gmap: gmap_build.xml annotate

annotate gmap_build.xml @ 2:f6ba0f12cca2 draft

Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013

author	peterjc
date	Wed, 28 Sep 2016 10:43:44 -0400
parents	74391fc6e3f2
children	488e9d642566

rev	line source
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	1 <tool id="gmap_build" name="GMAP Build" version="3.0.0">
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	2 <description>a database genome index for GMAP and GSNAP</description>
10e3476429b5 Uploaded jjohnson parents: diff changeset	3 <requirements>
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	4 <requirement type="package" version="2013-05-09">gmap</requirement>
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	5 </requirements>
10e3476429b5 Uploaded jjohnson parents: diff changeset	6 <version_string>gmap --version</version_string>
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	7 <command interpreter="command"> /bin/bash $shscript > $output </command>
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	8 <inputs>
10e3476429b5 Uploaded jjohnson parents: diff changeset	9 <!-- Name for this gmapdb -->
10e3476429b5 Uploaded jjohnson parents: diff changeset	10 <param name="refname" type="text" label="Name you want to give this gmap database" help="">
10e3476429b5 Uploaded jjohnson parents: diff changeset	11 <validator type="empty_field" message="A database name is required."/>
10e3476429b5 Uploaded jjohnson parents: diff changeset	12 </param>
10e3476429b5 Uploaded jjohnson parents: diff changeset	13 <!-- Input data -->
10e3476429b5 Uploaded jjohnson parents: diff changeset	14 <repeat name="inputs" title="Reference Sequence" min="1">
10e3476429b5 Uploaded jjohnson parents: diff changeset	15 <param name="input" type="data" format="fasta" label="reference sequence fasta" />
10e3476429b5 Uploaded jjohnson parents: diff changeset	16 </repeat>
10e3476429b5 Uploaded jjohnson parents: diff changeset	17
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	18 <param name="circular_chroms" type="text" value="" optional="true" label="Names of circular chromosomes"
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	19 help="a list of chromosomes, separated by commas, allow GSNAP and GMAP to align reads across the ends of the chromosome">
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	20 </param>
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	21
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	22 <param name="sort" type="select" label="Sort chromosomes" help="">
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	23 <option value="none">none - use chromosomes as found in FASTA file(s)</option>
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	24 <option value="alpha">alpha - sort chromosomes alphabetically (chr10 before chr 1)</option>
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	25 <option value="numeric-alpha">numeric-alpha - chr1, chr1U, chr2, chrM, chrU, chrX, chrY</option>
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	26 <option value="chrom">chrom - chr1, chr2, chrM, chrX, chrY, chr1U, chrU</option>
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	27 </param>
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	28
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	29 <param name="cmetindex" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Create cmetindex to process reads from bisulfite-treated DNA"/>
10e3476429b5 Uploaded jjohnson parents: diff changeset	30 <param name="atoiindex" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Create atoiindex to process reads under RNA-editing tolerance"/>
10e3476429b5 Uploaded jjohnson parents: diff changeset	31 <conditional name="splicesite">
10e3476429b5 Uploaded jjohnson parents: diff changeset	32 <param name="splice_source" type="select" label="Add splice and intron info from" >
10e3476429b5 Uploaded jjohnson parents: diff changeset	33 <option value="none"></option>
10e3476429b5 Uploaded jjohnson parents: diff changeset	34 <option value="refGeneTable">refGenes table from UCSC table browser</option>
10e3476429b5 Uploaded jjohnson parents: diff changeset	35 <option value="gtf">GTF</option>
10e3476429b5 Uploaded jjohnson parents: diff changeset	36 <option value="gff3">GFF3</option>
10e3476429b5 Uploaded jjohnson parents: diff changeset	37 </param>
10e3476429b5 Uploaded jjohnson parents: diff changeset	38 <when value="none"/>
10e3476429b5 Uploaded jjohnson parents: diff changeset	39 <when value="refGeneTable">
