Matt Ralston MatthewRalston

Sample service script for debianoids

Look at LSB init scripts for more information.

Copy to /etc/init.d:

# replace "$YOUR_SERVICE_NAME" with your service's name (whenever it's not enough obvious)

	>yaourt -S samtools

	==> Downloading samtools PKGBUILD from AUR...
	x .SRCINFO
	x .gitignore
	x PKGBUILD
	wookietreiber commented on 2015-10-25 17:09
	Thanks for letting me know, updated pkgrel.

	greyltc commented on 2017-05-20 09:46

	Using gcc for C compiler. If this is not what you want, set CC.
	Using /usr/libexec/gcc/xxxx/4.4.7/collect2 instead.

	src/Hackage/Security/TUF/Layout/Repo.hs:8:1: error:
	Could not find module ‘Distribution.Package’
	Perhaps you haven't installed the profiling libraries for package ‘Cabal-2.0.0.2’?
	Use -v to see a list of the files searched for.
	\|
	8 \| import Distribution.Package
	\| ^^^^^^^^^^^^^^^^^^^^^^^^^^^

	Ioannidis, John PA, et al. "Repeatability of published microarray gene expression analyses." Nature genetics 41.2 (2009): 149-155.
	Nekrutenko, Anton, and James Taylor. "Next-generation sequencing data interpretation: enhancing reproducibility and accessibility." Nature Reviews Genetics 13.9 (2012): 667-672.
	Peng, Roger D. "Reproducible research in computational science." Science (New York, Ny) 334.6060 (2011): 1226.
	Baggerly, Keith. "Disclose all data in publications." Nature 467.7314 (2010): 401.
	Van Noorden, Richard. "The trouble with retractions." Nature 478.7367 (2011): 26-28.
	Begley, C. Glenn, and Lee M. Ellis. "Drug development: Raise standards for preclinical cancer research." Nature 483.7391 (2012): 531-533.

	partner = Object.new
	def my_most_sincere_apology
	"I'm sorry for everything that I've done. But when I call you never seem to be home."
	end

	try:
	1000.times do \|t\|
	partner.call(:my_most_sincere_apology)
	end
	catch e:

	'''
	When you want to match files that only differ by one character: sample_1.fastq.gz sample_2.fastq.gz
	'''
	def is_hamming_match(seq1, seq2):
	if len(seq1) == len(seq2): # The sequences must be of equal length
	zipped = zip(seq1, seq2)
	is_mismatch = list([c1 != c2 for c1, c2 in zipped])
	if sum(is_mismatch) == 1: # The sequences must have only one mismatch
	mismatches = list([[c1, c2] for c1, c2 in zipped if c1 != c2])
	if mismatches[0] == ['1', '2'] or mismatches[0] == ['2', '1']: # The mismatch must only be the numbers 1 and 2

	fancy_scientific <- function(l) {
	# turn in to character string in scientific notation
	l <- format(l, scientific = TRUE)
	# quote the part before the exponent to keep all the digits
	l <- gsub("^(.*)e", "'\\1'e", l)
	# turn the 'e+' into plotmath format
	l <- gsub("e", "%*%10^", l)
	# return this as an expression
	parse(text=l)
	}

	#set -x
	##
	# Your previous /Users/Matthew/.bash_profile file was backed up as /Users/Matthew/.bash_profile.macports-saved_2013-04-01_at_23:07:38
	##

	export PATH=/usr/local/bin/:$PATH


	# MacPorts Installer addition on 2013-04-01_at_23:07:38: adding an appropriate PATH variable for use with MacPorts.
	export PATH=/opt/local/bin:/opt/local/sbin:/Users/Matthew/Documents/Bash_scripts:/Applications/circos-0.66/bin/:$PATH

	>./autogen.sh
	checking for aclocal... yes
	checking for autoheader... yes
	checking for autoconf... yes
	checking for libtoolize... yes
	checking for automake... yes
	running aclocal -I m4 (/opt/slurm-drmaa-slurm-drmaa-1.2.0-clusters)
	running libtoolize --automake --copy --force (/opt/slurm-drmaa-slurm-drmaa-1.2.0-clusters)
	running autoheader --warnings=all (/opt/slurm-drmaa-slurm-drmaa-1.2.0-clusters)
	running automake --foreign --add-missing --copy --warnings=all (/opt/slurm-drmaa-slurm-drmaa-1.2.0-clusters)