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

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Installation notes for DeconSeq version 0.4.3 2013-05-05

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Prerequisites

None

Installation

  1. $ cd /programinstallers/
  2. $ wget -N http://downloads.sourceforge.net/project/deconseq/standalone/deconseq-standalone-0.4.3.tar.gz
  3. Installation
    $ cd /usr/local/bin
  4. $ tar -zxvf /programinstallers/deconseq-standalone-0.4.3.tar.gz 
    deconseq-standalone-0.4.3/
deconseq-standalone-0.4.3/COPYING
deconseq-standalone-0.4.3/deconseq.pl
deconseq-standalone-0.4.3/bwasw_modified_source/
deconseq-standalone-0.4.3/bwasw_modified_source/bwtsw2.h
deconseq-standalone-0.4.3/bwasw_modified_source/bwtsw2_aux.c
deconseq-standalone-0.4.3/bwasw_modified_source/bwtsw2_main.c
deconseq-standalone-0.4.3/bwasw_modified_source/stdaln.c
deconseq-standalone-0.4.3/bwasw_modified_source/bwaMAC
deconseq-standalone-0.4.3/bwasw_modified_source/bwa64
deconseq-standalone-0.4.3/bwasw_modified_source/stdaln.h
deconseq-standalone-0.4.3/splitFasta.pl
deconseq-standalone-0.4.3/DeconSeqConfig.pm
deconseq-standalone-0.4.3/README
deconseq-standalone-0.4.3/bwaMAC
deconseq-standalone-0.4.3/ChangeLog
deconseq-standalone-0.4.3/bwa64
  5. Make version-independent symlink
    $ ln -s deconseq-standalone-0.4.3 deconseq
  6. $ cd deconseq
  7. $ chmod +x *.pl
  8. $ chmod +x bwa64
  9. Remove unneeded files
    $ rm bwaMAC
  10. $ rm bwasw_modified_source/ -rf
  11. Make a directory for databases
    $ mkdir /dcdata1/deconseq
  12. Change values in DeconSeqConfig.pm (if applicable)
    $ nano DeconSeqConfig.pm
    ...
    
use constant DB_DIR => '/dcdata1/deconseq/'; Note that path must end in /
    
...
    
use constant PROG_DIR => '/usr/local/bin/deconseq/'; Note that ./ did not work
    
...
    
use constant DBS => { hsref => { name => 'Human - Craig Venter (HuRef)',
                                 db =>   'hs_alt_HuRef_s1,hs_alt_HuRef_s2,hs_alt_HuRef_s3' },
                      arch =>  { name => 'Archaeal genomes [155 unique genomes, 02/12/11]',
                                 db =>   'archDB_s1' },
                      bact1 => { name => 'Bacterial genomes [2,206 unique genomes, 02/12/11]',
                                 db =>   'bactDB_s1,bactDB_s2,bactDB_s3' },
                      bact2 => { name => 'Bacterial genomes HMP [76,337 WGS sequences, 02/12/11]',
                                 db =>   'bacthmpDB_s1,bacthmpDB_s2' },
                      vir =>   { name => 'Viral genomes in RefSeq 45 [3,761 unique sequences, 02/12/11]',
                                 db =>   'virDB_s1' },
                      rib =>   { name => '18S sequences [57,317 unique sequences, 08/11/10]',
                                 db =>   'euk_18s_s1' }
              };
use constant DB_DEFAULT => 'bact1';
  13. Copy documentation for web page
    $ mkdir /U:/simonlabweb/bioinformatics/programs/deconseq
  14. $ cp -puv README /U:/simonlabweb/bioinformatics/programs/deconseq/README.txt
  15. $ cd ..
  16. Add to default PATH
    $ sudo nano /etc/profile
    ...
    PATH="$PATH:/usr/local/bin/deconseq"
    ...
  17. Download databases from ftp://edwards.sdsu.edu:7009/deconseq/db/ to the directory we made in step #11
    $ cd /dcdata1/deconseq
  18. $ for db in archDB_s1 bactDB_s1 bactDB_s2 bactDB_s3 bacthmpDB_s1 bacthmpDB_s2 euk_18s_s1 hs_alt_HuRef_s1 hs_alt_HuRef_s2 hs_alt_HuRef_s3 virDB_s1 ; do wget -N ftp://edwards.sdsu.edu:7009/deconseq/db/$db.tar.gz; tar -zxvf $db.tar.gz; done
  19. $ rm *.gz
  20. Add to default PATH for all users
    $ sudo nano /etc/profile
    …
    PATH="$PATH:/usr/local/bin/deconseq"
    …