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Seeking advice on PathSeq

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  • #46
    Installation on cluster

    Hi Chandra,

    One quick question. Do you provide an installer to setup and run PathSeq on a local cluster/server? It would be great if we have one. BWA based alignment against other genomic databases can be performed even on cluster with in an hour. Do you have any plan to release such a version, it will be a great help to the research community

    Thanks and look forward to your comments

    Best

    Praveen.

    Comment


    • #47
      Hi Praveen,

      I just made the Pathseq_BWA.

      I released it for beta tester.

      This weekend, i will upload the latest one.

      Thanks
      Chandra



      Originally posted by pravee1216 View Post
      Hi Chandra,

      One quick question. Do you provide an installer to setup and run PathSeq on a local cluster/server? It would be great if we have one. BWA based alignment against other genomic databases can be performed even on cluster with in an hour. Do you have any plan to release such a version, it will be a great help to the research community

      Thanks and look forward to your comments

      Best

      Praveen.

      Comment


      • #48
        Sounds good. When would it be available to us? Is this version capable to run on a server system?

        Thanks for the initiative of building this version

        Praveen.

        Comment


        • #49
          Hi Chandra,
          Any update on Pathseq_BWA?

          -Dinesh

          Comment


          • #50
            Hi Pathseq users,

            We released new version Pathseq version 1.2 that has following updates:

            http://www.broadinstitute.org/softwa...Downloads.html

            Update:
            1. BWA aligner replaces the MAQ aligner
            2. S3CMD has been updated
            3. Added new datatype called DATATYPE (WGS/RNASEQ). This helps the pipeline to select the databases (reference genomes)
            4. Hadoop framework has been updated to 1.0.3.

            Please kindly send me your comments and suggestions.

            Thanks
            Chandra

            Comment


            • #51
              Hi Chandra,

              Nice to see the update. Does this version support or run on a cluster system? Do you have any plan to release it?

              Thanks

              Praveen.

              Comment


              • #52
                Hi Praveen,

                What kind of cluster system you have?

                I am working on several other options, which will be released soon,

                Thanks
                Chandra
                Originally posted by pravee1216 View Post
                Hi Chandra,

                Nice to see the update. Does this version support or run on a cluster system? Do you have any plan to release it?

                Thanks

                Praveen.

                Comment


                • #53
                  Thanks for the update, Chandra. Will try it out and get back to you...

                  - Dinesh

                  Originally posted by pcs_murali View Post
                  Hi Pathseq users,

                  We released new version Pathseq version 1.2 that has following updates:

                  http://www.broadinstitute.org/softwa...Downloads.html

                  Update:
                  1. BWA aligner replaces the MAQ aligner
                  2. S3CMD has been updated
                  3. Added new datatype called DATATYPE (WGS/RNASEQ). This helps the pipeline to select the databases (reference genomes)
                  4. Hadoop framework has been updated to 1.0.3.

                  Please kindly send me your comments and suggestions.

                  Thanks
                  Chandra

                  Comment


                  • #54
                    Looks like there is a bug in Preprocessed_Reads.com file. Line 18 says exit and the script quits.
                    After commenting the line, the script runs fine.
                    Code:
                    @ n_para=$#
                    
                    # Reading environmental variables for running job from cluster.config and job.config
                    set para = `awk -f readconfig.awk T0=cluster.config T01=job.config < .empty.lst`
                    set fq1 = $1
                    
                    echo $para[15]
                    
                    [B]exit[/B]
                    
                    echo $fq1 > .tmp
                    set namefile = `awk '{ns=split($1, x, "/"); print x[ns];}' .tmp`
                    Last edited by DineshCyanam; 09-12-2012, 12:02 PM.

                    Comment


                    • #55
                      Alright... So I ran the new PathSeq_BWA version and here are the results. I had ~65 million filtered reads and it took ~8 hours to finish and produced 177308 unmapped reads. This was run on 19 nodes (+1 master node) as a large instance.

                      More when I'm done analyzing the results.

                      - Dinesh

                      Comment


                      • #56
                        Hi people of the thread...

                        Does PathSeq still requires the use of AWS for installation?

                        I just graduated from uni and would like to explore the use of PathSeq as it sounds fun! but if it still requires AWS and credit card then I might not be able to do so

                        However I do have access to unix cluster, but if the installation instruction from http://www.broadinstitute.org/softwa...tallation.html still holds true, then I don't think I have the resource to use AWS

                        On a side not, how much would AWS charge for a PathSeq run?

                        Cheers

                        Comment


                        • #57
                          Hi Zaki,

                          PathSeq that is downloaded from the URL is configured for the AWS. However, technically, it can run local hadoop cluster (which may need some changes to scripts).

                          AWS charge for PathSeq entirely depends on your data. We don't have any kind of affiliation to AWS.

                          Please let me know if you have unix cluster that is configured for hadoop?

                          Thanks
                          Chandra

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