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Work on UCloud

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R

Renv

create a .Renviron in the project folder and write the line:

RENV_PATHS_CACHE=/work/Renv

(Optional) Configure repository

create a .Rprofile in the project folder and write the line:

# Configure BioCManager to use Posit Package Manager:
options(BioC_mirror = "https://packagemanager.posit.co/bioconductor")
options(BIOCONDUCTOR_CONFIG_FILE = "https://packagemanager.posit.co/bioconductor/config.yaml")

# Configure a CRAN snapshot compatible with Bioconductor 3.19:
options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/jammy/latest"))

Python

Create a conda env.

SevenBridges

SevenBridges is a cloud based commericial bioinformatics platform. BD users can use BD pre-configured pipelines to process single cell RNA-seq data generated by BD Rhapsody system.

Transfer data from UCloud to SevenBridges.

Step 0: request an account from here.

Step 1: start a terminal APP and install SevenBridges command line tool (sb). Check the reference for any update.

Step 2: Authorize sb by sb configure. Refer to here to retrieve authentication tokens.

Step 3: Crete a project or identify the project path. Example: tuhu/chlamydia01.

Step 4: Upload the file, using the bd upload command. Example: sb upload start chlamydia-01-fastq/trim --destination tuhu/chlamydia01 --tag upload_trimmed_data

Download data from SevenBridges to UCloud

  • Start a Terminal application.

  • Install aria2c by:

sudo add-apt-repository ppa:savoury1/backports
sudo apt-get update
sudo apt-get install aria2
  • Follow the instructions here