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changeset 38:f1b32c09deaf draft

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Uploaded
author stef
date Fri, 10 Oct 2014 11:28:57 -0400
parents eb9a8e3a3682
children a793ffd0cd04
files falco-call.sh falco-call.xml falco-report.sh falco/amplicon-VcAn-TSACP.sh falco/init.sh falco/misc/amplicon-VcAn-TSACP.sh falco/misc/init.sh tool_dependencies.xml
diffstat 7 files changed, 67 insertions(+), 247 deletions(-) [+]
line wrap: on
line diff
--- a/falco-call.sh	Fri Oct 10 11:07:36 2014 -0400
+++ b/falco-call.sh	Fri Oct 10 11:28:57 2014 -0400
@@ -62,16 +62,17 @@
 echo "VCFOUT : "$vcf_out
 echo "INIT   : "$init_file
 
+echo "------ sourcing init_file"
 source $init_file
 
-echo "------ --- ------"
-echo "------ sam ------"
-echo "------ --- ------"
-$samtools
-echo "------ --- ------"
-echo "------ bcf ------"
-echo "------ --- ------"
-$bcftools
+#echo "------ --- ------"
+#echo "------ sam ------"
+#echo "------ --- ------"
+#$samtools
+#echo "------ --- ------"
+#echo "------ bcf ------"
+#echo "------ --- ------"
+#$bcftools
 #echo "--- snpsift ---"
 #java -jar $snpSift/SnpSift.jar
 #echo "--- snpeff ---"
@@ -85,17 +86,16 @@
 ## ----------
 ## create output files dir
 ## ----------
-#mkdir $out_path
-#mkdir $out_path/$bam_base
+mkdir $out_path
+mkdir $out_path/$bam_base
 
 ## ----------
 ## running analysis
 ## ----------
-echo "Starting VcAn"
 
 ## DEBUG
 #exit 0
-
+echo "Starting VcAn"
 $TOOLDIR/falco/amplicon-VcAn-TSACP.sh $bam_file $bam_base
 echo "...done with VcAn"
 #$TOOLDIR/falco/amplicon-AlVcAn-TSACP.sh ## this contains more
@@ -117,29 +117,29 @@
 ## ----------
 ## create index html for main galaxy output
 ## ----------
-# echo "<!DOCTYPE html>" >> $html_out
-# echo "<html>" >> $html_out
-# echo "<head>" >> $html_out
-# echo "<style>" >> $html_out
-# echo "    body{ padding: 0px 20px; }" >> $html_out
-# echo "    h1{ color: red; }" >> $html_out
-# echo "    table{ border: 1px solid black; padding: 5px }" >> $html_out
-# echo "</style>" >> $html_out
-# echo "</head>" >> $html_out
-# echo "<body>" >> $html_out
-# echo "	<h1>FALCO</h1>" >> $html_out
-# echo "	<a href=\"index.html\">HTML</a>" >> $html_out
-# echo "	<table><tbody>" >> $html_out
-# #for file in *.vcf *.txt *.tsv
-# for file in *
-# do
-# 	lineCount=`wc -l $file | cut -f 1 -d " "`
-# 	echo "	<tr><td><a href=\"$file\">$file</a> has $lineCount lines</td></tr>" >> $html_out
-# 	#echo "  <tr><td> HEAD: " `head $file` "</td></tr>" >> $html_out
-# done
-# echo "	</tbody></table>" >> $html_out
-# echo "</body>" >> $html_out
-# echo "</html>" >> $html_out
+echo "<!DOCTYPE html>" >> $html_out
+echo "<html>" >> $html_out
+echo "<head>" >> $html_out
+echo "<style>" >> $html_out
+echo "    body{ padding: 0px 20px; }" >> $html_out
+echo "    h1{ color: red; }" >> $html_out
+echo "    table{ border: 1px solid black; padding: 5px }" >> $html_out
+echo "</style>" >> $html_out
+echo "</head>" >> $html_out
+echo "<body>" >> $html_out
+echo "	<h1>FALCO</h1>" >> $html_out
+echo "	<a href=\"index.html\">HTML</a>" >> $html_out
+echo "	<table><tbody>" >> $html_out
+#for file in *.vcf *.txt *.tsv
+for file in *
+do
+	lineCount=`wc -l $file | cut -f 1 -d " "`
+	echo "	<tr><td><a href=\"$file\">$file</a> has $lineCount lines</td></tr>" >> $html_out
+	#echo "  <tr><td> HEAD: " `head $file` "</td></tr>" >> $html_out
+done
+echo "	</tbody></table>" >> $html_out
+echo "</body>" >> $html_out
+echo "</html>" >> $html_out
 