10e3476429b5 Uploaded jjohnson parents: diff changeset	40 <param name="refGenes" type="data" format="tabular" optional="true" label="UCSC refGenes table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/refGene.txt.gz" />
10e3476429b5 Uploaded jjohnson parents: diff changeset	41 <param name="col_skip" type="integer" value="1" label="Columns to skip before the id/name column (default 1)"
10e3476429b5 Uploaded jjohnson parents: diff changeset	42 help="Note that alignment tracks in UCSC sometimes have an extra column on the left.">
10e3476429b5 Uploaded jjohnson parents: diff changeset	43 <validator type="in_range" message="The number of colmumns to skip must >= 0." min="0."/>
10e3476429b5 Uploaded jjohnson parents: diff changeset	44 </param>
10e3476429b5 Uploaded jjohnson parents: diff changeset	45
10e3476429b5 Uploaded jjohnson parents: diff changeset	46 </when>
10e3476429b5 Uploaded jjohnson parents: diff changeset	47 <when value="gtf">
10e3476429b5 Uploaded jjohnson parents: diff changeset	48 <param name="gtfGenes" type="data" format="gtf" optional="true" label="Genes as GTF" help="" />
10e3476429b5 Uploaded jjohnson parents: diff changeset	49 </when>
10e3476429b5 Uploaded jjohnson parents: diff changeset	50 <when value="gff3">
10e3476429b5 Uploaded jjohnson parents: diff changeset	51 <param name="gff3Genes" type="data" format="gff3" optional="true" label="Genes in GFF3 format" help="" />
10e3476429b5 Uploaded jjohnson parents: diff changeset	52 </when>
10e3476429b5 Uploaded jjohnson parents: diff changeset	53 </conditional>
10e3476429b5 Uploaded jjohnson parents: diff changeset	54 <conditional name="dbsnp">
10e3476429b5 Uploaded jjohnson parents: diff changeset	55 <param name="snp_source" type="select" label="Add SNP info from" >
10e3476429b5 Uploaded jjohnson parents: diff changeset	56 <option value="none"></option>
10e3476429b5 Uploaded jjohnson parents: diff changeset	57 <option value="snpTable">UCSC SNP Table</option>
10e3476429b5 Uploaded jjohnson parents: diff changeset	58 <option value="snpFile">GMAP SNP File</option>
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	59 <option value="vcfFile">VCF File</option>
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	60 </param>
10e3476429b5 Uploaded jjohnson parents: diff changeset	61 <when value="none"/>
10e3476429b5 Uploaded jjohnson parents: diff changeset	62 <when value="snpTable">
10e3476429b5 Uploaded jjohnson parents: diff changeset	63 <param name="snps" type="data" format="tabular" optional="true" label="UCSC SNPs table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130.txt.gz" />
10e3476429b5 Uploaded jjohnson parents: diff changeset	64 <param name="snpsex" type="data" format="tabular" optional="true" label="UCSC SNP Exceptions table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130Exceptions.txt.gz" />
10e3476429b5 Uploaded jjohnson parents: diff changeset	65 <param name="weight" type="select" label="Include SNPs with at least Confidence Level" help="">
10e3476429b5 Uploaded jjohnson parents: diff changeset	66 <option value="1" selected="true">1 (High)</option>
10e3476429b5 Uploaded jjohnson parents: diff changeset	67 <option value="2">2 (Medium)</option>
10e3476429b5 Uploaded jjohnson parents: diff changeset	68 <option value="3">3 (All)</option>
10e3476429b5 Uploaded jjohnson parents: diff changeset	69 </param>
10e3476429b5 Uploaded jjohnson parents: diff changeset	70 </when>
10e3476429b5 Uploaded jjohnson parents: diff changeset	71 <when value="snpFile">
10e3476429b5 Uploaded jjohnson parents: diff changeset	72 <param name="snps" type="data" format="gmap_snps" optional="true" label="GMAP SNPs file"
10e3476429b5 Uploaded jjohnson parents: diff changeset	73 help="Format (3 columns):
10e3476429b5 Uploaded jjohnson parents: diff changeset	74 <br>>rs62211261 21:14379270 CG
10e3476429b5 Uploaded jjohnson parents: diff changeset	75 <br>>rs62211262 21:14379281 CG
10e3476429b5 Uploaded jjohnson parents: diff changeset	76 <br>Each line must start with a > character, then be followed by an
10e3476429b5 Uploaded jjohnson parents: diff changeset	77 identifier (which may have duplicates). Then there should be the
10e3476429b5 Uploaded jjohnson parents: diff changeset	78 chromosomal coordinate of the SNP. (Coordinates are all 1-based, so
10e3476429b5 Uploaded jjohnson parents: diff changeset	79 the first character of a chromosome is number 1.) Finally, there
10e3476429b5 Uploaded jjohnson parents: diff changeset	80 should be the two possible alleles: ( AC AG AT CG CT GT or AN CN GN TN)
10e3476429b5 Uploaded jjohnson parents: diff changeset	81 <br>These alleles must correspond to the possible nucleotides on the plus strand of the genome.
