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:

'long'

--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 as a comma-separated (.csv) or tab-separated (.tsv) file. The file must have a column named ‘sample_id’ containing the sample IDs.

Example CSV format: sample_id s12345 s67890

--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:

'long'

--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

--metadata <metadata>

Path to a CSV or TSV file containing metadata

--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]...

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. If not provided, the execution UID will be used

--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

single-job

solosis-cli jobrunner single-job [OPTIONS] [COMMAND_TO_EXEC]...

Options

-j, --job_name <job_name>

Optional name of the job. If not provided, the execution UID is used.

--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

Arguments

COMMAND_TO_EXEC

Optional argument(s)

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

solosis-cli scrna merge-h5ad [OPTIONS]

Options

--samplefile <samplefile>

Required Sample file text file

--merged_filename <merged_filename>

Required Output file name, e.g., merged.h5ad

--job_name <job_name>

Optional name for the LSF job. Defaults to merge_h5ad_<uid>.

--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

scanpy

solosis-cli scrna scanpy [OPTIONS]

Options

--samplefile <samplefile>

Required Sample file text file

--sample_basedir <sample_basedir>

Sample database folder

--job_name <job_name>

Optional name for the LSF job. Defaults to scanpy_<uid>.

--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