mutations_caller_pipeline_aws 0.0.11 → 0.0.12

data/bin/mutations_caller_pipeline_aws

@@ -20,7 +20,7 @@ ________________________________________________________________________________
   Also you should have the indices for bwa and GATK prepared.
   NOTE: Only paired end reads are supported!
 
-                      +++  C L U S T E R  V E R S I O N  +++
+                      +++  C L U S T E R  V E R S I O N - 0.0.12 +++
 
   config.yml should look like this:
   # config.yml

data/lib/mutations_caller_pipeline_aws/bwa_caller.rb

@@ -1,8 +1,9 @@
 class BwaCaller
 
   def self.call_paired_end(r1, r2, sai1, sai2,  out_file, index, log_file, bwa, samtools, job_prefix,account, debug)
-    cmd = "qsub -o #{log_file} -hold_jid bwa_aln_#{job_prefix} -V -cwd -b y -N bwa_#{job_prefix} -l h_vmem=9G -pe make 3  #{account}\
-           #{bwa} sampe -r '@RG\tID:foo\tSM:bar\tPL:Illumina' #{index} \
+    dummy = "\\\\\\"
+    cmd = "qsub -o #{log_file} -hold_jid bwa_aln_#{job_prefix} -V -cwd -b y -N bwa_#{job_prefix} -l h_vmem=6G -pe make 3  #{account}\
+           #{bwa} sampe -r '@RG#{dummy}tID:foo#{dummy}tSM:bar#{dummy}tPL:Illumina' #{index} \
           #{sai1} #{sai2}  #{r1} #{r2} \
           \\| #{samtools} view -Su - \\| #{samtools} sort - #{out_file}"
     puts cmd

data/lib/mutations_caller_pipeline_aws/gatk_caller.rb

@@ -3,11 +3,11 @@ class GatkCaller
   # Genotyper
   def self.call(log_dir, gatk, index_fa, read_bam, read_vcf, job_prefix, account, debug)
     cmd = "echo 'starting GATK for mutant at ' `date` >> #{log_dir}
-      qsub -o #{log_dir} -V -cwd -b y -N genotyper_#{job_prefix} -l h_vmem=3G -hold_jid recalibration_#{job_prefix} #{account}\
+      qsub -o #{log_dir} -V -cwd -b y -N genotyper_#{job_prefix} -l h_vmem=4G -hold_jid recalibration_#{job_prefix} #{account}\
       #{gatk} -l INFO -R #{index_fa} -T UnifiedGenotyper \
       -I #{read_bam} \
       -o #{read_vcf} \
-      --genotype_likelihoods_model BOTH || exit 1"
+      --genotype_likelihoods_model BOTH"
     puts cmd
     system(cmd) if debug == 1
   end
@@ -20,7 +20,7 @@ class GatkCaller
       -R #{index_fa} -T CountCovariates \
       -cov ReadGroupCovariate -cov QualityScoreCovariate -cov DinucCovariate \
       -cov CycleCovariate \
-      -recalFile #{recal_file}  || exit 1 "
+      -recalFile #{recal_file}"
     puts cmd
     system(cmd) if debug == 1
   end
@@ -34,7 +34,7 @@ class GatkCaller
       -I #{read_bam} \
       -T TableRecalibration \
       -o #{recal_bam} \
-      -recalFile #{recal_file} || exit 1"
+      -recalFile #{recal_file}"
     puts cmd
     system(cmd) if debug == 1
   end
@@ -47,7 +47,7 @@ class GatkCaller
       -I #{read_bam} \
       -R #{index_fa} \
       -T RealignerTargetCreator \
-      -o #{target_intervals} || exit 1 "
+      -o #{target_intervals}"
     puts cmd
     system(cmd) if debug == 1
   end
@@ -61,7 +61,7 @@ class GatkCaller
       -R #{index_fa} \
       -T IndelRealigner \
       -targetIntervals #{target_intervals} \
-      -o #{realigned_bam}  || exit 1"
+      -o #{realigned_bam}"
     puts cmd
     system(cmd) if debug == 1
   end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mutations_caller_pipeline_aws
 version: !ruby/object:Gem::Version
-  version: 0.0.11
+  version: 0.0.12
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-01-20 00:00:00.000000000 Z
+date: 2012-01-20 00:00:00.000000000Z
 dependencies: []
 description: Using BWA to align and GATK to call the bases
 email:
@@ -53,4 +53,3 @@ signing_key:
 specification_version: 3
 summary: Call Mutations for files.fq
 test_files: []
-has_rdoc: