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Douglas Russell dpwrussell

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@dpwrussell
dpwrussell / .gitignore
Last active January 12, 2022 22:02
MRE for https://forum.image.sc/t/omero-data-dir-not-respected-with-read-only-omero-rw-db/61644
*.sql
*.p12
*.key
*.pem
*.crt
*.jks
.env
@dpwrussell
dpwrussell / Dockerfile
Last active April 22, 2021 15:29
Passing file descriptors to Xvfb to retrieve allocated DISPLAY
FROM ubuntu:20.10
RUN apt-get -y update
RUN apt-get install -y python3 xvfb
ADD main.py main.py
CMD python3 main.py & python3 main.py
@dpwrussell
dpwrussell / .gitignore
Created December 23, 2019 14:25
Reproduce https://github.com/fabric8io/docker-maven-plugin/issues/1291
.classpath
.settings/
target/
.project
@dpwrussell
dpwrussell / Dockerfile
Created November 8, 2019 12:36
Docker x-forwarding experiment
FROM ubuntu
RUN apt-get -y update \
&& apt-get -y install xauth \
&& apt-get -y install libxt6 libxtst6 libgtk2.0-0 libnss3 libx11-xcb1 libxss1 libasound2 \
&& apt-get -y install x11-apps \
&& rm -rf /var/lib/apt/lists/*
@dpwrussell
dpwrussell / README.md
Last active March 3, 2020 15:46
MATLAB Reference Architecture CLI Example Usage

CLI Examples for MathWorks' Reference Architectures

These are examples of creating and deleting reference architectures for three MathWorks offerings; MATLAB, MATLAB Parallel Server and Network License Manager for MATLAB. There are examples for both AWS and Azure.

In each of the examples, the minimum parameters are supplied. The values for each parameter are specific to your AWS account and the deployment you with to create, so they should be set by the user. The documentation (linked to from each of the examples) goes into details of all possible parameters

@dpwrussell
dpwrussell / README.md
Created August 16, 2018 17:32
Create/Update/Delete Batch Cluster and Job Queue

Example Usage:

Create/Update/Delete of a batch cluster and job queue requires a YAML configuration file of the following shape.

Note: These values are not the actual values for our account.

Region: us-east-1
StackPrefix: stack-name
@dpwrussell
dpwrussell / README.md
Last active July 24, 2018 17:19
Create AWS user and add to specified group(s).

Example Usage:

python create_aws_user.py newuser \
  --group ComputationalScientist \
  --group SUDOers

This outputs a block of text which should be communicated to the user.

@dpwrussell
dpwrussell / rename.py
Created July 6, 2017 19:48
AT File Renaming
#!/usr/bin/env python3
import os
import re
r = re.compile(r'(\w\s-\s\d\d\(fld\s\d\swv\s\w+\s-\s[\w]+-\stime)(\s\d+)(\s-\s\d+\sms)(\)\.tif)')
d = os.path.abspath('files/')
all_files = [f for f in os.listdir(d) if os.path.isfile(os.path.join(d, f))]
@dpwrussell
dpwrussell / workshop.md
Last active August 8, 2017 05:30
OMERO User Meeting 2017 AWS Workshop

OMERO User Meeting 2017 AWS Workshop

https://tinyurl.com/ydz73puv

What is Docker?

  • ...an open source project to pack, ship and run any application as a lightweight container.

  • An abstraction layer to "containerize" any application and allow it to run on any infrastructure
  • Used to containerize OMERO, OMERO.web and and the additional components of OMERO.cloudarchive
@dpwrussell
dpwrussell / Dockerfile
Last active April 6, 2017 14:49
webtagging-docker52
FROM omero-grid-web52
MAINTAINER douglas_russell@hms.havard.edu
USER root
RUN pip install -i https://testpypi.python.org/pypi omero-webtagging-autotag \
&& pip install -i https://testpypi.python.org/pypi omero-webtagging-tagsearch
USER omero
RUN /home/omero/OMERO.server/bin/omero config append omero.web.apps '"omero_webtagging_autotag"' \
&& /home/omero/OMERO.server/bin/omero config append omero.web.ui.center_plugins '["Auto Tag", "omero_webtagging_autotag/auto_tag_init.js.html", "auto_tag_panel"]' \