Run on SSD, 16GB RAM, Intel i7-4770k CPU
Imports are done on an empty database.
largedb contains 87 million pre-imported variants.
meatcar
/ maven-install.sh
Last active
July 16, 2018 14:15
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| #!/bin/bash | |
| # Script for installing maven 3.2.2 on Centos6 | |
| # Run as root. | |
| if [[ $UID -ne 0 ]] | |
| then | |
| echo "$0 must be run as root" | |
| exit 1 | |
| fi |
meatcar
/ gist:dcbd8a78ca0be46236f2
Created
September 11, 2014 18:17
meatcar
/ gist:ae11509df7564dc2c16d
Created
September 11, 2014 17:55
meatcar
/ test.jv.vcf
Created
August 28, 2014 21:48
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ##fileformat=VCFv4.1 | |
| ##INFO=<ID=EFFECT,Number=1,Type=String,Description="variant effect (UTR5,UTR3,intronic,splicing,missense,stoploss,stopgain,startloss,duplication,frameshift-insertion,frameshift-deletion,non-frameshift-deletion,non-frameshift-insertion,synonymous)"> | |
| ##INFO=<ID=HGVS,Number=1,Type=String,Description="HGVS Nomenclature"> | |
| ##center=Complete Genomics | |
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT GS000036397 | |
| chr1 11854476 rs1801131 T . . PASS TYPE=SNP GT:DP:AD 0/0:79:79,79 | |
| chr1 11856378 rs1801133 G . . PASS TYPE=SNP GT:DP:AD 0/0:119:119,119 | |
| chr1 97547947 rs67376798 T . . PASS TYPE=SNP GT:DP:AD 0/0:47:47,47 | |
| chr1 97915614 rs3918290 C . . PASS TYPE=SNP GT:DP:AD 0/0:53:53,53 | |
| chr3 14187449 rs2228001 G T . PASS EFFECT=MISSENSE;HGVS=XPC:NM_001145769.1:exon16:c.2704C>A:p.Q902K;TYPE=SNP GT:DP:AD 0/1:38:22,16 |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| git clone [email protected]:charite/jannovar.git | |
| cd jannovar | |
| mvn install | |
| # SUCCESS | |
| java -jar target/jannovar-0.6-SNAPSHOT.jar --create-refseq | |
| java -jar target/jannovar-0.6-SNAPSHOT.jar -D data/refseq_hg19.ser -U data -g hg19 -V subset_vcfBeta-HG00731-200-37-ASM.vcf | |
| #Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: 2 | |
| # at java.lang.String.charAt(String.java:658) | |
| # at jannovar.annotation.BlockSubstitution.getAnnotationBlockPlusStrand(BlockSubstitution.java:158) |
meatcar
/ auth_check_example.js
Created
December 17, 2013 07:07
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| var User = function () { | |
| this.loggedIn = false; | |
| }; | |
| User.prototype.ensureLogin = function () { | |
| var dfd; | |
| if (this.loggedIn) { | |
| dfd = $.Deferred(); | |
| dfd.resolve(); |
meatcar
/ auth_check_example.js
Created
December 17, 2013 07:05
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| var User = function () { | |
| this.loggedIn = false; | |
| }; | |
| User.prototype.ensureLogin = function () { | |
| var dfd; | |
| if (this.loggedIn) { | |
| dfd = $.Deferred(); | |
| dfd.resolve(); |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| greywolf:~ $ cat /etc/hosts | grep wolf.cdf | |
| #128.100.31.102 airwolf airwolf.cdf | |
| 128.100.31.198 greywolf.cdf.toronto.edu greywolf greywolf.cdf vncsrv1 | |
| 128.100.31.200 werewolf.cdf.toronto.edu werewolf werewolf.cdf comp1srv | |
| 128.100.31.201 seawolf.cdf.toronto.edu seawolf seawolf.cdf comp2srv | |
| 128.100.31.202 skywolf.cdf.toronto.edu skywolf skywolf.cdf | |
| 128.100.31.203 redwolf.cdf.toronto.edu redwolf redwolf.cdf |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Descritpion='UofT wifi' | |
| Interface=wlp1s0 | |
| Connection=wireless | |
| Security=wpa-configsection | |
| IP=dhcp | |
| WPAConfigSection=( | |
| 'ssid="UofT"' | |
| 'key_mgmt=WPA-EAP' | |
| 'eap=PEAP' | |
| 'phase1="peapelabel=0"' |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| " ctrl-p replacement -------------------------------------------- | |
| nno <leader>t :<C-u>Unite file_mru file_rec/async:! -start-insert -buffer-name=files<CR> | |
| nno <leader>cd :<C-u>Unite directory_mru directory -start-insert -buffer-name=cd -default-action=cd<CR> |