Modify bcl2fastq/src/cmake/macros.cmake
Find the last block:
#
# Macro to find libraries, with support for static-only search
#
macro(bcl2fastq_find_header_or_die variable file)
# List all containers (only IDs) | |
docker ps -aq | |
# Stop all running containers | |
docker stop $(docker ps -aq) | |
# Remove all containers | |
docker rm $(docker ps -aq) | |
# Remove all images |
How to install sf 0.7-6 on macOS Mojave with MacPorts | |
Prerequisites: | |
- installing R, pkg-config, and gdal via MacPorts. | |
Note that proj (proj5) is automatically installed as a dependency for gdal. | |
- downloading the source tarball sf_0.7-6.tar.gz in the current directory | |
Then: |
#!/bin/sh | |
parse_yaml() { | |
local prefix=$2 | |
local s='[[:space:]]*' w='[a-zA-Z0-9_]*' fs=$(echo @|tr @ '\034') | |
sed -ne "s|^\($s\)\($w\)$s:$s\"\(.*\)\"$s\$|\1$fs\2$fs\3|p" \ | |
-e "s|^\($s\)\($w\)$s:$s\(.*\)$s\$|\1$fs\2$fs\3|p" $1 | | |
awk -F$fs '{ | |
indent = length($1)/2; | |
vname[indent] = $2; | |
for (i in vname) {if (i > indent) {delete vname[i]}} |
-- Remove the history from | |
rm -rf .git | |
-- recreate the repos from the current content only | |
git init | |
git add . | |
git commit -m "Initial commit" | |
-- push to the github remote repos ensuring you overwrite history | |
git remote add origin git@github.com:<YOUR ACCOUNT>/<YOUR REPOS>.git |
pandoc -f markdown -t mediawiki test.md -o test.wiki | |
# Thanks to @tillmanj for the updated formatting |
#!/bin/bash | |
# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress] | |
# | |
# Deinterleaves a FASTQ file of paired reads into two FASTQ | |
# files specified on the command line. Optionally GZip compresses the output | |
# FASTQ files using pigz if the 3rd command line argument is the word "compress" | |
# | |
# Can deinterleave 100 million paired reads (200 million total | |
# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s) | |
# |