Thursday, July 23, 2015

Notes on decrypting dbGaP datasets

1. Install aspera     download from http://downloads.asperasoft.com/downloads (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, cri-syncmon.cri.uchicago.edu 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 dbtest@gap-upload.ncbi.nlm.nih.gov:data/instant/haeky2/41316 . 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.

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