mvdbeek

***** Intermediate results will be written to /corral4/main/jobs/051/733/51733115/_job_tmp/tmpwi3q3lgp in docker. ****


***** Running the command:*****
time seq 0 5 | parallel -q --halt 2 --line-buffer /opt/deepvariant/bin/make_examples --mode calling --ref "reference.fasta" --reads "reads_alignment.bam" --examples "/corral4/main/jobs/051/733/51733115/_job_tmp/tmpwi3q3lgp/make_examples.tfrecord@6.gz" --channels "insert_size" --task {}

[W::hts_idx_load3] The index file is older than the data file: reads_alignment.bam.bai
[W::hts_idx_load3] The index file is older than the data file: reads_alignment.bam.bai
[W::hts_idx_load3] The index file is older than the data file: reads_alignment.bam.bai

mvdbeek

SELECT date_trunc('year', create_time) AS year, count(*) as created_in_year
  FROM galaxy_user
  WHERE purged = false and deleted = false
  GROUP BY year
  ORDER BY year;


--         year         | created_in_year
-- ---------------------+-----------------
--  2006-01-01 00:00:00 |             109

mvdbeek

import fcntl
import os
import stat
import subprocess
import threading
import time

import pytest

RWXR_XR_X = stat.S_IRWXU | stat.S_IRGRP | stat.S_IXGRP | stat.S_IROTH | stat.S_IXOTH

mvdbeek

TASK [galaxyproject.galaxy : Install Galaxy base dependencies] **********************************************************************************************************************
fatal: [cvmfs0-psu1.galaxyproject.org]: FAILED! => {"changed": false, "cmd": ["/cvmfs/test.galaxyproject.org/venv/bin/pip", "install", "--index-url", "https://wheels.galaxyproject.org/simple/", "--extra-index-url", "https://pypi.python.org/simple", "-r", "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/dependencies/pinned-requirements.txt"], "msg": "stdout: Looking in indexes: https://wheels.galaxyproject.org/simple/, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\nIgnoring asynctest: markers 'python_version >= \"3.7\" and python_version < \"3.8\"' don't match your environment\nIgnoring cached-property: markers 'python_version >= \"3.7\" and python_version < \"3.8\"' don't match your environment\nIgnoring colorama: markers 'python_version >= \"3.7\" and python_version < \"3.12\" and platform_system == \"Wi

mvdbeek

I put a few timers here and there, and it turns out we correctly load up the editor steps into the store; updateStep is only called 84 times, however changeStepMapOver is being called thousands of times.

relevant diff:

diff --git a/client/src/stores/workflowStepStore.ts b/client/src/stores/workflowStepStore.ts
index ca5f05f85c..0fd672d531 100644
--- a/client/src/stores/workflowStepStore.ts
+++ b/client/src/stores/workflowStepStore.ts

mvdbeek

import os
import subprocess
import time
from datetime import (
    date,
    datetime,
)

import click
import psutil

mvdbeek

from xsdata.formats.dataclass.parsers import XmlParser
from xsdata.formats.dataclass.parsers.config import ParserConfig

parser_config = ParserConfig(fail_on_unknown_attributes=True)
parser = XmlParser()

tool = parser.from_string("""<tool id="fastqc" name="FastQC" version="0.73+galaxy0">
    <description>
        Read Quality reports
    </description>

mvdbeek

sudo apt install slurmd slurmctld -y
sudo chmod 777 /etc/slurm-llnl
sudo cat << EOF > /etc/slurm-llnl/slurm.conf
# slurm.conf file generated by configurator.html.

# Put this file on all nodes of your cluster.

# See the slurm.conf man page for more information.

#

mvdbeek

flowchart LR
    A[User] -->|Upload Request with Fingerprint| B(Tus server)
    B --> |Auth Headers| C{Galaxy}
    C --> |200 OK| B
    B -->  D(Upload complete ?)
    D --> E(Yes)
    D --> F(No)

mvdbeek

import time
from multiprocessing import get_context


def import_test(log=False):
    now = time.time()
    from galaxy.metadata import set_metadata
    if log:
        print(time.time() - now)