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Bruno P. Kinoshita kinow

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View INSTALL_ECFLOW.md
# 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
cd $BOOST_ROOT
./bootstrap.sh --prefix=/home/kinow/Development/python/workspace/ecflow/boost
./b2 install
# boost_build.sh failed to locate /usr/bin/libcrypt.so ?
@kinow
kinow / RUN_AS_WORKFLOW.md
Last active Sep 3, 2022
First complete run of an Autosubmit workflow
View RUN_AS_WORKFLOW.md

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
kinow / README.md
Last active Sep 1, 2022
Re-creating streamflow-fl with other engines
View README.md

Autosubmit

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
kinow / FIRST_EXPERIMENT.md
Last active Jun 26, 2022
Running my first experiment with Autosubmit
View FIRST_EXPERIMENT.md

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,"swr.cn-south-1.myhuaweicloud.com/cngbdb/blast:1.2"])
File queryfa
String fname = '/sfs/blastdb/2019_ncov/nucl/v6/ncov'
String method = 'blastn'
Int outfmt = 7
@kinow
kinow / app.py
Created Apr 27, 2022
setuptools/discussions/3288
View app.py
def hello():
print("hello")
__version__ = '0.1'
@kinow
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: []
outputs:
@kinow
kinow / Testes.java
Last active Mar 13, 2022
GEOMETRY-142
View Testes.java
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
kinow / current.md
Last active Nov 30, 2021
Imaging.java public methods
View current.md

Not using parser parameters

Imaging.java has the following public methods that do not require parameters used by parsers.

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