Utilities for CCBR Bioinformatics Software
On biowulf you can access the latest release of
ccbr_tools
by loading the ccbrpipeliner module:
module load ccbrpipeliner
Outside of biowulf, you can install the package with pip:
pip install git+https://github.com/CCBR/Tools
Or specify any tagged version or branch:
pip install git+https://github.com/CCBR/Tools@v0.1.0
ccbr_tools --help
Usage: ccbr_tools [OPTIONS] COMMAND [ARGS]...
Utilities for CCBR Bioinformatics Software
For more options, run: tool_name [command] --help
Options:
-v, --version Show the version and exit.
-h, --help Show this message and exit.
Commands:
send-email Send an email (works on biowulf)
cite Print the citation in the desired format
version Print the version of ccbr_tools
All installed tools:
ccbr_tools
gb2gtf
hf
intersect
jobby
jobinfo
peek
import ccbr_tools.pkg_util
print(ccbr_tools.pkg_util.get_version())
0.1.3-dev
View the API reference for more information: https://ccbr.github.io/Tools/reference/
Command-line utilities in CCBR Tools.
ccbr_tools
gb2gtf
hf
intersect
jobby
jobinfo
peek
Run a command with --help
to learn how to use it.
Additional standalone scripts for various common tasks in scripts/ are added to the path when this package is installed. They are less robust than the CLI Utilities included in the package and do not have any unit tests.
add_gene_name_to_count_matrix.R
aggregate_data_tables.R
argparse.bash
cancel_snakemake_jobs.sh
create_hpc_link.sh
extract_value_from_json.py
extract_value_from_yaml.py
filter_bam_by_readids.py
filter_fastq_by_readids_highmem.py
filter_fastq_by_readids_highmem_pe.py
gather_cluster_stats.sh
gather_cluster_stats_biowulf.sh
get_buyin_partition_list.bash
get_slurm_file_with_error.sh
gsea_preranked.sh
karyoploter.R
make_labels_for_pipeliner.sh
rawcounts2normalizedcounts_DESeq2.R
rawcounts2normalizedcounts_limmavoom.R
run_jobby_on_nextflow_log
run_jobby_on_nextflow_log_full_format
run_jobby_on_snakemake_log
run_jobby_on_snakemake_log_full_format
spooker
which_vpn.sh
Please cite this software if you use it in a publication:
Sovacool K., Koparde V., Kuhn S., Tandon M., Huse S. (2024). CCBR Tools: Utilities for CCBR Bioinformatics Software (version v0.1.3). DOI: 10.5281/zenodo.13377166 URL: https://ccbr.github.io/Tools/
@misc{YourReferenceHere,
author = {Sovacool, Kelly and Koparde, Vishal and Kuhn, Skyler and Tandon, Mayank and Huse, Susan},
doi = {10.5281/zenodo.13377166},
month = {12},
title = {CCBR Tools: Utilities for CCBR Bioinformatics Software},
url = {https://ccbr.github.io/Tools/},
year = {2024}
}