abcupload 1.0.0

ABCOMICS Genomic Data Upload Tool — upload sequencing files to ABCOMICS

abcupload

ABCOMICS Genomic Data Upload Tool

A command-line tool to upload sequencing and genomic data files to the ABCOMICS platform. It handles the full two-step upload process automatically: requesting a signed URL from the API, then streaming the file directly to secure cloud storage with a live progress bar.

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Installation

pip install abcupload

Requires Python 3.8 or later. Dependencies (requests, rich) are installed automatically.

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Quick start

# Set your API key once (contact [e-mail] to receive it)
export ABCOMICS_API_KEY=your_key_here

# Upload a single file
abcupload -u abc-000001 -p PRJAB00001 -d sample_R1.fastq.gz

# Upload all FASTQ files in the current directory
abcupload -u abc-000001 -p PRJAB00001 -d '*.fastq.gz'

# Upload an entire directory (scans for all accepted formats)
abcupload -u abc-000001 -p PRJAB00001 -d /data/project/

# Upload multiple specific files
abcupload -u abc-000001 -p PRJAB00001 -d file1.bam,file2.bam

# Test mode — files are deleted after 24 hours
abcupload -u abc-000001 -p PRJAB00001 -d '*.fastq.gz' -t

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Usage

abcupload -u USERNAME -p PROJECT_ID -d DATA [OPTIONS]

required:
  -u USERNAME     ABCOMICS username          (e.g. abc-000001)
  -p PROJECT_ID   Project ID                 (e.g. PRJAB00001)
  -d DATA         What to upload:
                    single file  :  -d sample.fastq.gz
                    comma list   :  -d file1.fastq.gz,file2.bam
                    glob pattern :  -d '*.fastq.gz'
                    directory    :  -d /path/to/data/

options:
  -k API_KEY      API key  (alternative to ABCOMICS_API_KEY env var)
  -t              Test mode — files deleted after 24 h
  -o              Overwrite existing files without asking
  -h, --help      Show this help and exit
  -V, --version   Show version and exit

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Environment variable

Set your API key as an environment variable so you do not have to pass -k on every command:

# Add to ~/.bashrc or ~/.zshrc for persistence
export ABCOMICS_API_KEY=your_key_here

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Accepted file formats

Format	Extensions
FASTQ	.fastq, .fq, .fastq.gz, .fq.gz, .fastq.bz2, .fq.bz2
FASTA	.fasta, .fa, .fna, .faa, .ffn, .frn, .fasta.gz, .fa.gz, .fna.gz, .faa.gz
BAM / SAM / CRAM	.bam, .sam, .cram
Index files	.bai, .crai, .csi, .tbi
VCF / BCF	.vcf, .vcf.gz, .bcf, .bcf.gz
Annotation	.gff, .gff3, .gtf, .bed (and .gz variants)
Tabular	.csv, .tsv

Maximum file size: 500 GB.

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What happens under the hood

1. For each file, abcupload sends a POST request to the ABCOMICS API with your username, project ID, and filename.
2. The API validates the request and returns a time-limited signed URL pointing directly to the ABCOMICS cloud storage bucket.
3. abcupload streams the file to that URL with a live progress bar showing speed, percentage, and estimated time remaining.
4. If a file with the same name already exists, you are asked whether to overwrite it or skip it (or use -o to always overwrite).

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Development install

git clone https://github.com/african-bioinformatics-center/ABCOMICS_site.git
cd ABCOMICS_site/abcupload
pip install -e .

Build a distribution:

pip install build
python -m build
# output: dist/abcupload-1.0.0.tar.gz  and  dist/abcupload-1.0.0-py3-none-any.whl

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Author

Khadim Gueye — African Bioinformatics Center (ABCOMICS)
Contact: [e-mail]

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License

MIT