Microbase S3CMD and AWS Workflow to Analyse Next Gen Sequence Data

Wsdl

Wsdl Operation

Value

Value

Value

Script

try {
    Thread.sleep(10000);
} catch(InterruptedException ex) {
    Thread.currentThread().interrupt();
}
a = "1";
b = "10";

Script

StringBuilder sb = new StringBuilder();

sb.append("{\"inputFiles\":[{\"bucket\":\"");
sb.append(BucketName_);
sb.append("\",\"path\":\"");
sb.append(BucketPath_);
sb.append("\",\"name\":\"");
sb.append(BucketFilename_);
sb.append("\"}],\"requiredOutputFiles\":[{\"bucket\":\"");
sb.append(BucketName_);
sb.append("\",\"path\":\"");
sb.append(BucketPath_);
sb.append("\",\"name\":\"");

if (sff_or_fastq.equals("fastq")) 
{ 
	sb.append("Contigs.fasta"); 
	sb.append("\"},");
}

if (sff_or_fastq.equals("sff")) 
{ 
	sb.append("Contigs.fasta");
	sb.append("\"},");
	sb.append("{\"bucket\":\"");
	sb.append(BucketName_);
	sb.append("\",\"path\":\"");
	sb.append(BucketPath_);
	sb.append("\",\"name\":\"");
	sb.append("Contigs.xml"); 
	sb.append("\"},");
}

if (Fast_Slow_Blast.equals("fast")) 
{ 
	sb.append("{\"bucket\":\"");
	sb.append(BucketName_);
	sb.append("\",\"path\":\"");
	sb.append(BucketPath_);
	sb.append("\",\"name\":\"");
	sb.append("random.fasta"); 
	sb.append("\"},");
}

sb.append("{\"bucket\":\"");
sb.append(BucketName_);
sb.append("\",\"path\":\"");
sb.append(BucketPath_);
sb.append("\",\"name\":\"");
sb.append("organism.blast"); 
sb.append("\"},");

sb.append("{\"bucket\":\"");
sb.append(BucketName_);
sb.append("\",\"path\":\"");
sb.append(BucketPath_);
sb.append("\",\"name\":\"");
sb.append("organism.txt"); 
sb.append("\"},");

sb.append("{\"bucket\":\"");
sb.append(BucketName_);
sb.append("\",\"path\":\"");
sb.append(BucketPath_);
sb.append("\",\"name\":\"");
sb.append("Organism_ID.txt"); 
sb.append("\"}");

sb.append("],\"optionalOutputFiles\":[],\"commandLines\":[");

if (sff_or_fastq.equals("fastq")) 
{ 
	sb.append("\"mpirun -np 32 /home/ubuntu/ray-build/Ray -s ");
	sb.append(BucketFilename_);
	sb.append(" -o Ray_Sample_Taverna\",\"mv %working_dir/Ray_Sample_Taverna/Contigs.fasta %working_dir\",");
}
if (sff_or_fastq.equals("sff")) 
{
	sb.append("\"python /home/ubuntu/sff_extract_0_3_0.py %working_dir/");
	sb.append(BucketFilename_);
	sb.append("\",");
	sb.append("\"mv %working_dir/");
	sb.append(Project_Name);
	sb.append(".fastq %working_dir/sample_in.iontor.fastq\",");
	sb.append("\"mv %working_dir/");
	sb.append(Project_Name);
	sb.append(".xml %working_dir/sample_traceinfo_in.iontor.fastq\",");
	sb.append("\"mira --project=sample --job=denovo,genome,accurate,iontor --fastq\",");
	sb.append("\"mv %working_dir/sample_assembly/sample_d_results/sample_out.unpadded.fasta %working_dir/Contigs.fasta\",");
}
if (Fast_Slow_Blast.equals("fast")) 
{
	sb.append("\"cp /home/ubuntu/Java_Parsers/jar/ParseFastaUpdate.class %working_dir\",");
	sb.append("\"java ParseFastaUpdate Contigs.fasta random.fasta\",");
	sb.append("\"blastall -p blastn -a 16 -d /home/ubuntu/blast_nt_db_t/nt -i %working_dir/random.fasta -o output.blast\",");
}
if (Fast_Slow_Blast.equals("slow")) 
{ 
	sb.append("\"blastall -p blastn -a 16 -d /home/ubuntu/blast_nt_db_t/nt -i %working_dir/Contigs.fasta -o output.blast\",");
}
sb.append("\"java ParserBLASTUpdated output.blast organism.txt\"");
sb.append("]}");
json = sb.toString();