pansapiens

#!/bin/bash

# Given a directory of fastq files, use bbmerge to find adapters sequences for every sample,
# align and find the consensus. 
# Final consensus is in  r1_adapter.consensus.fa and r2_adapter.consensus.fa - trim by hand
# if the automatic trimming up the the first 'n' isn't sensible

# Requires: bbmerge.sh (bbmap), muscle, emboss (cons)

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

#!/bin/bash

R_TMUX_SESSION_NAME="${R_TMUX_SESSION_NAME:-vscode-r}"
TMUX_CMD=$(command -v tmux)

if ! [ -x "$(command -v tmux)" ]; then
    echo "Error: tmux is not installed."
    exit 1
fi

pansapiens

Gzip compression heatmap

Generates a heatmap plot showing the compression ratio of different block through a file.

Show interesting patterns in FASTQ files, and may be useful for diagnosing pathological or unusual data. I find using the zscore transformation for the plot is more informative.

Run like:

./compression_heatmap.py -b 1048576 -c rainbow -t zscore SRR11794587_2.fastq.gz

pansapiens

#!/usr/bin/env python
# A simple script to suck up HTML, convert any images to inline Base64
# encoded format and write out the converted file.
#
# Usage: python standalone_html.py <input_file.html> <output_file.html>
#
# TODO: Consider MHTML format: https://en.wikipedia.org/wiki/MHTML

import os
from bs4 import BeautifulSoup

pansapiens

from typing import Dict, List
import csv
from rest_framework import status
from rest_framework.response import Response
from rest_framework.parsers import JSONParser, BaseParser
from rest_framework.views import APIView

class CSVTextParser(BaseParser):
    """
    A CSV parser for DRF APIViews.

pansapiens

#!/bin/bash
# This script deinterleaves a FASTQ file generated by an MGI sequencer with two flowcell lanes
# where headers are in the format: @v300009551L1C002R003000000/1 with L1 or L2 indicating the lane
# This can be useful for some analyses since each lane can behave like a technical replicate (eg DADA2 error correction?)

set -e
set -o pipefail

input_fastq_gz="$1"  # input FASTQ file
samplename="$(basename $input_fastq_gz .fastq.gz)"

pansapiens

FROM centos:7
#
# You'll need to download bcl-convert-3.6.3-1.el7.x86_64.rpm from 
# https://support.illumina.com/downloads/bcl-convert-downloads.html
# Yay clickwrap licenses !
#
# Building:
#
# docker build -t bcl-convert:latest -t bcl-convert:3.6.3 .
# sudo singularity build bcl-convert.sif docker-daemon://bcl-convert:latest

pansapiens

#!/usr/bin/env python
import os
import shutil
import re
import sys
import difflib
import argparse


def parse_ssh_config(config_path):

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/.