Thursday, July 23, 2015

Notes on decrypting dbGaP datasets

1. Install aspera     download from (select aspera connect and then show all installers) 2. Download using aspera     working exampole download gtex to tarbell 11/25/214 (this didn’t work, may work) "/home/him1/.aspera/connect/bin/ascp" -QTr -l 300M -k 1 -i "/home/him1/.aspera/connect/etc/asperaweb_id_dsa.openssh" -W AB6D9CB19B62747EC89082FF7954E5F901C737E21A8D44CC3B2D4D2E94D0AA1E7C79C059D9E704B36AF81B523E9EA81C4D . 3. download manifest 4. get repository key 5. Decrypt (modified on 4/15/2015)     - download decryption tools from dbGaP     - run ./vdb-config -i from the sratoolkit bin directory     - press 4 and import repository key (prj_6981.ngc, this will create a working folder  /Users/haky/ncbi/dbGaP-6981/)     - from the working directory created by the ugly vdb-config run vbd-decrypt   > cd  /Users/haky/ncbi/dbGaP-6981/   >  ~/bin/sratoolkit.2.4.5-2-mac64/bin/vdb-decrypt /Volumes/Pegasus/im-lab/nas40t2/haky/Data/dbGaP/GTEx/43830  working examples: 5052 is the number of the project that requested the data access (5052=Phenotype Prediction IRB) 43831 is the download request id
>cd /Users/haky/ncbi/dbGaP-5052/ >~/bin/sratoolkit.2.4.5-2-mac64/bin/vdb-decrypt /Volumes/Pegasus/im-lab/nas40t2/Data/dbGaP/Framingham/44795/

I should clean it up but the instructions on decrypting were helpful.

No comments: