 
'configure' finished successfully (0.390s)
  7. $ ./waf build
    … 
    'build' finished successfully (0.852s)
  8. $ sudo ./waf install 
    Waf: Entering directory `/programinstallers/sprai-0.9.9.23/build'
+ install /usr/local/bin/ca_ikki_v5.pl (from ca_ikki_v5.pl)
+ install /usr/local/bin/dumbbell_filter.pl (from dumbbell_filter.pl)
+ install /usr/local/bin/bfmt72s (from build/bfmt72s)
+ install /usr/local/bin/myrealigner (from build/myrealigner)
+ install /usr/local/bin/nss2v_v3 (from build/nss2v_v3)
+ install /usr/local/bin/m52bfmt7 (from build/m52bfmt7)
+ install /usr/local/bin/ezez4qsub_vx1.pl (from ezez4qsub_vx1.pl)
+ install /usr/local/bin/ezez_vx1.pl (from ezez_vx1.pl)
+ install /usr/local/bin/fa2fq.pl (from fa2fq.pl)
+ install /usr/local/bin/fq2fa.pl (from fq2fa.pl)
+ install /usr/local/bin/fq2idfq.pl (from fq2idfq.pl)
+ install /usr/local/bin/fqfilt.pl (from fqfilt.pl)
+ install /usr/local/bin/get_top_20x_fa.pl (from get_top_20x_fa.pl)
+ install /usr/local/bin/partition_fa.pl (from partition_fa.pl)
+ install /usr/local/bin/ezez4makefile_v4.pl (from ezez4makefile_v4.pl)
+ install /usr/local/bin/get_target_fasta_records.pl (from get_target_fasta_records.pl)
+ install /usr/local/bin/dfq2fq_v2.pl (from dfq2fq_v2.pl)
+ install /usr/local/bin/extract_fq.pl (from extract_fq.pl)
+ install /usr/local/bin/check_redundancy.pl (from check_redundancy.pl)
+ install /usr/local/bin/check_circularity.pl (from check_circularity.pl)
+ install /usr/local/bin/bfmtx2m4.pl (from bfmtx2m4.pl)
Waf: Leaving directory `/programinstallers/sprai-0.9.9.23/build'
'install' finished successfully (0.059s)
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  14. Cleanup
    $ cd /programinstallers ; rm sprai-$ver -rf