10e3476429b5 Uploaded jjohnson parents: diff changeset	82 If the one of these two letters does not match the allele in the reference
10e3476429b5 Uploaded jjohnson parents: diff changeset	83 sequence, that SNP will be ignored in subsequent processing as a probable error.
10e3476429b5 Uploaded jjohnson parents: diff changeset	84 The N stands for any other allele." />
10e3476429b5 Uploaded jjohnson parents: diff changeset	85 </when>
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	86 <when value="vcfFile">
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	87 <param name="snps" type="data" format="vcf" optional="true" label="VCF SNPs file"
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	88 help="Example: ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	89 The VCF file contains multiple versions of dbSNP, so if you want a
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	90 particular version, such as 135. The vcf_iit program tries to pick
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	91 a subset of SNPs that somewhat parallel
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	92 the ones without exceptions in the UCSC dbSNP file. It keeps all SNPs
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	93 that have been validated (marked in the VCF file as "VLD") or have a
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	94 submitter link-out ("SLO"). Otherwise, it excludes SNPs that are
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	95 individual genotypes ("GNO"). If none of these conditions hold, then
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	96 the SNP is allowed. "/>
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	97 <param name="vcf_version" type="text" value="" optional="true" label="dbSNP version"
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	98 help="The VCF file contains multiple versions of dbSNP, so if you want a particular version, such as 135"/>
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	99 </when>
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	100 </conditional>
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	101
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	102 <param name="kmer" type="select" multiple="true" force_select="true" label="kmer size" help="Use smaller values when building indexes on machines with limited RAM">
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	103 <option value="12">12 (64MB RAM)</option>
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	104 <option value="13">13 (256MB RAM)</option>
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	105 <option value="14">14 (1GB RAM)</option>
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	106 <option value="15" selected="true">15 (4GB RAM)</option>
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	107 </param>
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	108
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	109 </inputs>
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	110 <stdio>
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	111 <exit_code range="1" level="fatal" description="Error running gmap_build" />
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	112 </stdio>
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	113 <outputs>
10e3476429b5 Uploaded jjohnson parents: diff changeset	114 <!--
10e3476429b5 Uploaded jjohnson parents: diff changeset	115 <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/>
10e3476429b5 Uploaded jjohnson parents: diff changeset	116 -->
10e3476429b5 Uploaded jjohnson parents: diff changeset	117 <data format="gmapdb" name="output" label="${tool.name} on ${on_string} gmapdb ${refname}" />
10e3476429b5 Uploaded jjohnson parents: diff changeset	118 </outputs>
10e3476429b5 Uploaded jjohnson parents: diff changeset	119 <configfiles>
10e3476429b5 Uploaded jjohnson parents: diff changeset	120 <configfile name="shscript">
10e3476429b5 Uploaded jjohnson parents: diff changeset	121 #!/bin/bash
10e3476429b5 Uploaded jjohnson parents: diff changeset	122 #set $ds = chr(36)
