Interactive jobs
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= Deep sequencing for short fragment alignment (DeepAligner) = | = Deep sequencing for short fragment alignment (DeepAligner) = | ||
| - | ''Section contributed by | + | ''Section contributed by OU & SZTAKI'' |
The DeepAligner application’s workflow has been developed as a Parameter Study workflow with usage of autogenerator port (second small box around left top box in Fig xs1.) and collector job (right bottom box in Fig. xs1). The preprocessor job generates a set of input files from some pre-adjusted parameter. Then the second job (middle box in Fig. x1) will be executed as many times as the input files specify. The second job is an MPI based BLAST executable (MPIBlast) which aligns short sequences. The inputs of the MPI job are the sets of sequences (defined by the researcher) and the already deployed sequence database fragments. The last job of the workflow is a Collector which is used to collect several files and then process them as a single input. Collectors force delayed job execution until the last file of the input file set to be collected has arrived to the Collector job. The workflow engine computes the expected number of input files at run time. When all the expected inputs arrived to the Collector it starts to process all the incoming inputs files as a single input set. Finally output files will be generated, and will be stored on a Storage Element of the DCI shown as little box around the Collector in Fig 1. | The DeepAligner application’s workflow has been developed as a Parameter Study workflow with usage of autogenerator port (second small box around left top box in Fig xs1.) and collector job (right bottom box in Fig. xs1). The preprocessor job generates a set of input files from some pre-adjusted parameter. Then the second job (middle box in Fig. x1) will be executed as many times as the input files specify. The second job is an MPI based BLAST executable (MPIBlast) which aligns short sequences. The inputs of the MPI job are the sets of sequences (defined by the researcher) and the already deployed sequence database fragments. The last job of the workflow is a Collector which is used to collect several files and then process them as a single input. Collectors force delayed job execution until the last file of the input file set to be collected has arrived to the Collector job. The workflow engine computes the expected number of input files at run time. When all the expected inputs arrived to the Collector it starts to process all the incoming inputs files as a single input set. Finally output files will be generated, and will be stored on a Storage Element of the DCI shown as little box around the Collector in Fig 1. | ||
Revision as of 23:29, 24 April 2012
CMSLTM @IMBB
Jobs were submitted to the PBS queue manager
Example script:
#!/bin/bash #PBS -q lifesci #PBS -l nodes=2:ppn=5 #PBS -l walltime=10:00:00 # PBS_O_WORKDIR=/home/gkastel/layer_V1/experiment/ # PBS_NODEFILE="/home/gkastel/layer_V1/experiment/nodelist.txt" MPIEXEC="/usr/mpi/gcc/openmpi-1.4.3/bin/mpiexec" cd $PBS_O_WORKDIR NPROCS=10 NRNIV=/home/gkastel/src/nrn-7.1/x86_64/bin/nrniv NLIBS=/home/gkastel/layer_V1/mechanism/x86_64/.libs/libnrnmech.so date +%s > times.txt echo >> times.txt $MPIEXEC -np NPROCS $NRNIV -dll "$NLIBS" -mpi finalpar.hoc date +%s >> times.txt
Invocation:
qsub script-name.sh
Deep sequencing for short fragment alignment (DeepAligner)
Section contributed by OU & SZTAKI
The DeepAligner application’s workflow has been developed as a Parameter Study workflow with usage of autogenerator port (second small box around left top box in Fig xs1.) and collector job (right bottom box in Fig. xs1). The preprocessor job generates a set of input files from some pre-adjusted parameter. Then the second job (middle box in Fig. x1) will be executed as many times as the input files specify. The second job is an MPI based BLAST executable (MPIBlast) which aligns short sequences. The inputs of the MPI job are the sets of sequences (defined by the researcher) and the already deployed sequence database fragments. The last job of the workflow is a Collector which is used to collect several files and then process them as a single input. Collectors force delayed job execution until the last file of the input file set to be collected has arrived to the Collector job. The workflow engine computes the expected number of input files at run time. When all the expected inputs arrived to the Collector it starts to process all the incoming inputs files as a single input set. Finally output files will be generated, and will be stored on a Storage Element of the DCI shown as little box around the Collector in Fig 1.
Fig 1: DeepAligner workflow with the MPI based Blast job in the middle More information: [1]
In-silico Disease Gene Mapper
Section contributed by OU & SZTAKI
The in-silico Disease Gene Mapper (DiseaseGeneMapper) was ported successfully with the workflow based gUSE development environment. The ported DiseaseGeneMapper application is operated as an on-line service on the HP-SEE’s Bioinformatics eScience Gateway.
DiseaseGene (In-silico Disease Gene Mapper) [2]
