biospectrabysequencing / gbs_moa Goto Github PK
View Code? Open in Web Editor NEWWorkflow for GBS in moa template format
License: Other
Workflow for GBS in moa template format
License: Other
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.
It is on CentOS 6.6 using pip to install python dependencies.
## Location
$ which moa
/usr/bin/moa
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)
version?
: . hramwd@genome7 ~ [] ; uname -n
genome7.pfr.co.nz
: . hramwd@genome7 ~ [] ; python --version
Python 2.6.6
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
This is a placeholder to discuss what we are doing in terms of Quality control of BBS data
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
Sending an email to [email protected] to test out bip.io...
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/
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.
Theses Moa examples are pretty dirty so a spring clean of logs and other stuff belonging in .gitignores is required on a dev branch
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