- awscli
- boto3
- sqlite3
- requests
- qacct (Sun Grid Engine)
- parallel (Linux command)
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
...
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,
...
},
},
...
}
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]
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
See document LICENSE.