bsc provides a command line interface to common requests on the Illumina's BaseSpace cloud API.
- Install the python sdk.
- Fill in your credentials on the ~/.basespacepy.cfg file (more details on the link above).
The script can be used by itself as a command line program, (try --help) or as a module, check out the as_module_example.py file.
$ ./bsc.py -a list_projects
proj_name proj_id
NextSeq 500: TruSeq PCR Free WGS_RTA2.1.3.0 (NA12878) 8705697
NextSeq 500 v2: Nextera Rapid Capture Exome (CEPH Trio) 19559545
$ ./bsc.py -a list_samples -p 19559545
experiment_name sample_name sample_id
NextSeq 500 v2: NRC NA12878_Rep1 21472706
NextSeq 500 v2: NRC NA12892_Rep1 21472707
NextSeq 500 v2: NRC NA12891_Rep1 21472708
$ ./bsc.py -a list_samplefiles -s 21472706 -l all
file_size file_path file_id
672601396 NA12878-Rep1_S1_L001_R1_001.fastq.gz 1411485021
687038064 NA12878-Rep1_S1_L001_R2_001.fastq.gz 1411485022
674214209 NA12878-Rep1_S1_L002_R1_001.fastq.gz 1411485023
686805446 NA12878-Rep1_S1_L002_R2_001.fastq.gz 1411485024
661133853 NA12878-Rep1_S1_L003_R1_001.fastq.gz 1411485025
672065598 NA12878-Rep1_S1_L003_R2_001.fastq.gz 1411485026
686304285 NA12878-Rep1_S1_L004_R1_001.fastq.gz 1411485027
697163335 NA12878-Rep1_S1_L004_R2_001.fastq.gz 1411485028