Andrew Perry pansapiens

## get_latest_container.sh
#!/bin/bash
#
# ./get_latest_container.sh
# Given a bioconda package name as the first argument, downloads
# the most recent corresponding Singularity image from quay.io/biocontainers
#
# Usage:
#
#   ./get_latest_container.sh <package_name>
#

## _README.md

      
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                pansapiens
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              April 14, 2022 11:01
            
              
                The Aspera ascp key you are looking for
              
          
    Installing and running ascp is a PITA.
Here's the private key you need (at least for NCBI/ENA downloads).
ascp is now available in a Docker container. This makes things easier.
Do this:
# We need the not-actually-secret private key that comes packaged with Aspera Connect but is inexplicably not used as the default
# when no key is specified. Here's one I prepared earlier.


## make_tiled_composite_video.py
#!/usr/bin/env python
"""
Given a list of video files, creates a tiled output video with each
input video playing simulutaneously with mixed audio.
The result is something like a composite security camera feed, or the
"Brady Bunch" opening credits.

DISCLAIMER: The author holds no responsibility for your actions if you
become criminally insane from watching all nine Puppet Master films
simultaneously. You have been warned.

## Dockerfile
FROM continuumio/miniconda3

#
# docker build -t pansapiens/rnasik:latest -t pansapiens/rnasik:1.5.4 .
# docker run --rm -it -v $(pwd):/data pansapiens/rnasik --help
#

RUN conda install --yes -c conda-forge mamba
RUN mamba install --yes -c bioconda -c conda-forge -c serine -c serine/label/dev -c anaconda -c defaults -c r -c conda-forge/label/broken \
                           python=3.6 rnasik=1.5.4 qualimap=2.2.2b=0 "pandas<1" && \

## grab_from_cloudstor_pw_protect.py
#!/usr/bin/env python3

# https://colab.research.google.com/drive/1CGOygPAmjTxWnmsywv178dh3u36ZRBgv

# You'll need to install the `robobrowser` Python package.
# Do it in a virtualenv like:
#
# python3 -m venv ~/.virtualenvs/cloudstor
# source ~/.virtualenvs/cloudstor/activate
# pip3 install robobrowser

## test_signals.ipynb

      
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                pansapiens
                / test_signals.ipynb
            
            
              Created
              November 26, 2020 03:49
            
              
                test_signals.ipynb
              
          
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## switch_docker_image_library_path.sh
##
#  Update - no longer works. You need to also:
#  edit: /lib/systemd/system/docker.service
#  then run: sudo systemctl daemon-reload
#  see, https://medium.com/@ibrahimgunduz34/how-to-change-docker-data-folder-configuration-33d372669056
#
#  TODO: Fix this to use sed or similar to edit /lib/systemd/system/docker.service
##

# From: https://forums.docker.com/t/how-do-i-change-the-docker-image-installation-directory/1169

## Mutable Instruments - Firmware upload process.md

      
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              November 8, 2020 05:10
                — forked from JamesHagerman/Mutable Instruments - Firmware upload process.md
            
          
    How to get firmware onto mutable modules

On Ubuntu 20.04.
(I have not yet tried the Black Magic Probe and gdb parts)
Install compiler

First install the arm compiler:

  
## Dockerfile
FROM ubuntu:18.04
RUN apt-get -y update && \
    apt-get -y install git build-essential autogen autotools-dev automake \
                       libsdsl-dev libsdsl3 libsparsehash-dev zlib1g-dev libboost-all-dev libgomp1 && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/*
WORKDIR /
RUN git clone --depth 1 --branch 2.3.2 https://github.com/bcgsc/biobloom.git && \
    cd /biobloom && \
    git submodule update --init && ./autogen.sh && \

## custom_environments_in_jupyter.ipynb

      
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              July 21, 2020 01:53
            
              
                Using custom environments in Jupyter
              
          
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	#!/bin/bash
	#
	# ./get_latest_container.sh
	# Given a bioconda package name as the first argument, downloads
	# the most recent corresponding Singularity image from quay.io/biocontainers
	#
	# Usage:
	#
	# ./get_latest_container.sh <package_name>
	#
	#!/usr/bin/env python
	"""
	Given a list of video files, creates a tiled output video with each
	input video playing simulutaneously with mixed audio.
	The result is something like a composite security camera feed, or the
	"Brady Bunch" opening credits.

	DISCLAIMER: The author holds no responsibility for your actions if you
	become criminally insane from watching all nine Puppet Master films
	simultaneously. You have been warned.
	FROM continuumio/miniconda3

	#
	# docker build -t pansapiens/rnasik:latest -t pansapiens/rnasik:1.5.4 .
	# docker run --rm -it -v $(pwd):/data pansapiens/rnasik --help
	#

	RUN conda install --yes -c conda-forge mamba
	RUN mamba install --yes -c bioconda -c conda-forge -c serine -c serine/label/dev -c anaconda -c defaults -c r -c conda-forge/label/broken \
	python=3.6 rnasik=1.5.4 qualimap=2.2.2b=0 "pandas<1" && \
	#!/usr/bin/env python3

	# https://colab.research.google.com/drive/1CGOygPAmjTxWnmsywv178dh3u36ZRBgv

	# You'll need to install the `robobrowser` Python package.
	# Do it in a virtualenv like:
	#
	# python3 -m venv ~/.virtualenvs/cloudstor
	# source ~/.virtualenvs/cloudstor/activate
	# pip3 install robobrowser
	##
	# Update - no longer works. You need to also:
	# edit: /lib/systemd/system/docker.service
	# then run: sudo systemctl daemon-reload
	# see, https://medium.com/@ibrahimgunduz34/how-to-change-docker-data-folder-configuration-33d372669056
	#
	# TODO: Fix this to use sed or similar to edit /lib/systemd/system/docker.service
	##

	# From: https://forums.docker.com/t/how-do-i-change-the-docker-image-installation-directory/1169
	FROM ubuntu:18.04
	RUN apt-get -y update && \
	apt-get -y install git build-essential autogen autotools-dev automake \
	libsdsl-dev libsdsl3 libsparsehash-dev zlib1g-dev libboost-all-dev libgomp1 && \
	apt-get clean && \
	rm -rf /var/lib/apt/lists/*
	WORKDIR /
	RUN git clone --depth 1 --branch 2.3.2 https://github.com/bcgsc/biobloom.git && \
	cd /biobloom && \
	git submodule update --init && ./autogen.sh && \