BU-ISCIII provides a serie or services in its portfolio for supporting bioinformatics analysis to the labs in the Institute of Health Carlos III. bu-isciii tools is a set of helper tools for management of these bioinformatics analysis together with the LIMS (iSkyLIMS)
micromamba create -n buisciii -f environment.yml
micromamba activate buisciii
pip install --force-reinstall --upgrade git+https://github.com/bu-isciii/buisciii-tools.git@mainor
git checkout main
conda create -n buisciii -f environment.yml
conda activate
pip install .If you want to install the latest code in the repository:
micromamba create -n buisciii_dev -f environment.yml
micromamba activate buisciii_dev
pip install --force-reinstall --upgrade git+https://github.com/bu-isciii/buisciii-tools.git@developor locally:
git checkout develop
micromamba create -n buisciii_dev -f environment.yml
micromamba activate buisciii_dev
pip install .Run bu-isciii tools:
bu-isciii --helpOutputs the following:
Usage: bu-isciii [OPTIONS] COMMAND [ARGS]...
Options:
--version Show the version and exit.
-v, --verbose Print verbose output to the console.
-l, --log-file <filename> Save a verbose log to a file.
-u, --api_user TEXT User for the API logging
-p, --api_password TEXT Password for the API logging
-c, --cred_file TEXT Config file with API logging credentials
--help Show this message and exit
Commands:
list List available bu-isciii services.
clean Service cleaning.
new-service Create new service, it will create folder and copy...
scratch Copy service folder to scratch directory for execution.
copy-sftp Copy resolution FOLDER to sftp, change status of...
finish Service cleaning, remove big files, rename folders before...
bioinfo-doc Create the folder documentation structure in bioinfo_doc...
archive Archive services or retrieve services from archive
autoclean-sftp Clean old sftp services
fix-permissions Fix permissionsList available bu-isciii services:
bu-isciii listHelp:
Usage: bu-isciii list [OPTIONS] <service>
List available bu-isciii services.
Options:
--help Show this message and exit.Output:
┏━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Service name ┃ Description ┃ Github ┃
┡━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│ assembly_annotation │ Nextflow assembly pipeline to assemble │ https://github.com/Daniel-VM/bacass/... │
│ │ bacterial genomes │ │
│ mtbseq_assembly │ Mycobacterium tuberculosis mapping, │ https://github.com/ngs-fzb/MTBseq_source │
│ │ variant calling and detection of │ │
│ │ resistance using MTBseq │ │
│ mtbseq │ Mycobacterium tuberculosis mapping, │ https://github.com/ngs-fzb/MTBseq_source │
│ │ variant calling and detection of │ │
│ │ resistance using MTBseq │ │
│ pikavirus │ PikaVirus, a mapping-based tool for │ https://github.com/BU-ISCIII/PikaVirus │
│ │ metagenome analysis of virus. │ │
│ plasmidid_assembly │ Plasmid identification tool based on │ https://github.com/BU-ISCIII/plasmidID │
│ │ mapping and assisted by assembly │ │
│ wgmlst_taranis │ Multilocus sequence typing (MLST) using │ https://github.com/BU-ISCIII/taranis │
│ │ Taranis │ │
│ wgmlst_chewbbaca │ Multilocus sequence typing (MLST) using │ https://github.com/B-UMMI/chewBBACA │
│ │ chewBBACA │ │
│ viralrecon │ Viral genome reconstruction analysis for │ https://github.com/BU-ISCIII/viralrecon │
│ │ SARS-COV-2 data │ │
│ rnaseq │ RNA-seq analysis │ https://github.com/nf-core/rnaseq │
│ lowfreq_panel │ Low frequency variant calling from │ │
│ │ enrichment panel. │ │
│ snippy │ Rapid haploid variant calling and core │ https://github.com/tseemann/snippy │
│ │ genome alignment │ │
│ seek_and_destroy │ Simple pipeline for basic quality │ https://github.com/GuilleGorines/Seek-Des… │
│ │ control, host removal and exploratory │ │
│ │ analysis of samples. │ │
│ ariba_characterization │ │ │
│ mag_met │ 1- Bioinformatics best-practise analysis │ https://github.com/nf-core/mag or │
│ │ for taxonomic classification and │ https://github.com/nf-core/taxprofiler │
│ │ profiling; 2- Bioinformatics best-practise│ │
│ │ analysis pipeline for assembly, binning │ │
└────────────────────────┴───────────────────────────────────────────┴────────────────────────────────────────────┘Example of usage:
bu-isciii new-service <resolution_id>Help:
Usage: bu-isciii new-service [OPTIONS] <resolution id>
Create new service, it will create folder and copy template depending on
selected service.
Options:
-p, --path PATH Path to create the service folder
-n, --no_create_folder No create service folder, only resolution
-a, --ask_path Please ask for path.
