Still doesn't make sense.

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.

• DBI
• DBD::SQLite
• forks
• forks::shared
• File::Which
• Perl::Unsafe::Signals
• Bit::Vector
• Inline::C
• IO::All
• IO::Prompt

1. Type 'perl -MCPAN -e shell' to access the CPAN shell. You may
   have to answer some configuration questions if this is your first time
   starting CPAN. You can normally just hit enter to accept CPAN defaults.
   You may have to be logged in as 'root' or use sudo to install modules
   via CPAN. If you don't have root access, then install local::lib from
   http://www.cpan.org using the bootstrap method to setup a non-root CPAN
   install location.
2. Type 'install DBI' in CPAN to install the first module, then type
   'install DBD::SQLite' to install the next one, and so on.
3. Alternatively you can download modules from http://www.cpan.org/.
   Just follow the instructions that come with each module to install.

2. Install BioPerl 1.6 or higher.

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

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

1. 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
2. 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).
3. 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.
4. Unpack RepeatMasker to the directory of your choice (i.e. /usr/local).
5. 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.
6. 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).
7. Add the location where you installed RepeatMasker to your PATH variable in
   .bash_profile (i.e. export PATH="/usr/local/RepeatMasker:$PATH").
8. 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
9. 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

1. Unpack the MAKER tar file into the directory of your choice (i.e.
   /usr/local).
2. Go to the MAKER src/ directory.
3. Configure using --> perl Build.PL
4. Install using --> ./Build install
5. 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"
6. Add the location where you installed MAKER to your PATH variable in
   .bash_profile (i.e. export PATH=/usr/local/maker/bin:$PATH).
7. You can now run a test of MAKER by following the instructions in the MAKER
   README file.

(OPTIONAL COMPONENTS)

1. Augustus 2.0 or higher. Download from http://bioinf.uni-greifswald.de/augustus/
2. GeneMark-ES. Download from http://exon.biology.gatech.edu
3. FGENESH 2.4 or higher. Purchase from http://www.softberry.com
4. GeneMarkS. Download from http://exon.biology.gatech.edu

!!Read their installation documentation.

Move it to something like Naturalis/puppet-MAKER, test it.

...from /docs/ARANGS16

We need help please :)
@jwill123
For the Maker installation we are doing, we would need to know where you will install snap, since we have to set an environment variable to this location : export ZOE="where_snap_is/Zoe".
Many thanks!

• install GATK in a docker containe. GATK github repository
• call genotypes using gatk
• install ANGSD in a docker container
• calculate genotype likelihood with ANGSD
• extend pipeline script to include genotype calling and genotype likelihood
• run pipeline
• compare results between threshold genotype calling and genotype likelihood
• push GATK and ANGSD containers to Docker hub for later re-usage