old_contents: #!/usr/bin/python
  import os
  
  docker_id = "0ede86ece3ce"
  f = open("filenames_1.txt", "r")
  for filename in f:
      filename = filename.rstrip()
      analysis_id = filename.replace(".fastq.tar.gz", "")
      filepath = "/home/ubuntu/SCRATCH/%s" %(filename)
      print analysis_id
      output = "/home/ubuntu/SCRATCH/geuvadis_results/%s" %(analysis_id)
      if not os.path.isdir(output):
  	os.mkdir(output)
  
      os.system("docker run
      -v /home/ubuntu/:/host/home
      -v /etc:/host/etc
      -v /mnt/SCRATCH:/home/ubuntu/SCRATCH/
      -i
      -t %s /usr/bin/python /home/ubuntu/expression/pipeline_elastic_cluster_new.py
      --analysis_id %s
      --gtf /home/ubuntu/SCRATCH/geuvadis_genome/gencode.v19.annotation.hs37d5_chr.gtf
      --input_file %s
      --p 8
      --star_pipeline /home/ubuntu/expression/icgc_rnaseq_align/star_align.py
      --output_dir %s
      --genome_fasta_file /home/ubuntu/SCRATCH/geuvadis_genome/hs37d5.fa
      --genome_dir /home/ubuntu/SCRATCH/geuvadis_genome/star_genome/
      --quantMode TranscriptomeSAM
      --cufflinks_pipeline /home/ubuntu/expression/compute_expression.py
      --ref_flat /home/ubuntu/SCRATCH/geuvadis_genome/refFlat.txt"
      %(docker_id, analysis_id, filepath, output))
  
  
  
  
  
  
  
new_contents: #!/usr/bin/python
  import os
  
  docker_id = "0ede86ece3ce"
  f = open("filenames_1.txt", "r")
  for filename in f:
      filename = filename.rstrip()
      analysis_id = filename.replace(".fastq.tar.gz", "")
      filepath = "/home/ubuntu/SCRATCH/%s" %(filename)
      print analysis_id
      output = "/home/ubuntu/SCRATCH/geuvadis_results/%s" %(analysis_id)
      if not os.path.isdir(output):
  	os.mkdir(output)
  
      os.system("docker run\
      -v /home/ubuntu/:/host/home\
      -v /etc:/host/etc\
      -v /mnt/SCRATCH:/home/ubuntu/SCRATCH/\
      -i\
      -t %s /usr/bin/python /home/ubuntu/expression/pipeline_elastic_cluster_new.py\
      --analysis_id %s\
      --gtf /home/ubuntu/SCRATCH/geuvadis_genome/gencode.v19.annotation.hs37d5_chr.gtf\
      --input_file %s\
      --p 8\
      --star_pipeline /home/ubuntu/expression/icgc_rnaseq_align/star_align.py\
      --output_dir %s\
      --genome_fasta_file /home/ubuntu/SCRATCH/geuvadis_genome/hs37d5.fa\
      --genome_dir /home/ubuntu/SCRATCH/geuvadis_genome/star_genome/\
      --quantMode TranscriptomeSAM\
      --cufflinks_pipeline /home/ubuntu/expression/compute_expression.py\
      --ref_flat /home/ubuntu/SCRATCH/geuvadis_genome/refFlat.txt"
      %(docker_id, analysis_id, filepath, output))
  
  
  
  
  
  
  
subject: update scripts