RADD

Notes:

One time setup

  1. Apply for Sockeye allocation: https://flex.redcap.ubc.ca/surveys/?s=7MKJT898LK
  2. Setup Multi-factor authentication. This is mandatory step or you will not be able to SSH.
  3. Install myVPN:
    • Set up guide for Mac users
    • Window users may need to email and request OneDrive link to download an installer, as Lisa did in April, 2024

One time setup

  1. Connect to myvpn.ubc.ca through myVPN app

  2. Connect to to Sockey through terminal using Secure Socket Shell protocol (SSH): 
    ssh username@sockeye.arc.ubc.ca
  3. Navigate to project folder: 
    cd /arc/project/st-username-1/RADD

Running part 1

  1. Interactively

    • Use apptainer prepared by Chris see logs

    See slide 7

    If this runs and produces the following output:

    ``` Detecting mass traces at 25 ppm ... OK Detecting chromatographic peaks in 41125 regions of interest ... OK: 9122 found. [1/83] 2-Fluorodeschloroketamine ... [2/83] 2-Methyl AP-237 ... [3/83] 3,4-Difluoro-U-47700 ... [4/83] 3-Hydroxyphenazepam ... [5/83] 4-Trifluoromethyl-U-47700 ... [6/83] 4F-ABINACA ... [7/83] 4F-Ethylphenidate ... [8/83] 4F-MDMB-BICA ... [9/83] 5-Methoxy MiPT ... [10/83] 5F-CUMYL-PINACA ... [11/83] 5F-EDMB-PICA ... [12/83] 5F-EMB-PICA ... [13/83] 5F-MDMB PICA ... [14/83] 8-Aminoclonazolam ... [15/83] AB-FUBINACA ... [16/83] ADB-4en-PINACA ... [17/83] ADB-BINACA ... [18/83] ADB-FUBIATA ... [19/83] ADB-HEXINACA ... [20/83] ADB-PHENITACA ... [21/83] Adinazolam ... [22/83] Alpha-PCYP ... [23/83] Alpha-PiHP ... [24/83] AP-237 ... [25/83] AP-238 ... [26/83] Benocyclidine ... [27/83] Bentazepam ... [28/83] Bromazolam ... [29/83] Bromofentanyl ... [30/83] Brorphine ... [31/83] Brotizolam ... [32/83] Butonitazene ... [33/83] BZO-HEXOXIZID ... [34/83] Chlorofentanyl ... [35/83] Ciclotizolam ... [36/83] Cl-PCP ... [37/83] Clonazolam ... [38/83] Clotiazepam ... [39/83] Delorazepam ... [40/83] Desalkylgidazepam ... [41/83] Deschloroetizolam ... [42/83] Diclazepam ... [43/83] Dipyanone ... [44/83] EDMB-PINACA ... [45/83] Estazolam ... [46/83] Etaqualone ... [47/83] Etodesnitazene ... [48/83] Etonitazene ... [49/83] Eutylone ... [50/83] F-PCP ... [51/83] Flubromazepam ... [52/83] Flubromazolam ... [53/83] Fluclotizolam ... [54/83] Flunitazene ... [55/83] Fluorofentanyl ... [56/83] FUB-144 ... [57/83] Furanyl UF-17 ... [58/83] Gidazepam ... [59/83] Loprazolam ... [60/83] Lormetazepam ... [61/83] MDMB-4en-BINACA ... [62/83] MDMB-5Br-INACA ... [63/83] Meclonazepam ... [64/83] MeO-PCE ... [65/83] Methoxpropamine ... [66/83] Methylenedioxy-PV8 ... [67/83] Metizolam ... [68/83] Metonitazene ... [69/83] N,N-Dimethylpentylone ... [70/83] N-Ethyl-U-47700 ... [71/83] N-Ethylpentedrone ... [72/83] N-methyl-U-47931E ... [73/83] N-Methylhexylone ... [74/83] n-Piperidinyl etonitazene ... [75/83] N-Pyrrolidino Etonitazene ... [76/83] Napthyl-U-47700 ... [77/83] Nitrazolam ... [78/83] para-Methyl AP-237 ... [79/83] Phenazepam ... [80/83] Pyrazolam ... [81/83] Tenocyclidine ... [82/83] U-47931E ... [83/83] Zapizolam ... [1] "writing to /scratch/st-cfjell-1/output/ms_data/expedited_2023//2023-0001BG01.rds" ``` The script is working perfectly fine and you can run all the tests.

  2. Submit as a batch array of jobs: see how-to notes

  3. Reformat .rds to .csv using R script

    • rds_to_csv.R
Archive 3a. Reformat RDS to .csv / .xlsx using Python script - ```rds_to_csv.py```

Part 2

Part 3

Part 4

[Pending]

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