10e3476429b5 Uploaded jjohnson parents: diff changeset	123 #set $gt = chr(62)
10e3476429b5 Uploaded jjohnson parents: diff changeset	124 #set $lt = chr(60)
10e3476429b5 Uploaded jjohnson parents: diff changeset	125 #set $ad = chr(38)
10e3476429b5 Uploaded jjohnson parents: diff changeset	126 ## #set $ref_files = ''
10e3476429b5 Uploaded jjohnson parents: diff changeset	127 ## #for $i in $inputs:
10e3476429b5 Uploaded jjohnson parents: diff changeset	128 ## #set $ref_files = $ref_files $i.input
10e3476429b5 Uploaded jjohnson parents: diff changeset	129 ## #end for
10e3476429b5 Uploaded jjohnson parents: diff changeset	130 ## echo $ref_files
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	131 #set circular = ""
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	132 #if $circular_chroms.__str__.strip() != '':
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	133 #set circular = ('').join([' -c ','"', $circular_chroms.__str__,'"'])
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	134 #end if
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	135 #import os.path
10e3476429b5 Uploaded jjohnson parents: diff changeset	136 #set $gmapdb = $output.extra_files_path
10e3476429b5 Uploaded jjohnson parents: diff changeset	137 #set $mapsdir = $os.path.join($os.path.join($gmapdb,str($refname)), str($refname) + '.maps')
10e3476429b5 Uploaded jjohnson parents: diff changeset	138 mkdir -p $gmapdb
10e3476429b5 Uploaded jjohnson parents: diff changeset	139 ## export GMAPDB required for cmetindex and atoiindex
10e3476429b5 Uploaded jjohnson parents: diff changeset	140 export GMAPDB=$gmapdb
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	141 #if $kmer:
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	142 #for $k in $kmer.__str__.split(','):
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	143 gmap_build -D $gmapdb -d $refname -s $sort $circular -k $k #for i in $inputs# ${i.input}#end for#
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	144 #end for
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	145 #else:
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	146 gmap_build -D $gmapdb -d $refname -s $sort $circular #for i in $inputs# ${i.input}#end for#
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	147 #end if
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	148 get-genome -D $gmapdb -d '?' \| sed 's/^Available .*/gmap db: /'
10e3476429b5 Uploaded jjohnson parents: diff changeset	149 echo "kmers: " $kmer
10e3476429b5 Uploaded jjohnson parents: diff changeset	150 #if $splicesite.splice_source == 'refGeneTable':
10e3476429b5 Uploaded jjohnson parents: diff changeset	151 #if $splicesite.refGenes.__str__ != 'None':
10e3476429b5 Uploaded jjohnson parents: diff changeset	152 cat $splicesite.refGenes \| psl_splicesites -s $splicesite.col_skip \| iit_store -o $os.path.join($mapsdir,'splicesites')
10e3476429b5 Uploaded jjohnson parents: diff changeset	153 cat $splicesite.refGenes \| psl_introns -s $splicesite.col_skip \| iit_store -o $os.path.join($mapsdir,'introns')
10e3476429b5 Uploaded jjohnson parents: diff changeset	154 #end if
10e3476429b5 Uploaded jjohnson parents: diff changeset	155 #elif $splicesite.splice_source == 'gtf':
10e3476429b5 Uploaded jjohnson parents: diff changeset	156 #if $splicesite.gtfGenes.__str__ != 'None':
10e3476429b5 Uploaded jjohnson parents: diff changeset	157 cat $splicesite.gtfGenes \| gtf_splicesites \| iit_store -o $os.path.join($mapsdir,'splicesites')
10e3476429b5 Uploaded jjohnson parents: diff changeset	158 cat $splicesite.gtfGenes \| gtf_introns \| iit_store -o $os.path.join($mapsdir,'introns')
10e3476429b5 Uploaded jjohnson parents: diff changeset	159 #end if
10e3476429b5 Uploaded jjohnson parents: diff changeset	160 #elif $splicesite.splice_source == 'gff3':
10e3476429b5 Uploaded jjohnson parents: diff changeset	161 #if $splicesite.gff3Genes.__str__ != 'None':
10e3476429b5 Uploaded jjohnson parents: diff changeset	162 cat $splicesite.gff3Genes \| gff3_splicesites \| iit_store -o $os.path.join($mapsdir,'splicesites')
