mfcovington

(currently in progress)

#iPlant Data Store Tutorial

There are multiple ways to access files and directories on the iPlant Data Store (aka iRODS[1]). Here we will cover three methods, each with their pros and cons.

1. Browser-based Access --- User-friendly, but low throughput and 2GB upload limit
2. iCommands --- High throughput with maximum user control, but must be comfortable with the Command-Line Interface
3. iDrop --- High throughput and ability to schedule periodic transfers, but iDrop is in beta release and may have bugs

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chr     pos     ref_base        snp_base        genotype        insert_position SNP_CLASS
SL2.40ch00      16576   T       C       PEN     NA      SNP
SL2.40ch00      16757   A       G       PEN     NA      SNP
SL2.40ch00      16759   A       C       PEN     NA      SNP
SL2.40ch00      16806   T       C       PEN     NA      SNP
SL2.40ch00      17034   C       G       PEN     NA      SNP
SL2.40ch00      17136   G       A       PEN     NA      SNP
SL2.40ch00      17140   C       A       PEN     NA      SNP
SL2.40ch00      17595   A       C       PEN     NA      SNP
SL2.40ch00      17622   A       G       PEN     NA      SNP

mfcovington

#Bitbucket Tutorial for UCD PlantBio Perl Club

###What is Bitbucket?

Like [github][github], [bitbucket][bitbucket] is a web-based bosting service for git repositories (bitbucket hosts Mercurial repositories, too). As a research group at a university, a very attractive feature of bitbucket is that accounts created with an email address from an educational institution are automagically upgraded to unlimited private respositories and private collaborators. Only paid github accounts have access to privacy.

###Goal of this Tutorial

• Create an empty git repository on bitbucket
• Make a local clone of the repository and add some content

mfcovington

#!/usr/bin/env perl
# fasta_flattener.pl 
# Mike Covington
# created: 2012-06-14
#
# Description: flatten a FASTA file by removing white space
#
use strict;
use warnings;
use Bio::SeqIO;

mfcovington

Downloads and manuals:

• SHORE
• SHOREmap
• SHORE example

#TEMPLATES

mfcovington

Sublime Text 2 – Useful Shortcuts (Mac OS X)

General

⌘T	go to file
⌘⌃P	go to project
⌘R	go to methods
⌃G	go to line
⌘KB	toggle side bar
⌘⇧P	command prompt

mfcovington

<!-- Paste into Settings/Markdown/MarkdownHeader in Notesy for Github-style Markdown -->

<!--
<link rel="stylesheet" type="text/css" href="css/foo.css"/>
-->

<style type="text/css">
<!--

/* 

mfcovington

##Definitions lists don't work:

Term : Definition

Apple : Pomaceous fruit of plants of the genus Malus. : An american computer company.

Term 1

mfcovington

#!/usr/bin/env perl
# filter_blast_rm_chimeras.pl
# Mike Covington
# created: 2012-11-26
#
# Description: filter BLAST results to separate queries that hit
# multiple distinct regions from those that hit a single region
#
use strict;
use warnings;

mfcovington

html,
body {
    color: black;
}

* {
    margin: 0;
    padding: 0;
}