--help Show this message and exit.Example of usage:
bu-isciii scratch --direction service_to_scratch <resolution_id>Help:
Usage: bu-isciii scratch [OPTIONS] <resolution id>
Copy service folder to scratch directory for execution.
Options:
-p, --path PATH Absolute path to the folder containing
service to copy
-a, --ask_path Please ask for service path.
-t, --tmp_dir PATH Directory to which the files will be
transfered for execution. Default:
/data/bi/scratch_tmp/bi/
-d, --direction [service_to_scratch|scratch_to_service|remove_scratch]
Direction of the rsync command.
service_to_scratch from /data/bi/service to
/data/bi/scratch_tmp/bi/.scratch_to_service:
From /data/bi/scratch_tmp/bi/ to
/data/bi/service
--help Show this message and exit.Example of usage:
bu-isciii finish <resolution_id>Help:
Usage: bu-isciii finish [OPTIONS] <resolution id>
Service cleaning, remove big files, rename folders before copy and copy
resolution FOLDER to sftp.
Options:
-p, --path PATH Absolute path to the folder containg the service to
reaname and copy
-a, --ask_path Please ask for path, not assume pwd.
-s, --sftp_folder PATH Absolute path to directory to which the files will
be transfered
-t, --tmp_dir PATH Absolute path to the scratch directory containing
the service.
--help Show this message and exit.Finish module performs de following modules at onin this order, at once:
Example of usage:
bu-isciii clean <resolution_id>Help:
Usage: bu-isciii clean [OPTIONS] <resolution id>
Service cleaning. It will either remove big files, rename folders before
copy, revert this renaming, show removable files or show folders for no
copy.
Options:
-p, --path PATH Absolute path to the folder containing
service to clean
-a, --ask_path Please ask for path
-s, --option [full_clean|rename_nocopy|clean|revert_renaming|show_removable|show_nocopy]
Select what to do inside the cleanning step:
full_clean: delete files and folders to
clean, rename no copy and deleted folders,
rename_nocopy: just rename no copy folders,
clean: delete files and folders to
clean,revert_renaming: remove no_copy and
delete tags,show_removable: list folders and
files to remove and show_nocopy: show
folders to rename with no_copy tag.
--help Show this message and exit.bu-isciii scratch --direction scratch_to_service <resolution_id>Example of usage:
bu-isciii copy-sftp <resolution_id>Help:
Usage: bu-isciii copy-sftp [OPTIONS] <resolution id>
Copy resolution FOLDER to sftp, change status of resolution in iskylims and
generate md, pdf, html.
Options:
-p, --path PATH Absolute path to directory containing files to
transfer
-a, --ask_path Please ask for path
-s, --sftp_folder PATH Absolute path to directory to which the files will
be transfered
--help Show this message and exit.Example of usage:
bu-isciii bioinfo-doc <resolution_id>Help:
Usage: bu-isciii bioinfo-doc [OPTIONS] <resolution id>
Create the folder documentation structure in bioinfo_doc server
Options:
-p, --path PATH Absolute path to bioinfo_doc directory.
-a, --ask_path Please ask for path, not assume
/data/bioinfo_doc/.
-t, --type [service_info|delivery]
Select the documentation that will generate
-s, --sftp_folder PATH Absolute path to sftp folfer containing
service folder
-r, --report_md PATH Absolute path to markdown report to use
instead of the one in config file
-m, --results_md PATH Absolute path to markdown report to use
instead of the one in config file
-e, --email_psswd TEXT Password for [email protected]
--help Show this message and exit.Example of usage:
bu-isciii archive --date_from 2022-01-01 --date_until 2023-01-01Help:
Usage: bu-isciii archive [OPTIONS]
Archive services or retrieve services from archive
Options:
-s, --service_id TEXT service id, pe SRVCNM787
-sf, --service_file TEXT file with services ids, one per line
-t, --ser_type [services_and_colaborations|research]
Select which folder you want to archive.
-o, --option [archive|retrieve_from_archive]
Select either you want to archive services
or retrieve a service from archive.
-sp, --skip_prompts Avoid prompts (except on service choosing)
-df, --date_from TEXT The date from which start search (format
'YYYY-MM-DD')
-du, --date_until TEXT The date from which end search (format
'YYYY-MM-DD')
-f, --output_name TEXT Tsv output path + filename with archive
stats and info
--help Show this message and exit.Example of usage:
bu-isciii autoclean-sftpHelp:
Usage: bu-isciii autoclean-sftp [OPTIONS]
Clean old sftp services
Options:
-s, --sftp_folder PATH Absolute path to sftp folder
-d, --days INTEGER Integer, remove files older than a window of `-d
[int]` days. Default 14 days.
--help Show this message and exit.Example of usage:
bu-isciii fix-permissions -d /data/biHelp:
Usage: bu-isciii fix-permissions [OPTIONS]
Fix permissions
Options:
-d, --input_directory PATH Input directory to fix permissions (absolute path) [required]
--help Show this message and exit.Python package idea and design is really inspired in nf-core/tools.