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jacob-ogre / NUCmer_parallel.txt
Created June 17, 2014 01:43
NUCmer parallelization and --prefix
tl; dr: If parallelizing NUCmer by dividing a query into pieces, use the --prefix
flag to ensure separate mgap files are created rather than the single out.mgap.
### Fuller explanation ###
Trying to parallelize NUCmer alignment of assembly contigs to PacBio reads I ran
(repeatedly) into the error:
ERROR: Could not parse input from 'Query File'.
Please check the filename and format, or file a bug report
@jacob-ogre
jacob-ogre / R-For-Loop.sublime-snippet
Last active December 15, 2015 20:41
R: For-loop
<snippet>
<content><![CDATA[for(${1:i} in ${2:seq}) {
${3:#do something}
}]]></content>
<tabTrigger>for</tabTrigger>
<scope>source.r, source.rd.console</scope>
<description>For Loop</description>
</snippet>
@jacob-ogre
jacob-ogre / R-Plot.sublime-snippet
Created April 5, 2013 16:13
R: Basic-Plot
<snippet>
<content><![CDATA[plot(${1:predictor/factor}, ${2:response},
xlab="${3:xlabel}",
ylab="${4:ylabel}",
main="${5:main}")]]></content>
<tabTrigger>plo</tabTrigger>
<scope> source.r, source.rd.console</scope>
<description>plot</description>
</snippet>
@jacob-ogre
jacob-ogre / R-If-Else.sublime-snippet
Last active December 15, 2015 20:41
R: If-Else-loop
<snippet>
<content><![CDATA[if(${1:test}){
${2:yes}
} else {
${3:no}
}
]]></content>
<tabTrigger>ife</tabTrigger>
<scope>source.r, source.rd.console</scope>
<description>Ifelse</description>
@jacob-ogre
jacob-ogre / Princomp.sublime-snippet
Created April 6, 2013 01:19
R: princomp
<snippet>
<content><![CDATA[
${1:variable} <- princomp(na.omit(cbind(${2:v1}, ${3:v2})))]]></content>
<tabTrigger>prin</tabTrigger>
<scope> source.r, source.rd.console</scope>
<description>principal components rmode</description>
</snippet>
@jacob-ogre
jacob-ogre / Correlation.sublime-snippet
Created April 6, 2013 01:40
R: correlation
<snippet>
<content><![CDATA[
${1:variable} <- cor(${2:var/mat}, ${3:var,} use=${4:"complete.obs"})]]></content>
<tabTrigger>cor</tabTrigger>
<scope> source.r, source.rd.console</scope>
<description>correlation</description>
</snippet>
@jacob-ogre
jacob-ogre / Function_Doc.sublime-snippet
Created April 6, 2013 12:20
R: Function Documentation
<snippet>
<content><![CDATA[
# ${1:summary}
#
# USAGE:
# ${2:fx_call}(${3:vars})
#
# ARGS:
# ${4:args}
#
@jacob-ogre
jacob-ogre / macfanctl.conf
Created May 18, 2013 16:00
A config file to keep a Macbook Pro 5,5 cool while running Linux mint
# Config file for macfanctl daemon
#
# Note: 0 < temp_X_floor < temp_X_ceiling
# 0 < fan_min < 6200
fan1_min: 2000
temp_avg_floor: 35
temp_avg_ceiling: 45
@jacob-ogre
jacob-ogre / JWM_file_header
Last active December 17, 2015 12:19
A header
# CC0, a GPL-compliant copyright; this code is released to the public domain.
# See <http://creativecommons.org/publicdomain/zero/1.0/>
#
# Written in MONTH YEAR by AUTHOR(S), email
#
@jacob-ogre
jacob-ogre / .vimrc
Created May 20, 2013 13:40
My .vimrc, which captures most of the functionality of Sublime Text 2 while using all open-source software. One particularly important difference (for me) is that the use of tmux and vim-slime permits running a script in one pane and an REPL in a second pane, and sending lines/blocks of, e.g., R code from pane 0 to pane 1 (or whatever arrangemen…
color desert
filetype plugin on
syntax on
let mapleader = ","
let g:mapleader = ","
let g:slime_target = "tmux"
let python_highlight_all = 1
map <F12> :let &background = ( &background == "dark"? "light" : "dark" )<CR>