Pierre Lindenbaum lindenb
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lindenb
/ R01.mk
Last active
August 29, 2015 13:55
how to use <a href="http://www.r-project.org/"><b>R</b></a> as the main <b>SHELL</b> of <a href="https://www.gnu.org/software/make/manual/html_node/index.html">GNU-Make</a> instead of using a classical linux shell like bash
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| .PHONY: all clean | |
| SHELL = ./mockR | |
| .SHELLFLAGS= -e | |
| .ONESHELL: | |
| CHROM=1 2 | |
| UCSC=http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/ | |
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| var mysql = require('mysql'); | |
| var connection = mysql.createConnection({ | |
| debug:true, | |
| trace:true, | |
| host : 'genome-mysql.cse.ucsc.edu', | |
| port : 3306, | |
| database: 'hg19', | |
| user : 'genome', |
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| .PHONY:all | |
| PROXY1= ## -httpproxy:host:port | |
| PROXY2= ## -Dhttp.proxyHost=host -Dhttp.proxyPort=port | |
| all: Test.class | |
| java ${PROXY2} -cp tmp:. Test | |
| Test.class : Test.java tmp/uk/ac/ebi/webservices/whatizit/ws/ObjectFactory.java tmp/gov/nih/nlm/ncbi/eutils/entrez/eutils/esearch/ObjectFactory.java | |
| javac -sourcepath tmp:. $< |
lindenb
/ Makefile
Created
March 12, 2014 11:12
Answer to https://twitter.com/BioMickWatson/status/443694391350525953 : clipped sequences ignored by samtools. Added 8 bases to all reads in 5' and 3': only a few SNPs found.
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| sam.dir=/commun/data/packages/samtools-0.1.19 | |
| bwa=/commun/data/packages/bwa-0.7.6a/bwa | |
| .PHONY:all reads | |
| all: test.vcf | |
| test.vcf: test.bam.bai | |
| ${sam.dir}/samtools mpileup -uf ex1.fa test.bam | ${sam.dir}/bcftools/bcftools view -vcg - > $@ | |
| test.bam.bai : ex1.fa.bwt f1.fq f2.fq |
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| import java.io.*; | |
| class Test | |
| { | |
| private static class Source | |
| implements Runnable | |
| { | |
| private PipedOutputStream pipedOutputStream=new PipedOutputStream(); | |
| private InputStream in; | |
| Source(InputStream in) throws IOException |
lindenb
/ newick.js
Last active
August 29, 2015 13:58
answer to biostar http://www.biostars.org/p/97409/ "Collapse clades in a Newick tree with average distance to tips < x"
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| <html xmlns="http://www.w3.org/1999/xhtml"> | |
| <head> | |
| <script> | |
| var newick= null; | |
| /* parser generated by jison 0.4.13 */ | |
| /* | |
| Returns a Parser object of the following structure: | |
| Parser: { |
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| BEGIN { | |
| inE=0; | |
| inS=0; | |
| def=""; | |
| } | |
| /\/\// { | |
| inS=0; | |
| inE=0; | |
| next; | |
| } |
lindenb
/ bookmarklet.js
Created
April 30, 2014 20:33
copy of http://angel.net/~nic/passwdlet.domain.html
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| javascript:var%20b64pad='';var%20chrsz=8;function%20b64_sha1(s){return%20binb2b64(core_sha1(str2binb(s),s.length*chrsz));}function%20core_sha1(x,len){x[len%3E%3E5]|=0x80%3C%3C(24-len);x[((len+64%3E%3E9)%3C%3C4)+15]=len;var%20w=Array(80);var%20a=1732584193;var%20b=-271733879;var%20c=-1732584194;var%20d=271733878;var%20e=-1009589776;for(var%20i=0;i%3Cx.length;i+=16){var%20olda=a;var%20oldb=b;var%20oldc=c;var%20oldd=d;var%20olde=e;for(var%20j=0;j%3C80;j++){if(j%3C16)w[j]=x[i+j];else%20w[j]=rol(w[j-3]^w[j-8]^w[j-14]^w[j-16],1);var%20t=safe_add(safe_add(rol(a,5),sha1_ft(j,b,c,d)),safe_add(safe_add(e,w[j]),sha1_kt(j)));e=d;d=c;c=rol(b,30);b=a;a=t;}a=safe_add(a,olda);b=safe_add(b,oldb);c=safe_add(c,oldc);d=safe_add(d,oldd);e=safe_add(e,olde);}return%20Array(a,b,c,d,e);}function%20sha1_ft(t,b,c,d){if(t%3C20)return%20(b&c)|((~b)&d);if(t%3C40)return%20b^c^d;if(t%3C60)return%20(b&c)|(b&d)|(c&d);return%20b^c^d;}function%20sha1_kt(t){return%20(t%3C20)?1518500249:(t%3C40)?1859775393:(t%3C60)?-1894007588:-899497514;}functio |
lindenb
/ galaxy.txt
Last active
August 29, 2015 14:01
discussion for https://biostar.usegalaxy.org/p/7619
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| @JAVA_EXE@ |
lindenb
/ uniprot.js
Created
May 20, 2014 17:32
Calling uniprot using CORS ( http://www.html5rocks.com/en/tutorials/cors/?redirect_from_locale=fr and https://twitter.com/jervenbolleman/status/468777355289178112 )
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| <html> | |
| <script> | |
| // Create the XHR object. | |
| function createCORSRequest(method, url) { | |
| var xhr = new XMLHttpRequest(); | |
| if ("withCredentials" in xhr) { | |
| // XHR for Chrome/Firefox/Opera/Safari. | |
| xhr.open(method, url, true); | |
| } else if (typeof XDomainRequest != "undefined") { |
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