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

#!/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

#!/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

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


def parse_ssh_config(config_path):

pansapiens

#!/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>
#

pansapiens

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" && \

pansapiens

pansapiens

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:

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