On Sherlock, run pyenv local dvv_seq in your cloned directory
Add the following to your $HOME/.bash_profile (using the appropriate path to your cloned directory):
export PYTHONPATH="/path/to/SingleCellSequencing:$PYTHONPATH"To import the necessary shared libraries, you will need to execute the following each time after you log in to Sherlock (alternatively, you can add it as a line to your $HOME/.bash_profile):
module load dvv_seq-
Create an account at mongolab.com
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Sign in and get to the home screen
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Next to "MongoDB Deployments" you'll see three buttons. Click the one that says "Create new".
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For "Cloud provider", select "amazon web services". For "Location": "Amazon's US East (Virginia) Region (us-east-1)".
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Under "Plan", choose "Single-node" and select "Sandbox" (...it's free).
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For "Database name" write "single_cell_sequencing".
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Click "Create new MongoDB deployment".
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Back on the home screen, click on "single_cell_sequencing".
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Click on the "Users" tab and then select "Add a database user".
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Choose a username and password. Note that in fireworks, the password is stored in plaintext.
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Note that the information shown at the top ("To connect using the shell") contains the database hostname and database port (the part after the colon is the port).
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Run
python initialize.py -
Run
lpad resetand chooseYes if prompted
To queue a set of directories to process, run:
python fw_queue.py /path/to/directory/containing/librariesTo see a list of help options, run:
python fw_queue.py --helpTo run fireworks interactively (after having queued your jobs), run:
rlaunch rapidfireThis is useful for debugging, but you probably don't want to use it in production because it runs serially.
Do not do this on a login node (your tasks are too computationally expensive)
To run using the scheduler:
qlaunch -r rapidfire --nlaunches infinite --sleep 5This command will run forever until you Ctrl-C to kill it once you see that all the output and analysis files have been generated.
qlaunch is relatively lightweight, so you can probably get away with running it on a login node.