10e3476429b5 Uploaded jjohnson parents: diff changeset	163 cat $splicesite.gff3Genes \| gff3_introns \| iit_store -o $os.path.join($mapsdir,'introns')
10e3476429b5 Uploaded jjohnson parents: diff changeset	164 #end if
10e3476429b5 Uploaded jjohnson parents: diff changeset	165 #end if
10e3476429b5 Uploaded jjohnson parents: diff changeset	166 #if $dbsnp.snp_source != 'none' and $dbsnp.snps.__str__ != 'None':
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	167 #if $dbsnp.snp_source == 'snpTable':
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	168 #if $dbsnp.snpsex.__str__ != 'None':
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	169 cat $dbsnp.snps \| dbsnp_iit -w $dbsnp.weight -e $dbsnp.snpsex \| iit_store -o $os.path.join($mapsdir,'snps')
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	170 #else:
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	171 cat $dbsnp.snps \| dbsnp_iit -w $dbsnp.weight \| iit_store -o $os.path.join($mapsdir,'snps')
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	172 #end if
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	173 #elif $dbsnp.snp_source == 'vcfFile':
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	174 #if $dbsnp.vcf_version and len($dbsnp.vcf_version.__str__.strip()) > 0:
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	175 cat $dbsnp.snps \| vcf_iit -v $dbsnp.vcf_version.__str__.strip() \| iit_store -o $os.path.join($mapsdir,'snps')
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	176 #else:
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	177 cat $dbsnp.snps \| vcf_iit \| iit_store -o $os.path.join($mapsdir,'snps')
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	178 #end if
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	179 #else:
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	180 cat $dbsnp.snps \| iit_store -o $os.path.join($mapsdir,'snps')
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	181 #end if
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	182 snpindex -d $refname -v snps
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	183 echo "snpindex" -d $refname -v snps
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	184 #end if
10e3476429b5 Uploaded jjohnson parents: diff changeset	185 #if $cmetindex.__str__ == 'yes':
10e3476429b5 Uploaded jjohnson parents: diff changeset	186 cmetindex -d $refname
10e3476429b5 Uploaded jjohnson parents: diff changeset	187 echo "cmetindex" -d $refname
10e3476429b5 Uploaded jjohnson parents: diff changeset	188 #end if
10e3476429b5 Uploaded jjohnson parents: diff changeset	189 #if $atoiindex.__str__ == 'yes':
10e3476429b5 Uploaded jjohnson parents: diff changeset	190 atoiindex -d $refname
10e3476429b5 Uploaded jjohnson parents: diff changeset	191 echo "atoiindex" -d $refname
10e3476429b5 Uploaded jjohnson parents: diff changeset	192 #end if
10e3476429b5 Uploaded jjohnson parents: diff changeset	193 get-genome -D $gmapdb -d $refname -m '?' \| sed 's/^Available maps .*/maps: /'
10e3476429b5 Uploaded jjohnson parents: diff changeset	194 </configfile>
10e3476429b5 Uploaded jjohnson parents: diff changeset	195 </configfiles>
10e3476429b5 Uploaded jjohnson parents: diff changeset	196
10e3476429b5 Uploaded jjohnson parents: diff changeset	197 <tests>
10e3476429b5 Uploaded jjohnson parents: diff changeset	198 </tests>
10e3476429b5 Uploaded jjohnson parents: diff changeset	199
10e3476429b5 Uploaded jjohnson parents: diff changeset	200 <help>
10e3476429b5 Uploaded jjohnson parents: diff changeset	201
10e3476429b5 Uploaded jjohnson parents: diff changeset	202 GMAP Build
10e3476429b5 Uploaded jjohnson parents: diff changeset	203
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	204 GMAP Build creates an index of a genomic sequence for mapping and alignment using GMAP_ (Genomic Mapping and Alignment Program for mRNA and EST sequences) and GSNAP_ (Genomic Short-read Nucleotide Alignment Program). (GMAP Build uses GMAP commands: gmap_build, iit_store, psl_splicesites, psl_introns, gtf_splicesites, gtf_introns, gff3_splicesites, gff3_introns, dbsnp_iit, snpindex, cmetindex, and atoiindex.)
