This page was last updated on Friday, 02-Dec-2016 09:17:00 CST

Installation notes for REAPR version v1.0.17 - July 12, 2013

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Prerequisites

• Note, REAPR comes with SMALT included
  SMALT is recommended to map the reads. REAPR has been tested using versions 0.6.4 and 0.7.0.1 of SMALT, but we have noticed issues with writing a BAM file directly (with the SMALT option -f bam). Please use -f samsoft when running SMALT, then import to BAM with samtools or Picard.
• R installed and in your path (http://www.r-project.org/)
• The following Perl modules need to be installed:
  • File::Basename
  • File::Copy
  • File::Spec
  • File::Spec::Link
  • Getopt::Long
  • List::Util
  $ sudo cpan File::Basename File::Copy File::Spec File::Spec::Link Getopt::Long List::Util
• Optionally, you might want to have Artemis installed
  (http://www.sanger.ac.uk/resources/software/artemis/) to view the output.
  It must be at least Artemis version 15.0.0.
• REAPR comes with its own versions of bamtools, cmake, samtools, snpomatic, and tabix.
  There is no way to tell the installer if you already have some of these installed, and the programs are hardcoded to use certain versions, e.g. libbamtools.so.2.1.0.

Installation

1. $ cd /programinstallers/
2. $ ver="1.0.17"
3. $ wget -N ftp://ftp.sanger.ac.uk/pub4/resources/software/reapr/Reapr_$ver.tar.gz
4. $ wget -N ftp://ftp.sanger.ac.uk/pub4/resources/software/reapr/Reapr_$ver.test_data.tar.gz
5. $ cd /usr/local/bin
6. $ tar -zxvf /programinstallers/Reapr_$ver.tar.gz
7. Make a version-independent symlink
   $ ln -s Reapr_$ver Reapr
8. $ cd Reapr
9. $ cp -puv manual.pdf /programinstallers/web/reapr/ && cp -puv README /programinstallers/web/reapr/README.txt
10. Compile source code
    $ ./install.sh
11. Add Reapr to the default PATH
    $ sudo nano /etc/profile
    ...
    PATH="$PATH:/usr/local/bin/Reapr"
    ...
12. Test the installation. Log out and back in to have PATH set.
    $ cd /programinstallers
13. $ tar -zxvf Reapr_$ver.test_data.tar.gz
14. $ cd Reapr_$ver.test_data
15. Run the tests. Return code should be zero if no errors occur, otherwise consult the log file
    $ ./test.sh &> test.log ; echo $?
    0
16. Cleanup
    $ cd .. ; rm Reapr_$ver.test_data -rf
17. $ tar -zxvf Reapr_$ver.tar.gz
18. $ cd Reapr_$ver
19. Copy files for web page
    $ mkdir web/reapr
20. $ cp -puv manual.pdf web/reapr/ ← this file missing in version 1.0.17, was present in 1.0.16 and 1.0.18, see manual online at ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_1.0.17.manual.pdf
21. $ cp -puv README web/reapr/README.txt
22. Compile
    $ ./install.sh
23. Manual installation without source code
    $ cd /usr/local/bin
24. $ mkdir Reapr_$ver
25. $ ln -s Reapr_$ver Reapr
26. Installation for ver 1.0.16 or 1.0.18 was
    $ cp -puv /programinstallers/Reapr_$ver/src/{*pl,task_score,task_stats,task_break,bam2fragCov,bam2insert,bam2fcdEstimate,make_plots,fa2gaps,fa2gc,scaff2contig,n50,task_gapresize,task_fcdrate,bam2perfect} /usr/local/bin/Reapr/
    

    `reapr.pl' -> `/usr/local/bin/reapr/reapr.pl'
    `task_facheck.pl' -> `/usr/local/bin/reapr/task_facheck.pl'
    `task_perfectfrombam.pl' -> `/usr/local/bin/reapr/task_perfectfrombam.pl'
    `task_perfectmap.pl' -> `/usr/local/bin/reapr/task_perfectmap.pl'
    `task_plots.pl' -> `/usr/local/bin/reapr/task_plots.pl'
    `task_preprocess.pl' -> `/usr/local/bin/reapr/task_preprocess.pl'
    `task_smaltmap.pl' -> `/usr/local/bin/reapr/task_smaltmap.pl'
    `task_summary.pl' -> `/usr/local/bin/reapr/task_summary.pl'
    `task_score' -> `/usr/local/bin/reapr/task_score'
    `task_stats' -> `/usr/local/bin/reapr/task_stats'
    `task_break' -> `/usr/local/bin/reapr/task_break'
    `bam2fragCov' -> `/usr/local/bin/reapr/bam2fragCov'
    `bam2insert' -> `/usr/local/bin/reapr/bam2insert'
    `bam2fcdEstimate' -> `/usr/local/bin/reapr/bam2fcdEstimate'
    `make_plots' -> `/usr/local/bin/reapr/make_plots'
    `fa2gaps' -> `/usr/local/bin/reapr/fa2gaps'
    `fa2gc' -> `/usr/local/bin/reapr/fa2gc'
    `scaff2contig' -> `/usr/local/bin/reapr/scaff2contig'
    `n50' -> `/usr/local/bin/reapr/n50'
    `task_gapresize' -> `/usr/local/bin/reapr/task_gapresize'
    `task_fcdrate' -> `/usr/local/bin/reapr/task_fcdrate'
    `bam2perfect' -> `/usr/local/bin/reapr/bam2perfect'

27. Also copy supplied already compiled SMALT to the REAPR directory
    $ cp -puv /programinstallers/Reapr_$ver/third_party/smalt_x86_64 /usr/local/bin/Reapr/smalt
28. This library is hard-coded into the programs
    $ sudo cp -puv Reapr_1.0.18/third_party/bamtools/lib/libbamtools.so.2.1.0 /usr/local/lib/bamtools/
29. Add Reapr to the default PATH
    $ sudo nano /etc/profile
    ...
    PATH="$PATH:/usr/local/bin/Reapr"
    ...
30. To use our installed versions of bamtools, cmake, samtools, snpomatic, and tabix, we need to make some links in the Reapr directory
    $ cd /usr/local/bin/Reapr
31. $ mkdir tabix && cd tabix && ln -s /usr/local/bin/tabix && ln -s /usr/local/bin/bgzip ; cd -
32. $ ln -s /usr/local/bin/bamtools
33. $ ln -s /usr/local/bin/samtools (Must be 0.x version of samtools)
34. $ ln -s /usr/local/bin/findknownsnps
35. This is so we can use reapr instead of reapr.pl
    $ ln -s reapr.pl reapr
36. For this way of installing, need to change line 11 of /usr/local/bin/Reapr/task_pipeline.pl
    from
    my $reapr_dir = abs_path(File::Spec->catfile($scriptdir, File::Spec->updir()));
    to
    my $reapr_dir = $scriptdir; #abs_path(File::Spec->catfile($scriptdir, File::Spec->updir()));
37. Test the installation. Log out and back in to have PATH set.
    $ cd /programinstallers
38. $ tar -zxvf Reapr_$ver.test_data.tar.gz
39. $ cd cd Reapr_$ver.test_data
40. Run the test. Return code should be zero if no errors occur
    $ ./test.sh &> test.log ; echo $?
    0
41. $ cd ..
42. Cleanup
    $ rm /programinstallers/{Reapr_$ver,Reapr_$ver.test_data} -rf