CGC Tutorial

Upload files to CGC

Command to upload (an example)

/home/fangl10/apps/cgc-uploader/bin/cgc-uploader.sh -t xxxxxAuthenticationKeyxxxxxx --project xiaowen/fda-seqc2-wg-1 --tag bamSurgeon --manifest-file $ABSOLUTE/PATH/TO/file-manifest.tsv --manifest-metadata

Optionally create a .meta file for each file to be uploaded (an example)

{

  "sample_id": "bwa.tumorDesignate_IL_N_2",

  "library_id": "bwa",

  "platform": "illumina HiSeq"

}

Download

/home/fangl10/apps/aria2-1.33.1-linux-gnu-64bit-build1/aria2c --check-certificate=false -i download_link.txt