API

solosis-cli

solosis-cli [OPTIONS] COMMAND [ARGS]...

Options

--debug: Enable debug mode

alignment

Commands for running alignment tools.

solosis-cli alignment [OPTIONS] COMMAND [ARGS]...

cellranger-arc-count

solosis-cli alignment cellranger-arc-count [OPTIONS]

Options

--libraries <libraries>: Path to a single libraries file

--librariesfile <librariesfile>: Path to a CSV containing paths to multiple library files

--create-bam: Generate BAM files for each library

--version <version>: Cell Ranger ARC version to use (e.g., ‘2.0.2’)

--debug: Enable debug mode

--mem <mem>

Memory limit (in MB)

Default:: 64000

--cpu <cpu>

Number of CPU cores

Default:: 4

--queue <queue>

Queue to which the job should be submitted

Default:: 'normal'

--gpu

Request a GPU with default settings

Default:: False

--time <time>: Number of GPUs to request

cellranger-count

solosis-cli alignment cellranger-count [OPTIONS]

Options

--sample <sample>: Sample ID (string)

--samplefile <samplefile>: Path to a CSV or TSV file containing sample IDs

--create-bam: Generate BAM files for each sample

--chemistry <chemistry>

Chemistry assay to define

Options:: SC5P-R2 | SC5P-PE-v3 | SC5P-R2 | SC5P-R2-v3 | SC3Pv1 | SC3Pv3 | SC3Pv2 | SC3Pv4 | SC3Pv3LT | SC3Pv3HT | SFRP | MFRP

--version <version>: Cell Ranger version to use (e.g., ‘7.2.0’)

--debug: Enable debug mode

--mem <mem>

Memory limit (in MB)

Default:: 64000

--cpu <cpu>

Number of CPU cores

Default:: 4

--queue <queue>

Queue to which the job should be submitted

Default:: 'normal'

--gpu

Request a GPU with default settings

Default:: False

--time <time>: Number of GPUs to request

cellranger-vdj

solosis-cli alignment cellranger-vdj [OPTIONS]

Options

--sample <sample>: Sample ID (string)

--samplefile <samplefile>: Path to a CSV or TSV file containing sample IDs

--version <version>: Cell Ranger version to use (e.g., ‘7.2.0’)

--debug: Enable debug mode

--mem <mem>

Memory limit (in MB)

Default:: 64000

--cpu <cpu>

Number of CPU cores

Default:: 4

--queue <queue>

Queue to which the job should be submitted

Default:: 'normal'

--gpu

Request a GPU with default settings

Default:: False

--time <time>: Number of GPUs to request

history

Commands for managing history.

solosis-cli history [OPTIONS] COMMAND [ARGS]...

clear

solosis-cli history clear [OPTIONS]

Options

-h, --hours <hours>: Age of logs to clear in hours.

--debug: Enable debug mode

uid

solosis-cli history uid [OPTIONS] UID

Options

--debug: Enable debug mode

Arguments

UID: Required argument

view

solosis-cli history view [OPTIONS]

Options

-n, --lines <lines>: Number of recent history entries to show.

--debug: Enable debug mode

irods

Commands for working with iRODS.

solosis-cli irods [OPTIONS] COMMAND [ARGS]...

iget-cellranger

solosis-cli irods iget-cellranger [OPTIONS]

Options

--sample <sample>: Sample ID (string).

--samplefile <samplefile>: Path to a CSV or TSV file containing sample IDs.

--debug: Enable debug mode

--mem <mem>

Memory limit (in MB)

Default:: 4000

--cpu <cpu>

Number of CPU cores

Default:: 2

--queue <queue>

Queue to which the job should be submitted

Default:: 'small'

--gpu

Request a GPU with default settings

Default:: False

--time <time>: Number of GPUs to request

iget-fastqs

solosis-cli irods iget-fastqs [OPTIONS]

Options

--sample <sample>: Sample ID (string)

--samplefile <samplefile>: Path to a CSV or TSV file containing sample IDs

--debug: Enable debug mode

imeta-report

solosis-cli irods imeta-report [OPTIONS]

Options

--sample <sample>: Sample ID (string).

--samplefile <samplefile>: Path to a CSV or TSV file containing sample IDs.

--debug: Enable debug mode

jobrunner

Farm related commands

solosis-cli jobrunner [OPTIONS] COMMAND [ARGS]...

command

Run a single command on the farm.

solosis-cli jobrunner command [OPTIONS] [COMMAND_TO_EXEC]...

Options

--cpu <cpu>: CPUs used

--queue <queue>: queue name

--time <time>: time for running

--cores <cores>: # of cores

--mem <mem>: mem in MB

-j, --job_name <job_name>: Name of the job

Arguments

COMMAND_TO_EXEC: Optional argument(s)

run_ipynb

solosis-cli jobrunner run_ipynb [OPTIONS]

Options

-n, --notebook <notebook>: Required Path to the notebook to run

-j, --job_name <job_name>: Name of the job

--debug: Enable debug mode

--mem <mem>

Memory limit (in MB)

Default:: 64000

--cpu <cpu>

Number of CPU cores

Default:: 1

--queue <queue>

Queue to which the job should be submitted

Default:: 'normal'

--gpu

Request a GPU with default settings

Default:: False

--time <time>: Number of GPUs to request

scrna

Commands for single-cell RNA-seq tools.

solosis-cli scrna [OPTIONS] COMMAND [ARGS]...

cellbender

solosis-cli scrna cellbender [OPTIONS]

Options

--metadata <metadata>: Path to a CSV or TSV file containing metadata

--total-droplets-included <total_droplets_included>: Choose a number that goes a few thousand barcodes into the ‘empty droplet plateau’

--expected-cells <expected_cells>: Base this on either the number of cells expected a priori from the experimental design

--debug: Enable debug mode

--mem <mem>

Memory limit (in MB)

Default:: 64000

--cpu <cpu>

Number of CPU cores

Default:: 2

--queue <queue>

Queue to which the job should be submitted

Default:: 'normal'

--gpu

Request a GPU with default settings

Default:: True

--time <time>: Number of GPUs to request

merge-h5ad

Merges multiple h5ads objects…

Please run solosis-cli sc-rna scanpy –samplefile … command first.

Example: /lustre/scratch126/cellgen/team298/soft/bin/examples/irods_download.txt Input file should have 3 mandatory columns: 1st column: sanger_id, 2nd column: sample_name, LAST column: irods path

solosis-cli scrna merge-h5ad [OPTIONS]

Options

--samplefile <samplefile>: Required Sample file text file

--merged_filename <merged_filename>: Required Output file name: Eg. merged.h5ad

scanpy

Basic Scanpy workflow for scRNA-seq data, generates Jupyter Notebook …

Example: /lustre/scratch126/cellgen/team298/soft/bin/examples/irods_download.txt Input file should have 3 mandatory columns: 1st column: sanger_id, 2nd column: sample_name, LAST column: irods path

solosis-cli scrna scanpy [OPTIONS]

Options

--samplefile <samplefile>: Required Sample file text file

--sample_basedir <sample_basedir>: sample database folder