mpkocher

#!/usr/bin/env Rscript

# ls /pbi/dept/secondary/siv/smrtlink/smrtlink-*
ALPHA <- "alpha"
BETA <- "beta"
BIHOURLY <- "bi-hourly"
NIGHLTLY <- "nightly"
SIV <- "siv"
SIV_ALPHA <- "siv-alpha"

mpkocher

<?xml version="1.0" encoding="utf-8" ?>
<chunk-operator id="pbsmrtpipe.operators.chunk_laa_ds">

    <task-id>pblaa.tasks.laa</task-id>

    <scatter>
        <scatter-task-id>pbsmrtpipe.tasks.subreadset_barcode_scatter</scatter-task-id>
        <chunks>
            <chunk out="$chunk.subreadset_id" in="pblaa.tasks.laa:0"/>
        </chunks>

mpkocher

# Required pbcommand >= 0.3.14
from pbcommand.pb_io.report import dict_to_report
from pbcommand.services import ServiceAccessLayer as S
from pbcommand.pb_io import load_report_from_json

sal = S("smrtlink-beta", 8081)

J_ID = 3349
R_UUID = "a37453c1-3463-4dbc-945a-f5cf2db1c812"

mpkocher

import jenkins
from collections import namedtuple
# pip install python-jenkins

Resource = namedtuple("Resource", "jenkins rpm transformer")
RELEASE_NAME = "-dromedary-"


def split_name(n):
    return n.split(RELEASE_NAME)[-1]

mpkocher

Transfer Scheme Notes

• The Scheme "id" must be ([A-z0-9-_]*)
• scheme must be "srs" (SSH+rsync) or "rsync" (rsync server)
• user non-empty string
• host non-empty string
• port int
• auth string /path/to/file
• path (see below)

mpkocher

{
    "_changelist": "UNKNOWN", 
    "_version": "0.3.5", 
    "attributes": [
        {
            "id": "mapping_stats.mapped_subread_bases_n", 
            "name": "Mapped Subread Bases", 
            "value": 281731533
        }, 
        {

mpkocher

{
    "entryPoints": [
        {
            "_comment": "datasetId can be provided as the DataSet UUID or Int. The entryId(s) can be obtained by running 'pbsmrtpipe show-pipeline-templates {PIPELINE-ID}'", 
            "datasetId": "1a369917-507e-4f70-9f38-69614ff828b6", 
            "entryId": "eid_ref_dataset", 
            "fileTypeId": "PacBio.DataSet.ReferenceSet"
        }
    ], 
    "name": "MK Dev pbservice Job", 

mpkocher

from collections import defaultdict
from pbcommand.services import ServiceAccessLayer as Sal, JobTypes

SALS = {}


def register_sal(host, port):
    s = Sal(host, port)
    SALS[host] = s
    return s

mpkocher

<?xml version="1.0" ?>
<pipeline-template-preset id="MyPreset">

    <!-- Pbsmrtpipe Engine Options -->
    <options>
    <!-- Enable Distributed Mode -->
        <option id="pbsmrtpipe.options.distributed_mode">
            <value>False</value>
        </option>
        <!-- Enable file chunking -->

mpkocher

{
    "num_3_seen": 13,
    "num_5_seen": 11,
    "num_filtered_short_reads": 0,
    "num_fl": 9,
    "num_flc": 0,
    "num_flnc": 9,
    "num_flnc_bases": 35563,
    "num_nfl": 13,
    "num_nflc": null,