biospectrabysequencing/gbs_moa

Workflow for GBS in moa template format

gbs_moa's Issues

github pages

I've pushed some content to the gh-pages branch (dd21d9a). Hence the emails about failing builds there...

I don't know if there is other content being served from http://www.biospectrabysequencing.org/, but utilising github pages may be a way to go. The help docs guide through the DNS changes required.

Quality control of BBS data

This is a placeholder to discuss what we are doing in terms of Quality control of BBS data

Plant and Food Research

We have some perl scripts, knitr Rmarkdown scripts, and a shiny application looking at quality control aspects of GBS restriction sites for bam alignments.

The shiny application does some exploratory analysis summarizing 96 wells * 2 bam files for ~1.5 Million restriction sites/tags in real time checking the sampled yield distributions versus the known population of restriction sites for samples, investigatng coverage depth, and fragment distribution before considering SNP discovery.

The perl script sanity checks restriction fragments (probably unnecessary), and summarises sites in the following form;

$ perl gbsSites.pl
NAME
    gbsSites.pl - BAM to location terminal ends

DESCRIPTION
    Process a bam file for GBS restriction sites

SYNOPSIS
     gbsSites.pl [options]

    Where options and [defaults] are:

     -bam <BAM file>    Path to a bam file. Multiple options allowed      []

     -enzyme <Enzyme name> Which restriction enzyme? BamHI, ApeKI etc     [BamHI]

     -format < narrow|wide > Options: 'wide' or 'narrow' formats          [wide]

     -out <output file> Filename for tab delimited report                 [report.txt]

## Example output
Sample  Chromosome      cutSite Count   fwdCount        revCompCount
[BAMFile]   1       8312    1       0       1
[BAMFile]   1       17201   340     340     0
[BAMFile]   1       33026   2       0       2
[BAMFile]   1       35031   1       1       0
[BAMFile]   1       50458   54      0       54

Moa installation is not working correctly

It is on CentOS 6.6 using pip to install python dependencies.

## Location
$ which moa
/usr/bin/moa

Dependences on PFR systems

CentOS

What CentOS version are we running?

: . hramwd@genome7 ~ [] ; uname -n
genome7.pfr.co.nz
: . hramwd@genome7 ~ [] ; cat /etc/redhat-release
Red Hat Enterprise Linux Server release 6.6 (Santiago)

Python

version?

: . hramwd@genome7 ~ [] ; uname -n
genome7.pfr.co.nz
: . hramwd@genome7 ~ [] ; python --version
Python 2.6.6

Moa

Some Moa dependencies;

: . hramwd@genome7 ~ [] ; yum list 2>/dev/null | grep python-dev
python-devel.x86_64               2.6.6-52.el6       @rhel-x86_64-server-6
dbus-python-devel.i686            0.83.0-6.1.el6     rhel-6-server-optional-rpms
dbus-python-devel.x86_64          0.83.0-6.1.el6     rhel-6-server-optional-rpms
gstreamer-python-devel.i686       0.10.16-1.1.el6    rhel-6-server-optional-rpms
gstreamer-python-devel.x86_64     0.10.16-1.1.el6    rhel-6-server-optional-rpms
nautilus-python-devel.i686        0.7.0-3.el6.1      epel
nautilus-python-devel.x86_64      0.7.0-3.el6.1      epel
python-devel.i686                 2.6.6-52.el6       rhel-6-server-rpms
qscintilla-python-devel.noarch    2.4-1.el6          epel

Just followed the same install instructions on an Ubuntu machine I’ve got and that works. I’m going to have to track down a CentOS 6.5 install (don’t have a VM of it anywhere unfortunately) and see if I can get it to install and run on there too. -- Shane

Workshop replicated?

I'd like to start a discussion on the target of the gbs_moa repository. In its current state I believe it is accurately extending the workshop that @relshire presented in Feb 2014 in doing the same as the bash scripts did, but with the addition of Moa as a controlling meta layer.

I'd like this revision to be tagged as such, if agreement is made that it accurately represents the commands run during that workshop in a moa-fied way.

I'd like this to happen so we can decide on and work on where we are going next.

Spring cleaning required on main!

Theses Moa examples are pretty dirty so a spring clean of logs and other stuff belonging in .gitignores is required on a dev branch

Missing LICENSE information

I could not see which licence you are using in the README file, nor is a LICENSE file present as GitHub suggest: https://help.github.com/articles/open-source-licensing/

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