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