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Bruno P. Kinoshita kinow

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# 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 Sep 3, 2022
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 Sep 1, 2022
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 Jun 26, 2022
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
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 Apr 27, 2022
def hello():
__version__ = '0.1'
kinow / hello.cwl
Created Mar 20, 2022
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 Mar 13, 2022
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;
kinow /
Last active Nov 30, 2021 public methods

Not using parser parameters has the following public methods that do not require parameters used by parsers.

  • hasImageFileExtension(File)
  • hasImageFileExtension(String)
View gist:afee6282c97edf090ee1b1d79b20453f
using Pkg
using Neo4jBolt
using Neo4jBolt
driver = Neo4jBoltDriver("bolt://localhost:7687", auth=("neo4j", "s3cr3t"))