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rvosa / arangs2016

Automated and Reproducible Analysis of Next Generation Sequencing data (ARANGS16)
http://gtpb.igc.gulbenkian.pt/bicourses/ARANGS16
MIT License
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packaging MAKER as a box #10

Open rvosa opened 8 years ago

rvosa commented 8 years ago

The MAKER pipeline for eukaryote genome annotation is very complicated to install. It would be very nice if it could be packaged inside a Vagrant box. Here's the instructions, just to give you an idea what a pain this is:

How to Install Standard MAKER

DETAILED INSTALL (for installing prerequisites manually)

1. You need to have perl 5.8.0 or higher installed.

You can verify this by typing perl -v on the command line in a terminal. You will also need to install the following perl modules from CPAN.

Download the Core Package from http://www.bioperl.org

Quick and dirty installation: (with this option, not all of bioperl will work, but what MAKER uses will)

  1. Download and unpack the most recent BioPerl package to a directory of your choice, or use Git to access the most current version of BioPerl. See http://www.bioperl.org for details on how to download using Git. You will then need to set PERL5LIB in your .bash_profile to the location of bioperl (i.e. export PERL5LIB="/usr/local/bioperl-live:$PERL5LIB").

Full BioPerl instalation via CPAN- (you will need sudo privileges, root access, or CPAN configured for local installation to continue with this option)

  1. Type perl -MCPAN -e shell into the command line to set up CPAN on your computer before installing bioperl (CPAN helps install perl dependencies needed to run bioperl). For the most part just accept any default options by hitting enter during setup.
  2. Type install Bundle::CPAN on the cpan command line. Once again just press enter to accept default installation options.
  3. Type install Module::Build on the cpan command line. Once again just press enter to accept default installation options.
  4. Type install Bundle::BioPerl on the cpan command line. Once again press enter to accept default installation options.

Full BioPerl instalation from download

  1. Unpack the downloaded bioperl tar file to the directory of your choice or use Git to get the most up to date version. Then use the terminal to find the directory and type perl Build.PL in the command line, then type ./Build test, then if all tests pass, type ./Build install. This will install BioPerl where perl is installed. Press enter to accept all defaults.

    3. Install either WuBlast or NCBI-BLAST using instruction in 3a and 3b

    3a. Install WuBlast 2.0 or higher (Alternatively install NCBI-BLAST in 3b)

(WuBlast has become AB-Blast and is no longer freely available, so if you are not lucky enough to have an existing copy of WuBlast, you can use NCBI BLAST or BLAST+ instead)

  1. Unpack the tar file into the directory of your choice (i.e. /usr/local).
  2. Add the following in your .bash_profile (value depend on where you chose to install wublast):
        export WUBLASTFILTER="/usr/local/wublast/filter"
        export WUBLASTMAT="/usr/local/wublast/matrix"

Add the location where you installed WuBlast to your PATH variable in .bash_profile (i.e. export PATH="/usr/local/wublast:$PATH").

3b. Install NCBI-BLAST 2.2.X or higher (Alternatively install WuBlast in 3a)

  1. Unpack the tar file into the directory of your choice (i.e. /usr/local).
  2. Add the location where you installed NCBI-BLAST to your PATH variable in .bash_profile (i.e. export PATH="/usr/local/ncbi-blast:$PATH").

    4. Install SNAP. Download from http://korflab.ucdavis.edu/software.html

  3. Unpack the SNAP tar file into the directory of your choice (ie /usr/local)
  4. Add the following to your .bash_profile file (value depends on where you choose to install snap): export ZOE="/usr/local/snap/Zoe"
  5. Navigate to the directory where snap was unpacked (i.e. /usr/local/snap) and type make
  6. Add the location where you installed SNAP to your PATH variable in .bash_profile (i.e. export PATH="/usr/local/snap:$PATH").

    5. Install RepeatMasker. Download from http://www.repeatmasker.org

  7. The most current version of RepeatMasker requires a program called TRF. This can be downloaded from http://tandem.bu.edu/trf/trf.html and here: http://rvosa.github.io/arangs2016/downloads/arangs2016-trf.bin
  8. The TRF download will contain a single executable file. You will need to rename the file from whatever it is to just 'trf' (all lower case).
  9. Make TRF executable by typing chmod a+x trf. You can then move this file wherever you want. I just put it in the .../RepeatMasker directory.
  10. Unpack RepeatMasker to the directory of your choice (i.e. /usr/local).
  11. If you do not have WuBlast installed, you will need to install RMBlast. We do not recomend using cross_match, as RepeatMasker performance will suffer.
  12. Now in the RepeatMasker directory type perl ./configure in the command line. You will be asked to identify the location of perl, rmblast/wublast, and trf. The script expects the paths to the folders containing the executables (because you are pointing to a folder the path must end in a '/' character or the configuration script throws a fit).
  13. Add the location where you installed RepeatMasker to your PATH variable in .bash_profile (i.e. export PATH="/usr/local/RepeatMasker:$PATH").
  14. You must register at http://www.girinst.org and download the Repbase repeat database, Repeat Masker edition, for RepeatMasker to work. Alternatively: Download from here http://rvosa.github.io/arangs2016/downloads/repeatmaskerlibraries-20150807.tar.gz
  15. Unpack the contents of the RepBase tarball into the RepeatMasker/Libraries directory.

    6. Install Exonerate 2.2. Download from http://www.ebi.ac.uk/~guy/exonerate

For linux x86_64 there are pre-compiled binaries. Use those.

  1. Exonerate has pre-compiled binaries for many systems; however, for Mac OS-X you will have to download the source code and compile it yourself by following steps b though d.
  2. You need to have Glib 2.0 installed. The easiest way to do this on a Mac is to install fink and then type fink install glib2-dev in the terminal.
  3. Change to the directory containing the Exonerate package to be compiled.
  4. To install exonerate in the directory /usr/local/exonerate, type: ./configure -prefix=/usr/local/exonerate -> then type make -> then type make install
  5. Add the location where you installed exonerate to your PATH variable in .bash_profile (i.e. export PATH="/usr/local/exonerate/bin:$PATH").

    7. Install MAKER. Download from http://www.yandell-lab.org

  6. Unpack the MAKER tar file into the directory of your choice (i.e. /usr/local).
  7. Go to the MAKER src/ directory.
  8. Configure using --> perl Build.PL
  9. Install using --> ./Build install
  10. Remember to add the following to your .bash_profile if you haven't already: export ZOE="where_snap_is/Zoe" export AUGUSTUS_CONFIG_PATH="where_augustus_is/config"
  11. Add the location where you installed MAKER to your PATH variable in .bash_profile (i.e. export PATH=/usr/local/maker/bin:$PATH).
  12. You can now run a test of MAKER by following the instructions in the MAKER README file.

    (OPTIONAL COMPONENTS)

  13. Augustus 2.0 or higher. Download from http://bioinf.uni-greifswald.de/augustus/
  14. GeneMark-ES. Download from http://exon.biology.gatech.edu
  15. FGENESH 2.4 or higher. Purchase from http://www.softberry.com
  16. GeneMarkS. Download from http://exon.biology.gatech.edu

!!Read their installation documentation.

hettling commented 8 years ago

As of commit 4d597437235494adaf56658fd7588bd446304141 there is a skeleton Vagrant file that is going to call all the puppet manifests.

hettling commented 8 years ago

The approach is that the Vagrantfile points to the manifests directory. Puppet will then look for a default.pp automatically, which will contain the import statements for the other manifests in the right order.