Paolo Di Tommaso pditommaso
pditommaso
/ Git notes
Last active
February 14, 2017 17:52
— forked from richardcornish/git.md
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| Start | |
| ===== | |
| 1. Install Git | |
| http://git-scm.com/download/mac | |
| (But consider using Homebrew) | |
| 2. Make a GitHub account | |
| https://github.com/ | |
| 3. Open Terminal |
pditommaso
/ bash.generate.random.alphanumeric.string.sh
Last active
August 29, 2015 14:17
— forked from earthgecko/bash.generate.random.alphanumeric.string.sh
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| #!/bin/bash | |
| # bash generate random alphanumeric string | |
| # | |
| dd bs=18 count=1 if=/dev/urandom 2>/dev/null | base64 | tr +/ 0A |
pditommaso
/ reseqtut_lmw.py
Last active
August 29, 2015 14:17
— forked from samuell/reseqtut_lmw.py
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| import luigi | |
| from luigis_monkey_wrench import * | |
| REF='human_17_v37.fasta' | |
| INDIVIDUALS=['NA06984','NA07000'] | |
| SAMPLES=['1','2'] | |
| BASENAME='.ILLUMINA.low_coverage.17q_' | |
| PICARDDIR='/sw/apps/bioinfo/picard/1.69/kalkyl/' | |
| KNOWNSITES='/proj/g2014207/labs/gatk/ALL.chr17.phase1_integrated_calls.20101123.snps_indels_svs.genotypes.vcf' |
pditommaso
/ diff2html.sh
Created
September 23, 2016 09:49
— forked from stopyoukid/diff2html.sh
Script that takes a git diff and outputs an html file in GitHub style
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| #!/bin/bash | |
| # | |
| # Convert diff output to colorized HTML. | |
| # (C) Mitch Frazier, 2008-08-27 | |
| # http://www.linuxjournal.com/content/convert-diff-output-colorized-html | |
| # Modified by stopyoukid | |
| # | |
| html="<html><head><meta charset=\"utf-8\"><title>Pretty Diff</title><style>body {text-align: center;}#wrapper {display: inline-block;margin-top: 1em;min-width: 800px;text-align: left;}h2 {background: #fafafa;background: -moz-linear-gradient(#fafafa, #eaeaea);background: -webkit-linear-gradient(#fafafa, #eaeaea);-ms-filter: \"progid:DXImageTransform.Microsoft.gradient(startColorstr='#fafafa',endColorstr='#eaeaea')\";border: 1px solid #d8d8d8;border-bottom: 0;color: #555;font: 14px sans-serif;overflow: hidden;padding: 10px 6px;text-shadow: 0 1px 0 white;margin: 0;}.file-diff {border: 1px solid #d8d8d8;margin-bottom: 1em;overflow: auto;padding: 0.5em 0;}.file-diff > div {width: 100%:}pre {margin: 0;font-family: \"Bitstream Vera Sans Mono\", Courier, monospace;font-size: 12px;line-height: 1.4em;text-indent: 0.5em;}.file {color: |
pditommaso
/ Hello.g4
Created
March 26, 2017 13:55
— forked from mattmcd/Hello.g4
Simple ANTLR4 grammar example
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| // define a grammar called Hello | |
| grammar Hello; | |
| r : 'hello' ID; | |
| ID : [a-z]+ ; | |
| WS : [ \t\r\n]+ -> skip ; |
pditommaso
/ NF_logo.png
Created
June 14, 2017 15:53
— forked from ewels/NF_logo.png
NextFlow Multipart HTML Emails
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| Save NextFlow logo as this file. |
pditommaso
/ raid_ephemeral.sh
Last active
December 23, 2017 23:14
— forked from joemiller/raid_ephemeral.sh
detect all ephemeral disks on EC2 then stripe together in a raid-0 vol mounted at /mnt
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| #!/bin/bash | |
| # | |
| # this script will attempt to detect any ephemeral drives on an EC2 node and create a RAID-0 stripe | |
| # mounted at /mnt. It should be run early on the first boot of the system. | |
| # | |
| # Beware, This script is NOT fully idempotent. | |
| # | |
| METADATA_URL_BASE="http://169.254.169.254/2012-01-12" | |
| yum -y -d0 install mdadm curl |
pditommaso
/ 00_cmd.sh
Created
January 24, 2018 23:14
— forked from lh3/00_cmd.sh
Scripts and command lines to create universal mask for hs37d5
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| # | |
| # generate 01compositional.bed.gz | |
| # | |
| # low-complexity by mDUST | |
| mdust hs37d5.fa -c -w7 -v28 \ | |
| | hs37d5.mdust-w7-v28.txt \ | |
| | cut -f1,3,4 \ | |
| | gawk -vOFS="\t" '{--$2;print}' \ | |
| | bgzip > 01compositional/hs37d5.mdust-w7-v28.bed.gz |
pditommaso
/ dgm.groovy
Created
January 16, 2019 20:56
— forked from wololock/dgm.groovy
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| @Grab(group = "org.reflections", module = "reflections", version = "0.9.11") | |
| import groovy.json.JsonOutput | |
| import org.codehaus.groovy.reflection.GeneratedMetaMethod | |
| import org.reflections.Reflections | |
| import org.reflections.util.ConfigurationBuilder | |
| def reflections = new Reflections(new ConfigurationBuilder().build()) | |
| def json = reflections.getSubTypesOf(GeneratedMetaMethod).collect { |
pditommaso
/ dgm.json
Created
January 16, 2019 20:58
— forked from wololock/dgm.json
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| [ | |
| { | |
| "name": "org.codehaus.groovy.runtime.dgm$0", | |
| "allDeclaredConstructors": true, | |
| "allPublicConstructors": true, | |
| "allDeclaredMethods": true, | |
| "allPublicMethods": true | |
| }, | |
| { | |
| "name": "org.codehaus.groovy.runtime.dgm$1", |