This script creates a staging folder of symlinks that point to local files in order to facilitate an upload of those files with a given directory structure / file naming convention.
Usage:
bash stage_upload_folder.sh [options]
-i|--input-file [Path to input file]
-o|--output-path [Path to write output]
Options:
-i, --input-file Path to two-column TSV input file:
column 1 = full paths to local files/folders
column 2 = full path of remote copy
-o, --output-path Path where output will be written
(will be created if it does not exist)
This script is a wrapper for the fastq-dump utility of the SRA Toolkit. It retrieves sequencing reads in FASTQ format (gzipped) from the NCBI Sequencing Read Archive (SRA) for a given set of SRR accession numbers, provided in a newline-delimited input file. It creates files named with the SRR accession and the sequence (read/mate) number (e.g., SRRnnnnnnnn_1.fastq.gz, SRRnnnnnnnn_2.fastq.gz, etc.)
It is intended for use with a cluster running Grid Engine and Environment Modules. It may also be run as a standalone bash script using bash instead of qsub.
Usage:
qsub [qsub flags] retrieve_SRR_fastq_files.qsub
-i|--input-file [input filename]
-o|--output-path [path to FASTQ files]
Options:
-i, --input-file Path to newline-separated file containing SRR accessions
(e.g., download from 'Accession List' in SRA Run Selector)
-o, --output-path Path where FASTQ files will be written
(will be created if it does not exist)