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	205
10e3476429b5 Uploaded jjohnson parents: diff changeset	206 You will want to read the README_
10e3476429b5 Uploaded jjohnson parents: diff changeset	207
10e3476429b5 Uploaded jjohnson parents: diff changeset	208 Publication_ citation: Thomas D. Wu, Colin K. Watanabe Bioinformatics 2005 21(9):1859-1875; doi:10.1093/bioinformatics/bti310
10e3476429b5 Uploaded jjohnson parents: diff changeset	209
10e3476429b5 Uploaded jjohnson parents: diff changeset	210 .. _GMAP: http://research-pub.gene.com/gmap/
10e3476429b5 Uploaded jjohnson parents: diff changeset	211 .. _GSNAP: http://research-pub.gene.com/gmap/
10e3476429b5 Uploaded jjohnson parents: diff changeset	212 .. _README: http://research-pub.gene.com/gmap/src/README
10e3476429b5 Uploaded jjohnson parents: diff changeset	213 .. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859
10e3476429b5 Uploaded jjohnson parents: diff changeset	214
10e3476429b5 Uploaded jjohnson parents: diff changeset	215
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	216 circular chromosomes
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	217
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	218 Finally, you can provide information to gmap_build that certain
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	219 chromosomes are circular, with the -c or -\-circular flag. The value
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	220 for these flags is a list of chromosomes, separated by commas. The
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	221 gmap_build program will then allow GSNAP and GMAP to align reads
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	222 across the ends of the chromosome. For example, the mitochondrial
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	223 genome in human beings is circular.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	224
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	225
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	226 Detecting known and novel splice sites in GSNAP
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	227
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	228 GSNAP can detect splice junctions in individual reads.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	229 GSNAP allows for known splicing at two levels: at the level of known
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	230 splice sites and at the level of known introns. At the site level,
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	231 GSNAP finds splicing between arbitrary combinations of donor and
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	232 acceptor splice sites, meaning that it can find alternative splicing
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	233 events. At the intron level, GSNAP finds splicing only between the
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	234 set of given donor-acceptor pairs, so it is constrained not to find
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	235 alternative splicing events, only introns included in the given list.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	236 For most purposes, I would recommend using known splice sites, rather
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	237 than known introns, unless you are certain that all alternative
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	238 splicing events are known are represented in your file.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	239
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	240 Splice site files can be generated from a GTF file
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	241 or from refGenes table from UCSC.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	242
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	243
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	244 SNP-tolerant alignment in GSNAP
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	245
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	246 GSNAP has the ability to align to a reference space of all possible
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	247 major and minor alleles in a set of known SNPs provided by the user.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	248
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	249
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	250 Process known SNP data, either from older dbSNP files or from newer
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	251 files in VCF format. The older dbSNP files can be obtained from UCSC,
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	252 either from the Galaxy UCSC table browser or downloaded:
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	253
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	254 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130.txt.gz
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	255
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	256 For versions before snp132, you may also want to exclude exceptions,
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	257 which will require this file:
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	258
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	259 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130Exceptions.txt.gz
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	260
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	261 The option "-w weight" makes use of the dbSNP item weight, a value
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	262 from 1 to 3, where lower weight means higher confidence. Items will
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	263 be included if the item weight is the given value weight or less.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	264 The default value of -w is 1, which is the criterion UCSC uses to
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	265 build its ambiguous version of the genome. To allow all item weights,
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	266 specify "-w 3".