 ## ----------
 ## creating galaxy history outputs
--- a/falco-call.xml	Fri Oct 10 11:07:36 2014 -0400
+++ b/falco-call.xml	Fri Oct 10 11:28:57 2014 -0400
@@ -83,7 +83,7 @@
       manifest_file=$manifest_file
       bam_file=$bam
       bam_name=$bam.name
-      <!--html_out=$html_output-->
+      html_out=$html_output
       vcf_out=$vcf_output
       out_path=${vcf_output.files_path}
     </configfile>
@@ -98,7 +98,7 @@
   <!-- Main output is an html based report, additional on request -->
   <!-- ==================== -->
   <outputs>
-    <!--<data format="html" name="html_output" label="FALCO AAP (${jobName})" />-->
+    <data format="html" name="html_output" label="FALCO AAP (${jobName})" />
     <data format="vcf" name="vcf_output" label="FALCO AAP (${jobName}): VCF" />
   </outputs>
 
--- a/falco-report.sh	Fri Oct 10 11:07:36 2014 -0400
+++ b/falco-report.sh	Fri Oct 10 11:28:57 2014 -0400
@@ -12,7 +12,6 @@
 #vcf_out=$4
 #out_path=$5
 source $1
-JAR_PATH=$2
 #JAR_PATH=$3
 
 bam_base=`echo $bam_name | sed 's#.bam$##' - ` 
@@ -50,11 +49,11 @@
 
 ## executables
 #echo "snpEff=/ccagc/lib/snpEff/snpEff_v3_4" >> $init_file
-echo "snpEff=\$SNPEFF_JAR_PATH/" >> $init_file
+#echo "snpEff=\$SNPEFF_JAR_PATH/" >> $init_file
 #echo "snpSift=/ccagc/lib/SnpSift" >> $init_file
-echo "snpSift=\$SNPEFF_JAR_PATH/" >> $init_file
+#echo "snpSift=\$SNPEFF_JAR_PATH/" >> $init_file
 #echo "varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar" >> $init_file
-echo "varscan=\$JAVA_JAR_PATH/VarScan.v2.3.5.jar" >> $init_file
+#echo "varscan=\$JAVA_JAR_PATH/VarScan.v2.3.5.jar" >> $init_file
 
 ## files
 echo "targetBed=$BED_PATH" >> $init_file
@@ -77,12 +76,12 @@
 samtools
 echo "--- bcf ---"
 bcftools
-echo "--- snpsift ---"
-java -jar $snpSift/SnpSift.jar
-echo "--- snpeff ---"
-java -jar $snpEff/snpeff.jar
-echo "--- varscan ---"
-java -jar $varScan
+#echo "--- snpsift ---"
+#java -jar $snpSift/SnpSift.jar
+#echo "--- snpeff ---"
+#java -jar $snpEff/snpeff.jar
+#echo "--- varscan ---"
+#java -jar $varScan
 
 exit 0
 
--- a/falco/init.sh	Fri Oct 10 11:07:36 2014 -0400
+++ b/falco/init.sh	Fri Oct 10 11:28:57 2014 -0400
@@ -2,37 +2,37 @@
 
 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 
-#index=/ccagc/data/ref/hg19/stampy/hg19
-#hash=/ccagc/data/ref/hg19/stampy/hg19
-#faref=/ccagc/data/ref/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa
-#bwaref=/ccagc/data/ref/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa
+index=/ccagc/data/ref/hg19/stampy/hg19
+hash=/ccagc/data/ref/hg19/stampy/hg19
+faref=/ccagc/data/ref/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa
+bwaref=/ccagc/data/ref/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa
 #manifest=/ccagc/data/ref/manifests/TSACP/TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt
 #targetBed=/ccagc/data/ref/manifests/TSACP/TSACP.bed
 
