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Panel
titleblastparam.sh

#!/bin/sh

export PATH=$PATH:$VO_ACADEMICGRID_SW_DIR/blast/bin

export LFC_HOST=lfc.biruni.upm.my

FOLDER_PREFIX=/grid/academicgrid/farhan/blast/full

FOLDER_FASTA=$1

FOLDER_RESULT=$2

FASTA_FILE=frag$3.fasta

OUTPUT_FILE=$FASTA_FILE.xml

FASTA_LFC=$FOLDER_PREFIX/$FOLDER_FASTA/$FASTA_FILE

lcg-cp lfn:$FASTA_LFC file:$FASTA_FILE

export BLASTDB=/opt/blastdb

export BLASTMAT=$VO_ACADEMICGRID_SW_DIR/blast/data

echo "Blast started at `date`”

blastall -b 20 -v 20 -p blastx -e 0.001 -m 7 -d nr2go nr -i $FASTA_FILE -o $OUTPUT_FILE

echo "Blast ended at `date`"

lcg-cr -l lfn:$FOLDER_PREFIX/$FOLDER_RESULT/$OUTPUT_FILE -d dpm.biruni.upm.my file:$OUTPUT_FILE

...

 

Panel
titledag.jdl

[

Type = "dag";

InputSandbox = {"job.sh", "job2.sh"};

Nodes = [

  nodeA = [

    Description = [

    JobType = "Normal”;

    Executable = "job.sh";

    Arguments = "A”;

    StdOutput = "std.out”;

    StdError = "std.err”;

    InputSandbox = {root.InputSandbox[0]};

    OutputSandbox = {"std.out","std.err"};

    ];

  ];

  nodeB = [

    Description = [

    JobType = "Normal";

    Executable = "job2.sh";

    Arguments = "B";

    StdOutput = "std.out";

    StdError = "std.err";

    InputSandbox = {root.InputSandbox[1]};

    OutputSandbox = {"std.out","std.err"};

    ];

  ];

  nodeC = [

    Description = [

    JobType = "Normal";

    Executable = "job3.sh";

    Arguments = "C";

    StdOutput = "std.out";

    StdError = "std.err";

    InputSandbox = {"job3.sh"};   OutputSandbox = {"std.out","std.err"};

     ];

  ];

  nodeD = [

  Description = [

    JobType = "Normal";

    Executable = "job.sh";

    Arguments = "D";

    StdOutput = "std.out";

    StdError = "std.err";

    InputSandbox = {root.InputSandbox[0]};

    OutputSandbox = {"std.out","std.err"};

    ];

  ];

];

Dependencies = { {nodeA,nodeB},{nodeA,nodeC},{{nodeB,nodeC},nodeD} };

]

Panel
titlejob1.sh

#!/bin/bash

echo "Job $1 - `date` - BEGIN"

hostname

sleep 100

echo "Job $1 - `date` - END"

Panel
titlejob2.sh

#!/bin/bash

echo "This is job2"

echo "Job $1 - `date` - BEGIN"

hostname

sleep 100

echo "Job $1 - `date` - END"

Panel
titlejob3.sh

#!/bin/bash

echo "This is job3"

echo "Job $1 - `date` - BEGIN"

hostname

sleep 100

echo "Job $1 - `date` - END"