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Bruno P. Kinoshita kinow

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kinow / coverage.xml
Created May 19, 2023 20:50
cylc pytest-cov output
View coverage.xml
This file has been truncated, but you can view the full file.
<?xml version="1.0" ?>
<coverage version="7.2.5" timestamp="1684529350876" lines-valid="23787" lines-covered="17741" line-rate="0.7458" branches-valid="10117" branches-covered="6379" branch-rate="0.6305" complexity="0">
<!-- Generated by -->
<!-- Based on -->
<package name="flow" line-rate="0.7415" branch-rate="0.6293" complexity="0">
View gist:ce0435d4ffd1e4a2fcfede53735cd03e
This file has been truncated, but you can view the full file.
Apache Maven 3.8.5 (3599d3414f046de2324203b78ddcf9b5e4388aa0)
Maven home: /opt/apache-maven-3.8.5
Java version: 17.0.6, vendor: Private Build, runtime: /usr/lib/jvm/java-17-openjdk-amd64
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "5.15.0-69-generic", arch: "amd64", family: "unix"
[INFO] Scanning for projects...
# git clone ...ecflow
# git checkout 5.8.4
ln -s /home/kinow/Development/python/workspace/ecflow/ /tmp/ecflow_build/ecFlow-5.8.4-Source
export WK=/tmp/ecflow_build/ecFlow-5.8.4-Source
export BOOST_ROOT=/tmp/ecflow_build/boost_1_71_0
./ --prefix=/home/kinow/Development/python/workspace/ecflow/boost
./b2 install
# failed to locate /usr/bin/ ?
kinow /
Last active September 3, 2022 07:59
First complete run of an Autosubmit workflow

Managed to complete a run of an Autosubmit workflow today for the first time, running the commands that I wanted. Here's where I was erring, and what I did to fix it.

Ubuntu sshd configurations

When you use the PS platform type, you also need to enable an SSH server. Autosubmit reads the SSH config file to load the host configuration.

kinow /
Last active September 1, 2022 04:33
Re-creating streamflow-fl with other engines


Install Autosubmit with pip install autosubmit==3.*. Follow their tutorial to set up the workflow engine (basically autosubmit configure and autosubmit install to create the directories, files, and databases).

Create an experiment with autosubmit expid --HPC local --description "autosubmit-fl...", and edit the files expdef_a000.conf and jobs_a000.conf in the ~/autosubmit/a000/ directory. The important entries to add or modify in expdef_a000.conf are:

kinow /
Last active June 26, 2022 05:58
Running my first experiment with Autosubmit

Here's the step by step that I used to have a running workflow.

  1. Synced master branch
  2. Re-installed dependencies in venv, pip install -U -e .
  3. Removed old files, rm -rf ~/.autosubmit* and rm -rf ~/autosubmit
  4. Configured and installed Autosubmit, autosubmit configure, followed by autosubmit install
  5. Created a new dummy experiment with autosubmit expid -H local --dummy -d DummyExp
  6. Updated my experiment's platform file
kinow / blast.wdl
Created June 2, 2022 03:38
View blast.wdl
version 1.0
workflow blast {
input {
String? blast_docker_override
String blast_docker= select_first([blast_docker_override,""])
File queryfa
String fname = '/sfs/blastdb/2019_ncov/nucl/v6/ncov'
String method = 'blastn'
Int outfmt = 7
kinow /
Created April 27, 2022 12:29
def hello():
__version__ = '0.1'
kinow / hello.cwl
Created March 20, 2022 09:18
tests streamflow
View hello.cwl
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Hello World"
doc: "Outputs a message using echo"
inputs: []
kinow /
Last active March 13, 2022 02:32
package org.apache.commons.geometry.examples.tutorials;
import java.util.Map;
import org.apache.commons.geometry.core.collection.PointMap;
import org.apache.commons.geometry.core.internal.PointMapAsSetAdapter;
import org.apache.commons.geometry.euclidean.EuclideanCollections;
import org.apache.commons.geometry.euclidean.oned.Vector1D;
import org.apache.commons.numbers.core.Precision;