otomo

1. Dependency

awscli
boto3
sqlite3
requests
qacct (Sun Grid Engine)
parallel (Linux command)

2. Install

git clone https://github.com/aokad/otomo.git
cd otomo
python setup.py build install

Set aws account (If you want to upload output files to aws S3)

aws configure
...

3. QuickStart

1) setup

Create SQLiteDB

$ otomo setup --wdir ${gcat_workflow_work_dir}

vi config file (option)

$ vi ~/.otomo.cfg

[notify]
slack_url = 
channel = 
label = 

[upload]
endpoint_url = 
profile =

Add samples

$ otomo regsample --samples ${samples.json}

$ cat ${samples.json}
{
    "ERP001942_ERR205022" :
    {
        "study": "ERP001942",
        "runid": "ERR205022",
        "upload": 
        {
            "expression/ERP001942_ERR205022/ERP001942_ERR205022.txt.fpkm":                 s3://BUCKET/sra/expression/ERP001942_ERR205022/ERP001942_ERR205022.txt.fpkm,
            "expression/ERP001942_ERR205022/ERP001942_ERR205022.txt.gz":                   s3://BUCKET/sra/expression/ERP001942_ERR205022/ERP001942_ERR205022.txt.gz,
            "expression/ERP001942_ERR205022/ERP001942_ERR205022.txt.summary":              s3://BUCKET/sra/expression/ERP001942_ERR205022/ERP001942_ERR205022.txt.summary,
            ...
        },
    },
...
}

2) Running Job

Set Sample Status

$ otomo analysis --sample ${sample} --status ${status} \
  --description ${description} \
  --error_message ${error_message} \
  --stop_reason ${stop_reason}

status ... init/run/success/failure/stop/finish/analysis_error/upload_error/remove_error

option

decsription
error_message
stop_reason

Set Job Status

$ qacct -j "*" -o USER -d 1 > ./qacct.txt
$ otomo regjob --qacct ./qacct.txt

Upload output files to object storage

$ otomo upload --max [1000]

3) Job Report

Add job info

$ qacct -j "*" -o OWNER -d 1 > ./qacct.txt
$ otomo regjob --qacct ./aqcct.txt

View report

$ otomo qreport ${option}

Options

-f: failure only
-b begin_time: jobs started after
--max NUMBER: limited display jobs

4. License

See document LICENSE.