Ismail Moghul IsmailM
👋
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| # DIRECTORIES | |
| VEP=$HOME/data/.progz/ensembl-vep/vep.pl | |
| ANALYSIS_DIR=$HOME/data/analysis | |
| ### VEP --ASSEMBLY param | |
| ASSEMBLY_FASTA=${ANALYSIS_DIR}/reference/human_g1k_v37_decoy.fasta | |
| ### VEP Custom Annotation | |
| DBSNP_DB=${ANALYSIS_DIR}/dbsnp/All_20161121.vcf.gz | |
| KAVIAR_DB=${ANALYSIS_DIR}/kaviar/VEP_annotation.vcf.gz | |
| GNOMAD_DIR=${ANALYSIS_DIR}/gnomad |
IsmailM
/ gist:a44c186ef245d8c862b305af7444fc2f
Created
February 14, 2017 17:16
— forked from brentp/gist:819611
install annovar and use it to annotate a vcf with hg19
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| wget http://www.openbioinformatics.org/annovar/download/annovar.latest.tar.gz.mirror | |
| tar xzvf annovar.tar.gz | |
| cd annovar | |
| # download databases (goes to UCSC) | |
| ./annotate_variation.pl -buildver hg19 -downdb 1000g2010nov humandb | |
| ./annotate_variation.pl -buildver hg19 -downdb avsift humandb | |
| ./annotate_variation.pl -buildver hg19 -downdb refGene humandb | |
| ./annotate_variation.pl -buildver hg19 -downdb mce46way humandb/ | |
| ./annotate_variation.pl -buildver hg19 -downdb snp131 humandb/ |
IsmailM
/ .Rprofile.r
Created
February 9, 2017 14:54
— forked from stephenturner/.Rprofile.r
My .Rprofile
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| ## See http://gettinggeneticsdone.blogspot.com/2013/06/customize-rprofile.html | |
| ## Load packages | |
| library(BiocInstaller) | |
| ## Don't show those silly significanct stars | |
| options(show.signif.stars=FALSE) | |
| ## Do you want to automatically convert strings to factor variables in a data.frame? | |
| ## WARNING!!! This makes your code less portable/reproducible. |
IsmailM
/ gist:877c936d329fded0e97c9eb5eaa37b8d
Last active
February 2, 2017 16:53
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| function print_time { | |
| END=$(date +%s) | |
| DIFF=$(( $END - $1 )) | |
| dd=$(echo "$DIFF/86400" | bc) | |
| dt2=$(echo "$DIFF-86400*$dd" | bc) | |
| dh=$(echo "$dt2/3600" | bc) | |
| dt3=$(echo "$dt2-3600*$dh" | bc) | |
| dm=$(echo "$dt3/60" | bc) | |
| ds=$(echo "$dt3-60*$dm" | bc) | |
| if [ $dd -gt 0 ]; then |
IsmailM
/ gist:549d52f285d52e9b8acec809969f8ab0
Created
February 2, 2017 01:52
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| <!DOCTYPE html> | |
| <html> | |
| <head> | |
| <meta charset="utf-8"> | |
| <title>jQuery tablesorter 2.0 - Theme Materialize</title> | |
| <!-- jQuery --> | |
| <script src="js/jquery-latest.min.js"></script> | |
| <!-- Demo stuff --> |
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| PATH=$PATH:$HOME/bin:/Applications/Sublime\ Text\ 3.app/Contents/SharedSupport/bin | |
| function o { | |
| if [ "$1" != "" ]; then | |
| open $1 | |
| else | |
| open $PWD | |
| fi | |
| } |
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| { | |
| "always_show_minimap_viewport": true, | |
| "bold_folder_labels": true, | |
| "color_scheme": "Packages/Materialize/schemes/Material Solarized Dark.tmTheme", | |
| "detect_indentation": false, | |
| "font_face": "Operator Mono Book", | |
| "font_options": | |
| [ | |
| "gray_antialias" | |
| ], |
IsmailM
/ Flickr-justified-gallery.js
Created
July 26, 2016 18:32
Flickr Justified Gallery Wordpress Plugin Javascript Dependency
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| /*! Swipebox v1.4.1 | Constantin Saguin csag.co | MIT License | github.com/brutaldesign/swipebox */ | |
| !function(a,b,c,d){c.swipebox=function(e,f){var g,h,i={useCSS:!0,useSVG:!0,initialIndexOnArray:0,removeBarsOnMobile:!0,hideCloseButtonOnMobile:!1,hideBarsDelay:3e3,videoMaxWidth:1140,vimeoColor:"cccccc",beforeOpen:null,afterOpen:null,afterClose:null,nextSlide:null,prevSlide:null,loopAtEnd:!1,autoplayVideos:!1,queryStringData:{},toggleClassOnLoad:""},j=this,k=[],l=e.selector,m=c(l),n=navigator.userAgent.match(/(iPad)|(iPhone)|(iPod)|(Android)|(PlayBook)|(BB10)|(BlackBerry)|(Opera Mini)|(IEMobile)|(webOS)|(MeeGo)/i),o=null!==n||b.createTouch!==d||"ontouchstart"in a||"onmsgesturechange"in a||navigator.msMaxTouchPoints,p=!!b.createElementNS&&!!b.createElementNS("http://www.w3.org/2000/svg","svg").createSVGRect,q=a.innerWidth?a.innerWidth:c(a).width(),r=a.innerHeight?a.innerHeight:c(a).height(),s=0,t='<div id="swipebox-overlay"> <div id="swipebox-container"> <div id="swipebox-slider"></div> |
IsmailM
/ gist:c323f2ea31adf807f344e17428dc95c5
Created
May 25, 2016 13:44
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| #!/bin/sh | |
| #$ -cwd # Set the working directory for the job to the current directory | |
| #$ -V | |
| #$ -pe smp 4 # Request 4 CPU cores | |
| #$ -l h_rt=24:0:0 # Request 24 hour runtime | |
| #$ -l h_vmem=1G # Request 1GB RAM / core, i.e. 4GB total | |
| echo 'Hey World, I'm IsmailM" |
IsmailM
/ nginx-passenger-ssl.conf
Created
May 20, 2016 08:43
— forked from rkjha/nginx-passenger-ssl.conf
Nginx/Passenger config when using SSL with a Ruby/Rails Application.
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| # for redirecting hhtp traffic to https version of the site | |
| server { | |
| listen 80; | |
| server_name example.com; | |
| return 301 https://$server_name$request_uri; | |
| } | |
| # for redirecting to non-www version of the site | |
| server { | |
| listen 80; |