-#dbSnp=/ccagc/data/ref/dbSNP/common_no_known_medical_impact_00-latest.f.vcf
-#dbNSFP=/ccagc/data/ref/dbNSFP/dbNSFP2.0b3.txt
-#clinvar=/ccagc/data/ref/dbSNP/clinvar_00-latest.f.vcf
-#cosmic=/ccagc/data/ref/cosmic/CosmicCodingMuts_v64_26032013_noLimit_wgs.f.vcf
-#cosmicNC=/ccagc/data/ref/cosmic/CosmicNonCodingVariants_v64_26032013_noLimit_wgs.f.vcf
-#locifilt=/ccagc/data/ref/dbSNP/locifilt.tsv
-#canonicals=/ccagc/data/ref/manifests/TSACP/canonicals.tsv
+dbSnp=/ccagc/data/ref/dbSNP/common_no_known_medical_impact_00-latest.f.vcf
+dbNSFP=/ccagc/data/ref/dbNSFP/dbNSFP2.0b3.txt
+clinvar=/ccagc/data/ref/dbSNP/clinvar_00-latest.f.vcf
+cosmic=/ccagc/data/ref/cosmic/CosmicCodingMuts_v64_26032013_noLimit_wgs.f.vcf
+cosmicNC=/ccagc/data/ref/cosmic/CosmicNonCodingVariants_v64_26032013_noLimit_wgs.f.vcf
+locifilt=/ccagc/data/ref/dbSNP/locifilt.tsv
+canonicals=/ccagc/data/ref/manifests/TSACP/canonicals.tsv
 
 illmP5="AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC"
 illmP7="AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT"
 
-#adapt_clipper=/ccagc/lib/cutadapt/cutadapt-1.1/bin/cutadapt
-#qTrim=/ccagc/bin/fastq_quality_trimmer
-#stampy=/ccagc/lib/stampy/stampy-1.0.18/stampy.py
+adapt_clipper=/ccagc/lib/cutadapt/cutadapt-1.1/bin/cutadapt
+qTrim=/ccagc/bin/fastq_quality_trimmer
+stampy=/ccagc/lib/stampy/stampy-1.0.18/stampy.py
 #samtools=/ccagc/lib/samtools/samtools-0.1.18/samtools
 #bcftools=/ccagc/lib/samtools/samtools-0.1.18/bcftools/bcftools
-#snpEff=/ccagc/lib/snpEff/snpEff_3_0a
-#snpEff=/ccagc/lib/snpEff/snpEff_v3_4
-#snpSift=/ccagc/lib/SnpSift
+snpEff=/ccagc/lib/snpEff/snpEff_3_0a
+snpEff=/ccagc/lib/snpEff/snpEff_v3_4
+snpSift=/ccagc/lib/SnpSift
 
-#varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar
-#java=/usr/bin/java
-#bwa=/ccagc/lib/bwa/bwa-0.5.9/bwa
-#flash=/ccagc/lib/flash/FLASH-1.2.2/flash
+varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar
+java=/usr/bin/java
+bwa=/ccagc/lib/bwa/bwa-0.5.9/bwa
+flash=/ccagc/lib/flash/FLASH-1.2.2/flash
 
