SraMetaData#

Add to module run order:
#BioModule biolockj.module.getData.sra.SraMetaData

Description#

Extract metadata via pysradb from local copy of SRAmetadb.sqlite.

Properties#

Properties are the name=value pairs in the configuration file.

SraMetaData properties:#

Property Description
exe.pysradb executable
Path for the "pysradb" executable; if not supplied, any script that needs the pysradb command will assume it is on the PATH.
default: null
sra.metaDataDir file path
path to the directory where the SRAmetadb.sqlite database is stored.
default: null
sra.sraProjectId list
The project id(s) referencesing a project in the NCBI SRA. example: SRP009633, ERP016051
default: null

General properties applicable to this module:#

Property Description
cluster.batchCommand string
Terminal command used to submit jobs on the cluster
default: null
cluster.jobHeader string
Header written at top of worker scripts
default: null
cluster.modules list
List of cluster modules to load at start of worker scripts
default: null
cluster.prologue string
To run at the start of every script after loading cluster modules (if any)
default: null
cluster.statusCommand string
Terminal command used to check the status of jobs on the cluster
default: null
docker.saveContainerOnExit boolean
If Y, docker run command will NOT include the --rm flag
default: null
docker.verifyImage boolean
In check dependencies, run a test to verify the docker image.
default: null
script.defaultHeader string
Store default script header for MAIN script and locally run WORKER scripts.
default: #!/bin/bash
script.numThreads integer
Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter.
default: 8
script.numWorkers integer
Set number of samples to process per script (if parallel processing)
default: 1
script.permissions string
Used as chmod permission parameter (ex: 774)
default: 770
script.timeout integer
Sets # of minutes before worker scripts times out.
default: null

Details#

version: 0.0.0 The biolockj.module.getData.sra.SraMetaDB module is added a pre-requisite to ensure that the database is available.

Adds modules#

pre-requisite modules
biolockj.module.getData.sra.SraMetaDB
post-requisite modules
none found

Docker#

If running in docker, this module will run in a docker container from this image:

biolockjdevteam/pysradb:v1.3.18

This can be modified using the following properties:
SraMetaData.imageOwner
SraMetaData.imageName
SraMetaData.imageTag

Citation#

Module developed by Malcolm Zapatas and Ivory Blakley
BioLockJ v1.4.2