pansapiens

#!/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

pansapiens

alias default_account='sacctmgr --parsable2 show user -s andrewpe | tail -1 | cut -f 2 -d '\''|'\'''
alias fairshare='sshare -a --accounts $(default_account)'
alias jhistory='sacct -u ${USER} --starttime $(date -d "-1 month" +%Y-%m-%d) --format=User,JobID,Jobname,partition,state,exitcode,time,start,end,elapsed,MaxRss,MaxVMSize,nnodes,ncpus,nodelist'
alias jshow='scontrol show job'
alias jinfo='sacct --starttime $(date -d "-1 month" +%Y-%m-%d) --format=User,JobID,Jobname%64,partition,qos,ReqCPUS,ReqMem,state,exitcode,time,start,end,elapsed,MaxRss,MaxVMSize,nnodes,ncpus,nodelist -j'
alias node_types='sinfo -o '\''%c %m %n %R'\'' --sort '\''P'\'''
alias qhogs='sreport cluster UserUtilizationByAccount -t hours'
alias si='sinfo -o "%20P %5D %14F %8z %10c %10m %10d %11l %16f %N"'
alias sq='squeue -o "%8i %.60j %4t %10u %20q %20a %10g %20P %10Q %5D %2C %5m %11l %11L %R"'
alias squ='squeue -u $USER --format="%.18i %.9P %.60j %.8u %.8a %.2t %.10M %.6D %R"'

pansapiens

Bootstrap: localimage
From: deepvariant-0.6.1.simg

# Install Google Cloud SDK for the gcloud tool, then:
# We grab the official Docker image, push it to a locally running container repo, then get
# Singularity to pull it back.
# gcloud docker -- pull gcr.io/deepvariant-docker/deepvariant:0.6.1
# docker tag gcr.io/deepvariant-docker/deepvariant:0.6.1 localhost:5000/deepvariant:0.6.1
# docker run -d -p 5000:5000 --restart=always --name registry registry:2
# docker push localhost:5000/deepvariant:0.6.1

pansapiens

#!/usr/bin/env python

from __future__ import print_function
import sys
from collections import OrderedDict

# Usage:
# python csv_join_rm_mm.py my_dart_ref.csv my_blast_hits.csv >joined_hits.csv 2>warnings.txt

REF_DART_ID_PREFIX = "SNP_"

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:

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

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

#!/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

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

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.