 pairUp=$DIR/misc/pairUp.pl
 pileup2cov=$DIR/misc/pileup2cov.pl
--- a/falco/misc/amplicon-VcAn-TSACP.sh	Fri Oct 10 11:07:36 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,120 +0,0 @@
-#!/bin/bash
-
-DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-
-source $DIR/init.sh
-
-TMP=./tmp
-if [ ! -e $TMP ]
-then
-	mkdir $TMP
-fi
-
-bam=$1
-output=$2
-
-if [ ! -e $output.vcf ] 
-then
-# Use Extended BAQ!
-# Tweak indel settings -m and -F
-echo `date` " [$$] - $samtools mpileup -Euf $faref -L 1000000 -d 1000000 -m 150 -F 0.01 -o 20 $bam | bcftools view -bvcg - > $output.bcf"
-$samtools mpileup -Euf $faref -L 1000000 -d 1000000 -m 150 -F 0.01 -o 20 $bam | $bcftools view -bvcg - > $output.bcf
-echo `date` " [$$] - Done!"
-echo `date` " [$$] - bcftools view $output.bcf > $output.vcf"
-$bcftools view $output.bcf > $output.vcf
-echo `date` " [$$] - Done!"
-fi
-
-# Annotation
-#VcfIn=$output.vcf
-#VcfOut=$output.samtools.vcf
-
-#if [ ! -e $VcfOut ]
-#then
-# Samtools annotation
-#echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf"
-#$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf
-#echo `date` " [$$] - Done!"
-
-#echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf"
-#$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf
-#mv $output.snpeff.2.vcf $VcfOut
-#echo `date` " [$$] - Done!"
-
-#echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf"
-#$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf
-#mv $output.snpeff.3.vcf $VcfOut
-#echo `date` " [$$] - Done!"
-#fi 
-
-if [ ! -e $output.qc.ann.txt ]
-then
-echo `date` " [$$] - $pileup2cov2 $bam $faref $manifest $output $samtools"
-$pileup2cov2 $bam $faref $manifest $output $samtools
-echo `date` " [$$] - Done!"
-fi
-
-if [ ! -e $output.qc.ann.qual.txt ]
-then
-echo `date` " [$$] - RScript $addQual $output.qc.ann.txt $output.qc.ann.qual.txt $DIR/misc/func.R $locifilt"
-Rscript $addQual $output.qc.ann.txt $output.qc.ann.qual.txt $DIR/misc/func.R $locifilt
-echo `date` " [$$] - Done!"
-fi
-
-echo `date` " [$$] - $qcFilt $output.qc.ann.qual.txt $clinvar $cosmic $cosmicNC $output"
-$qcFilt $output.qc.ann.qual.txt $clinvar $cosmic $cosmicNC $output
-echo `date` " [$$] - Done!"
-
-echo `date` " [$$] - $qc2vcf $output.qc.ann.qual.filt.txt > $output.qc.ann.filt.vcf"
-$qc2vcf $output.qc.ann.qual.filt.txt > $output.qc.ann.filt.vcf
-echo `date` " [$$] - Done!"
-
-echo `date` " [$$] - $qc2vcf $output.qc.ann.qual.clinvar.txt > $output.qc.ann.clinvar.vcf"
-$qc2vcf $output.qc.ann.qual.clinvar.txt > $output.qc.ann.clinvar.vcf
-echo `date` " [$$] - Done!"
-
-
-
-#VcfIn=$output.qc.ann.filt.vcf
-#VcfOut=$output.qc.ann.filt.a.vcf
-
-#if [ ! -e $VcfOut ]
-#then
-
-# qc vcf annotation
-#echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf"
-#$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf
-#echo `date` " [$$] - Done!"
-
-#echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf"
-#$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf
-#mv $output.snpeff.2.vcf $VcfOut
-#echo `date` " [$$] - Done!"
-
-#echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf"
-#$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf
-#mv $output.snpeff.3.vcf $VcfOut
-#echo `date` " [$$] - Done!"
-#fi
-
-#VcfIn=$output.qc.ann.clinvar.vcf
-#	VcfOut=$output.qc.ann.clinvar.a.vcf
-
-#if [ ! -e $VcfOut ]
-#then
-
-# qc vcf annotation
-#echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf"
-#$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf
-#echo `date` " [$$] - Done!"
-
-#echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf"
-#$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf
-#mv $output.snpeff.2.vcf $VcfOut
-#echo `date` " [$$] - Done!"
-
-#echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf"
-#$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf
-#mv $output.snpeff.3.vcf $VcfOut
-#echo `date` " [$$] - Done!"
-#fi
--- a/falco/misc/init.sh	Fri Oct 10 11:07:36 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-#!/bin/bash
-
-DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-
-index=/ccagc/data/ref/hg19/stampy/hg19
-hash=/ccagc/data/ref/hg19/stampy/hg19
-faref=/ccagc/data/ref/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa
-bwaref=/ccagc/data/ref/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa
-#manifest=/ccagc/data/ref/manifests/TSACP/TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt
-#targetBed=/ccagc/data/ref/manifests/TSACP/TSACP.bed
-
-dbSnp=/ccagc/data/ref/dbSNP/common_no_known_medical_impact_00-latest.f.vcf
-dbNSFP=/ccagc/data/ref/dbNSFP/dbNSFP2.0b3.txt
-clinvar=/ccagc/data/ref/dbSNP/clinvar_00-latest.f.vcf
-cosmic=/ccagc/data/ref/cosmic/CosmicCodingMuts_v64_26032013_noLimit_wgs.f.vcf
-cosmicNC=/ccagc/data/ref/cosmic/CosmicNonCodingVariants_v64_26032013_noLimit_wgs.f.vcf
-locifilt=/ccagc/data/ref/dbSNP/locifilt.tsv
-canonicals=/ccagc/data/ref/manifests/TSACP/canonicals.tsv
-
-illmP5="AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC"
-illmP7="AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT"
-
-adapt_clipper=/ccagc/lib/cutadapt/cutadapt-1.1/bin/cutadapt
-qTrim=/ccagc/bin/fastq_quality_trimmer
-stampy=/ccagc/lib/stampy/stampy-1.0.18/stampy.py
-#samtools=/ccagc/lib/samtools/samtools-0.1.18/samtools
-#bcftools=/ccagc/lib/samtools/samtools-0.1.18/bcftools/bcftools
-snpEff=/ccagc/lib/snpEff/snpEff_3_0a
-snpEff=/ccagc/lib/snpEff/snpEff_v3_4
-snpSift=/ccagc/lib/SnpSift
-
-varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar
-java=/usr/bin/java
-bwa=/ccagc/lib/bwa/bwa-0.5.9/bwa
-flash=/ccagc/lib/flash/FLASH-1.2.2/flash
-
-pairUp=$DIR/misc/pairUp.pl
-pileup2cov=$DIR/misc/pileup2cov.pl
-pileup2cov2=$DIR/misc/perAmpliconAnalysis.pl
-addQual=$DIR/misc/addQual.R
-
-qc2vcf=$DIR/misc/qc2vcf.pl
-qcFilt=$DIR/misc/qcFilt.pl
-plots=$DIR/misc/plots.R
-plotsPng=$DIR/misc/plotsPng.R
-
-attachManifest=$DIR/misc/attachManifest.pl
-plots=$DIR/misc/plots.R
-VcAn=$DIR/amplicon-VcAn-TSACP.sh
-report=$DIR/amplicon-Report.sh
-
-alignmentStats=$DIR/misc/alignmentStats.pl
-errorRate=$DIR/misc/errorRate.pl
-plotQc=$DIR/misc/plotsQC.R
-
-#export PATH=$PATH:/ccagc/lib/samtools/samtools-0.1.18/
-source ./galaxy_init.sh
--- a/tool_dependencies.xml	Fri Oct 10 11:07:36 2014 -0400
+++ b/tool_dependencies.xml	Fri Oct 10 11:28:57 2014 -0400
@@ -13,7 +13,6 @@
     
     <package name="bcftools" version="2">
         <repository changeset_revision="5f9ba601748e" name="bcftools" owner="iuc" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-        <readme>Let's see where this msg appears...bcftools</readme>
     </package>
     
     <!--
@@ -21,7 +20,6 @@
         <repository name="package_snpeff_3_4" owner="jjohnson" prior_installation_required="TRUE" />
         <readme>Let's see where this msg appears...snpeff</readme>
     </package>
-    
     <package name="varscan" version="2">
         <repository name="varscan_version_2" owner="devteam" prior_installation_required="TRUE" />
         <readme>Let's see where this msg appears...varscan</readme>