Examples
Input
solosis-cli
Expected Output
Usage: solosis-cli [OPTIONS] COMMAND [ARGS]...
Command line utility for the Cellular Genetics programme at the Wellcome
Sanger Institute
Options:
--version Show the version and exit.
--help Show this message and exit.
Commands:
alignment Commands for running alignment tools.
filesystem Commands for file and directory operations.
irods Commands for working with iRODS.
ncl-bsu Commands for Newcastle University BSU.
sc-rna Commands for single-cell RNA-seq workflows.
Alignment
Cell Ranger ARC example using –sample
Input
solosis-cli alignment cellranger-arc --sample HCA_rFSKI14910984 --libraries /lustre/scratch126/cellgen/team298/lg28/irods_test/libARC.csv
Expected Output
SOLOSIS ~ version 0.3.0
[info] Starting Process: cellranger-arc
Job <192355> is submitted to queue <normal>.
Cell Ranger ARC example using –samplefile
Input
solosis-cli alignment cellranger-arc --samplefile /lustre/scratch126/cellgen/team298/lg28/irods_test/ARC.csv --libraries /lustre/scratch126/cellgen/team298/lg28/irods_test/libARC.csv
Expected Output
SOLOSIS ~ version 0.3.0
[info] Starting Process: cellranger-arc
Job <192355> is submitted to queue <normal>.
Cell Ranger count example using –sample
Input
solosis-cli alignment cellranger-count --sample HCA_SkO14189565
Expected Output
SOLOSIS ~ version 0.3.0
[info] Starting Process: cellranger-count
[info] loading Cell Ranger version 7.2.0
[action] executing command: /nfs/users/nfs_l/lg28/repos/solosis/bin/alignment/cellranger-count/submit.sh HCA_SkO14542036 7.2.0 --no-bam
[progress] starting Cell Ranger for samples: HCA_SkO14542036...
[progress] Cell Ranger submitted successfully:
** See avaiable options using: cellranger -h
Job <199964> is submitted to queue <normal>.
[success] cellranger submission complete. run `bjobs -w` for progress.
Cell Ranger count example using `–samplefile `
Input
solosis-cli alignment cellranger-count --samplefile /lustre/scratch126/cellgen/team298/lg28/irods_test/sol_input.csv
Expected Output
SOLOSIS ~ version 0.3.0
[info] Starting Process: cellranger-count
[info] loading Cell Ranger version 7.2.0
[action] executing command: /nfs/users/nfs_l/lg28/repos/solosis/bin/alignment/cellranger-count/submit.sh HCA_SkO14542035,HCA_SkO14542036 7.2.0 --no-bam
[progress] starting Cell Ranger for samples: HCA_SkO14542035,HCA_SkO14542036...
[progress] Cell Ranger submitted successfully:
** See avaiable options using: cellranger -h
Job <201312> is submitted to queue <normal>.
[success] cellranger submission complete. run `bjobs -w` for progress.
STARsolo example using –samplefile
Input
solosis-cli alignment starsolo --samplefile /lustre/scratch126/cellgen/team298/lg28/irods_test/sol_input.csv
Expected Output
SOLOSIS ~ version 0.3.0
[info] Starting Process: starsolo
[info] loading starsolo
[action] executing command: /nfs/users/nfs_l/lg28/repos/solosis/bin/alignment/starsolo/submit.sh HCA_SkO14542035,HCA_SkO14542036
[progress] starting starsolo for samples: HCA_SkO14542035,HCA_SkO14542036...
[progress] starsolo submitted successfully:
Job <201433> is submitted to queue <normal>.
Submitted array LSF job for 2 samples.
[success] starsolo submission complete. run `bjobs -w` for progress.
Filesystem
Disk-usage example
Input
solosis-cli filesystem disk-usage
Expected Output
SOLOSIS ~ version 0.3.0
[info] Starting Process: disk-usage
[progress] Calculating disk usage for team298 ...
[progress]
workspace size used avail use%
--------- ----- ------ ----- -----
Lustre 45T 41.03T 4T 91%
nfs 60T 49T 12T 81%
warehouse 1.0T 769G 256G 76%
File-count example
Input
solosis-cli filesystem file-count
Expected Output
SOLOSIS ~ version 0.3.0
[info] Launching: filecount
[progress]
Script completed. Email sent to lg28@sanger.ac.uk
irods
iget-cellranger example using –samplefile
Input
solosis-cli irods iget-cellranger --samplefile /lustre/scratch126/cellgen/team298/lg28/irods_test/sol_input.csv
Expected Output
SOLOSIS ~ version 0.3.0
[info] Starting Process: iget-cellranger
[success] Command executed successfully.
[info] Samples for download:
1. HCA_SkO14542035
2. HCA_SkO14542036
[success] LSF Job ID 202652 submitted to 'small' queue.
[info] Use `bjobs` to monitor job completion.
[info] View job logs at $HOME/logs.
iget-fastqs example using –samplefile
Input
solosis-cli irods iget-fastqs --samplefile /lustre/scratch126/cellgen/team298/lg28/irods_test/sol_input.csv
Expected Output
SOLOSIS ~ version 0.3.0
[info] Starting Process: iget-fastqs
[success] Command executed successfully.
[progress] samples without FASTQ files: ['HCA_SkO14542035', 'HCA_SkO14542036']
[progress] executing command: /nfs/users/nfs_l/lg28/repos/solosis/bin/irods/iget-fastqs/submit.sh HCA_SkO14542035,HCA_SkO14542036
[progress] starting process for samples: HCA_SkO14542035,HCA_SkO14542036...
\ #*spinner*
sc-rna
cellbender example using –samplefile
Input
solosis-cli sc-rna cellbender --samplefile /lustre/scratch126/cellgen/team298/lg28/irods_test/sol_input.csv --total_droplets_included 30000
Expected Output
SOLOSIS ~ version 0.3.0osis$
** See avaiable options using: cellbender remove-background -h
** Using custom python for this environment
python=3.10.12 cellbender=0.3.0 torch=2.3.1
Job <203560> is submitted to queue <gpu-normal>.
merge-h5ad example using –samplefile
Input
solosis-cli sc-rna merge-h5ad --samplefile /lustre/scratch126/cellgen/team298/lg28/irods_test/sol_input.csv --merged_filename merged.h5ad
Expected Output
SOLOSIS ~ version 0.3.0
Your run token is:
Generating a bsub script rna_merge_.bsub
Job <205162> is submitted to default queue <normal>.
scanpy example using –samplefile
Input
solosis-cli sc-rna scanpy --samplefile /lustre/scratch126/cellgen/team298/lg28/irods_test/sol_input.csv
Expected Output
SOLOSIS ~ version 0.3.0
(2) [Info] _HCA_SkO14542035 will be processed in /lustre/scratch126/cellgen/team298/sample_data//_HCA_SkO14542035/rna_scanpy/
(3) [Info] _HCA_SkO14542036 will be processed in /lustre/scratch126/cellgen/team298/sample_data//_HCA_SkO14542036/rna_scanpy/
[Info] batch job submitted. check using 'bjobs -w' command
Job <205522> is submitted to default queue <normal>.