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	267
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	268 The more recent SNP data are provided in VCF format, and can be
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	269 retrieved like this:
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	270
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	271 ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	272
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	273 The VCF file contains multiple versions of dbSNP, so if you want a
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	274 particular version, such as 135, you would use the flag "-v 135". The
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	275 vcf_iit program tries to pick a subset of SNPs that somewhat parallel
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	276 the ones without exceptions in the UCSC dbSNP file. It keeps all SNPs
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	277 that have been validated (marked in the VCF file as "VLD") or have a
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	278 submitter link-out ("SLO"). Otherwise, it excludes SNPs that are
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	279 individual genotypes ("GNO"). If none of these conditions hold, then
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	280 the SNP is allowed. These rules might not be the best ones; I made
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	281 them up by trying to compare version 135 of the VCF data with
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	282 version 135 of the UCSC dbSNP data.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	283
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	284 Alignment of reads from bisulfite-treated DNA in GSNAP
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	285
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	286 GSNAP has the ability to align reads from bisulfite-treated DNA, which
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	287 converts unmethylated cytosines to uracils that appear as thymines in
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	288 reads. GSNAP is able to identify genomic-T to read-C mismatches,
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	289 if a cmetindex is generated.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	290
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	291 RNA-editing tolerance in GSNAP
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	292
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	293 Just as GSNAP has a program cmetindex and a mode called "cmet" for
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	294 tolerance to C-to-T changes, it can be tolerant to A-to-G changes
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	295 using the program atoiindex and a mode called "atoi". This mode is
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	296 designed to facilitate alignments that are tolerant to RNA editing
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	297 where A's are converted to I's, which appear as G's to a sequencer.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	298
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	299 To process reads under RNA-editing tolerance, you will first need to
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	300 create th atoi index.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	301
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	302
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	303
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	304 K-mer size
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	305
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	306 You can control the k-mer size
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	307 for the genomic index with the -k flag, which can range from 12 to 15.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	308 The default value for -k is 15, but this requires your machine to have
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	309 4 GB of RAM to build the indices. If you do not have 4 GB of RAM,
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	310 then you will need to reduce the value of -k or find another machine.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	311 Here are the RAM requirements for building various indices::
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	312
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	313 k-mer of 12: 64 MB
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	314 k-mer of 13: 256 MB
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	315 k-mer of 14: 1 GB
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	316 k-mer of 15: 4 GB
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	317
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	318 These are the RAM requirements for building indices, but not to run
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	319 the GMAP/GSNAP programs once the indices are built, because the
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	320 genomic indices are compressed. For example, the genomic index for a
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	321 k-mer of 15 gives a gammaptrs file of 64 MB and an offsetscomp file of
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	322 about 350 MB, much smaller than the 4 GB that would otherwise be
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	323 required. Therefore, you may want to build your genomic index on a
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	324 computer with sufficient RAM, and distribute that index to be used by
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	325 computers with less RAM.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	326
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	327 The amount of compression can be controlled using the -b or -\-basesize
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	328 parameter to gmap_build. By default, the value for k-mer size is 15,
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	329 and the value for basesize is 12. If you select a different value for
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	330 k-mer size, then basesize is made by default to be equal to that k-mer
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	331 size.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	332
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	333 If you want to build your genomic databases with more than one k-mer
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	334 size, you can re-run gmap_build with different values of -k. This
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	335 will overwrite only the identical files from the previous runs. You
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	336 can then choose the k-mer size at run-time by using the -k flag for
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	337 either GMAP or GSNAP.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	338
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	339 </help>
10e3476429b5 Uploaded jjohnson parents: diff changeset	340 </tool>
10e3476429b5 Uploaded jjohnson parents: diff changeset	341

Mercurial > repos > jjohnson > gmap

annotate gmap_build.xml @ 2:f6ba0f12cca2 draft