view README~ @ 2:565c0e690238 draft

Added support for LJB2, COSMIC67, CLINVAR and NCI60. Fixed dgv annotation to use new UCSC table dgvMerged instead.

ANNOVAR needs to be installed manually in the following way:


1)	If you already have ANNOVAR installed on your system, simply edit the tool-data/annovar.loc file to reflect locations of 
	the perl scripts (annotate_variation.pl and convert2annovar.pl) and humandb directory (directory containing the annovar database files)
1b) Restart galaxy instance for changes in .loc file to take effect


2)	If you do not have ANNOVAR installed, request annovar download and sign license here: 
		http://www.openbioinformatics.org/annovar/annovar_download_form.php

	3)	Once downloaded, install annovar per the installation instructions and edit annovar.loc file to reflect location of directory containing perl scripts.
			tool uses annotate_variation.pl  and  convert2annovar.pl
	
	4)	Then download all desired databases for all desired builds as follows:
			annotate_variation.pl -downdb -buildver <build> [-webfrom annovar] <database> <humandb>
	
		where <humandb> is location where all database files should be stored
		and <database> is the database file to download, e.g. refGene (see bottom of document for all available database files at the time of writing this tool)
		and <build> can be hg18 or hg19 for humans, also other organisms available.
	
		list of all available databases can be found here: http://www.openbioinformatics.org/annovar/annovar_db.html
	
	5) edit the tool-data/annovar.loc file to reflect location of humandb folder
	5b) restart galaxy instance for changes in .loc file to take effect

6) Tool uses cgatools join for combining of files, this should be installed automatically with repository. If not, get a copy from Complete Genomics directly:
		wget http://sourceforge.net/projects/cgatools/files/1.7.1/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz
		tar xvzf cgatools-1.7.1.5-linux_binary-x86_64.tar.gz		

	and place the "cgatools" binary found in bin/ directory on your $PATH
	
	
list of files in my own humandb folder:

	hg18_ALL.sites.2012_04.txt
	hg18_ALL.sites.2012_04.txt.idx
	hg18_avsift.txt
	hg18_avsift.txt.idx
	hg18_CEU.sites.2010_07.txt
	hg18_CEU.sites.2010_07.txt.idx
	hg18_cg46.txt
	hg18_cg46.txt.idx
	hg18_cg69.txt
	hg18_cg69.txt.idx
	hg18_cytoBand.txt
	hg18_dgv.txt
	hg18_ensGeneMrna.fa
	hg18_ensGene.txt
	hg18_esp5400_aa.txt
	hg18_esp5400_aa.txt.idx
	hg18_esp5400_all.txt
	hg18_esp5400_all.txt.idx
	hg18_esp5400_ea.txt
	hg18_esp5400_ea.txt.idx
	hg18_esp6500_aa.txt
	hg18_esp6500_aa.txt.idx
	hg18_esp6500_all.txt
	hg18_esp6500_all.txt.idx
	hg18_esp6500_ea.txt
	hg18_esp6500_ea.txt.idx
	hg18_esp6500si_aa.txt
	hg18_esp6500si_aa.txt.idx
	hg18_esp6500si_all.txt
	hg18_esp6500si_all.txt.idx
	hg18_esp6500si_ea.txt
	hg18_esp6500si_ea.txt.idx
	hg18_example_db_generic.txt
	hg18_example_db_gff3.txt
	hg18_genomicSuperDups.txt
	hg18_gerp++gt2.txt
	hg18_gerp++gt2.txt.idx
	hg18_gwasCatalog.txt
	hg18_JPTCHB.sites.2010_07.txt
	hg18_JPTCHB.sites.2010_07.txt.idx
	hg18_keggMapDesc.txt
	hg18_keggPathway.txt
	hg18_kgXref.txt
	hg18_knownGeneMrna.fa
	hg18_knownGene.txt
	hg18_ljb_all.txt
	hg18_ljb_all.txt.idx
	hg18_ljb_lrt.txt
	hg18_ljb_lrt.txt.idx
	hg18_ljb_mt.txt
	hg18_ljb_mt.txt.idx
	hg18_ljb_phylop.txt
	hg18_ljb_phylop.txt.idx
	hg18_ljb_pp2.txt
	hg18_ljb_pp2.txt.idx
	hg18_ljb_sift.txt
	hg18_ljb_sift.txt.idx
	hg18_phastConsElements44way.txt
	hg18_refGeneMrna.fa
	hg18_refGene.txt
	hg18_refLink.txt
	hg18_snp128NonFlagged.txt
	hg18_snp128NonFlagged.txt.idx
	hg18_snp128.txt
	hg18_snp128.txt.idx
	hg18_snp129NonFlagged.txt
	hg18_snp129NonFlagged.txt.idx
	hg18_snp129.txt
	hg18_snp129.txt.idx
	hg18_snp130NonFlagged.txt
	hg18_snp130NonFlagged.txt.idx
	hg18_snp130.txt
	hg18_snp130.txt.idx
	hg18_snp131NonFlagged.txt
	hg18_snp131NonFlagged.txt.idx
	hg18_snp131.txt
	hg18_snp131.txt.idx
	hg18_snp132NonFlagged.txt
	hg18_snp132NonFlagged.txt.idx
	hg18_snp132.txt
	hg18_snp132.txt.idx
	hg18_tfbsConsSites.txt
	hg18_YRI.sites.2010_07.txt
	hg18_YRI.sites.2010_07.txt.idx
	hg19_AFR.sites.2012_04.txt
	hg19_AFR.sites.2012_04.txt.idx
	hg19_ALL.sites.2010_11.txt
	hg19_ALL.sites.2010_11.txt.idx
	hg19_ALL.sites.2012_02.txt
	hg19_ALL.sites.2012_02.txt.idx
	hg19_ALL.sites.2012_04.txt
	hg19_ALL.sites.2012_04.txt.idx
	hg19_AMR.sites.2012_04.txt
	hg19_AMR.sites.2012_04.txt.idx
	hg19_ASN.sites.2012_04.txt
	hg19_ASN.sites.2012_04.txt.idx
	hg19_avsift.txt
	hg19_avsift.txt.idx
	hg19_cg46.txt
	hg19_cg46.txt.idx
	hg19_cg69.txt
	hg19_cg69.txt.idx
	hg19_cosmic61.txt
	hg19_cosmic61.txt.idx
	hg19_cosmic63.txt
	hg19_cosmic63.txt.idx
	hg19_cosmic64.txt
	hg19_cosmic64.txt.idx
	hg19_cosmic65.txt
	hg19_cosmic65.txt.idx
	hg19_cytoBand.txt
	hg19_dgv.txt
	hg19_ensGeneMrna.fa
	hg19_ensGene.txt
	hg19_esp5400_aa.txt
	hg19_esp5400_aa.txt.idx
	hg19_esp5400_all.txt
	hg19_esp5400_all.txt.idx
	hg19_esp5400_ea.txt
	hg19_esp5400_ea.txt.idx
	hg19_esp6500_aa.txt
	hg19_esp6500_aa.txt.idx
	hg19_esp6500_all.txt
	hg19_esp6500_all.txt.idx
	hg19_esp6500_ea.txt
	hg19_esp6500_ea.txt.idx
	hg19_esp6500si_aa.txt
	hg19_esp6500si_aa.txt.idx
	hg19_esp6500si_all.txt
	hg19_esp6500si_all.txt.idx
	hg19_esp6500si_ea.txt
	hg19_esp6500si_ea.txt.idx
	hg19_EUR.sites.2012_04.txt
	hg19_EUR.sites.2012_04.txt.idx
	hg19_genomicSuperDups.txt
	hg19_gerp++gt2.txt
	hg19_gerp++gt2.txt.idx
	hg19_gwasCatalog.txt
	hg19_keggMapDesc.txt
	hg19_keggPathway.txt
	hg19_kgXref.txt
	hg19_knownGeneMrna.fa
	hg19_knownGene.txt
	hg19_ljb_all.txt
	hg19_ljb_all.txt.idx
	hg19_ljb_lrt.txt
	hg19_ljb_lrt.txt.idx
	hg19_ljb_mt.txt
	hg19_ljb_mt.txt.idx
	hg19_ljb_phylop.txt
	hg19_ljb_phylop.txt.idx
	hg19_ljb_pp2.txt
	hg19_ljb_pp2.txt.idx
	hg19_ljb_sift.txt
	hg19_ljb_sift.txt.idx
	hg19_phastConsElements46way.txt
	hg19_refGeneMrna.fa
	hg19_refGene.txt
	hg19_refLink.txt
	hg19_snp130NonFlagged.txt
	hg19_snp130NonFlagged.txt.idx
	hg19_snp130.txt
	hg19_snp130.txt.idx
	hg19_snp131NonFlagged.txt
	hg19_snp131NonFlagged.txt.idx
	hg19_snp131.txt
	hg19_snp132NonFlagged.txt
	hg19_snp132NonFlagged.txt.idx
	hg19_snp132.txt
	hg19_snp132.txt.idx
	hg19_snp135NonFlagged.txt
	hg19_snp135NonFlagged.txt.idx
	hg19_snp135.txt
	hg19_snp137NonFlagged.txt
	hg19_snp137NonFlagged.txt.idx
	hg19_snp137.txt
	hg19_tfbsConsSites.txt