pansapiens

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 && \

pansapiens

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.

pansapiens

pansapiens

pansapiens

import urllib.request as request
from collections import defaultdict
  
def parse_aaindex2(lines, default=None):
    """
    Parse the lines of an AAIndex2 substitution matrix, return a dict of the entire database keyed by
    AAIndex identifier.
    
    The aaindex[id]['matrix'] dictionary is the same structure as Biopython's `Bio.SubsMat.MatrixInfo`
    substitution matricies.

pansapiens

Superceded by https://github.com/MonashBioinformaticsPlatform/data-carpentry-genomics-ansible

Quick scripts for setting up Data Carpentry Genomics: https://datacarpentry.org/genomics-workshop/setup.html (option B)

pansapiens

#!/usr/bin/env Rscript

# Based on https://www.biostars.org/p/45791/#45804
#
# Usage:
#  ./gff2gtf.R genes.gff genes.gtf
#
# Dependencies can be easily installed like:
#  conda create -n gff2gtf bioconductor-rtracklayer
#  conda activate gff2gtf

pansapiens

RStudio in Singuarity

Further development in continuing here: https://github.com/MonashBioinformaticsPlatform/rocker-ultra

---

This is an attempt to simplify launching an RStudio server in Singularity with a single wrapper script, with managment of package directories per-version in your home directory, auto-free port finding, per-session password generation and SSH port forwarding instructions for free.

Loosely based on https://www.rocker-project.org/use/singularity/.

pansapiens

FROM continuumio/miniconda3
LABEL   maintainer="Andrew Perry <andrew.perry@monash.edu>"

ARG     KRAKEN_DB_URL=https://ccb.jhu.edu/software/kraken/dl/minikraken_20171019_4GB.tgz
ARG     CENTRIFUGE_DB_URL=ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz
ENV     KRAKEN_DB_PATH=/databases/minikraken
ENV     CENTRIFUGE_DB_PATH=/databases/centrifuge-db

ENV     KRAKEN_DEFAULT_DB=$KRAKEN_DB_PATH/minikraken_20171013_4GB
ENV     CENTRIFUGE_DEFAULT_DB=$CENTRIFUGE_DB_PATH/p_compressed+h+v

pansapiens

Keybase proof

I hereby claim:

• I am pansapiens on github.
• I am pansapiens (https://keybase.io/pansapiens) on keybase.
• I have a public key whose fingerprint is CC4E 5E55 3A06 BC36 2B20 F907 DB09 40BE B37B 0426

To claim this, I am signing this object: