| # Load GO and DE data to R | |
| ## @knitr prep_data | |
| # Install missing CRAN packages if needed | |
| # git.packages <- c("docopt/docopt.R") | |
| # github.packages <- c("argparser") | |
| install.deps <- function(p, repo="cran"){ | |
| call_install <- switch(repo,cran=c("install.packages(package, repos=\"http://cloud.r-project.org/\""), |
| #' call primer3 for a given set of DNAstringSet object | |
| #' Forked from https://gist.github.com/al2na/8540391 | |
| #' TODO: Add support for target amplicon region (Maybe as [] in the fasta input) | |
| #' @param seq: DNA template as a character string (required) | |
| #' @param fw_primer: optional forward (left) primer, if provided Primer3 will assess it and will try to find a suitable reverse primer. Default: NULL | |
| #' @param rv_primer: optional reverse (right) primer (must be reverse-complemented to the template), if provided Primer3 will assess it and will try to find a suitable forward primer. Default: NULL | |
| #' @param size_range: a string with space separated list of desired amplicon size ranges. Default: '151-500' | |
| #' @param Tm: range of melting temprature parameters as a numerical vector containing (min,optimal,max). default: c(55,57,58) | |
| #' @param name: name of the amplicon in 'chr_start_end' format | |
| #' @param sequence_target: a string containing space separated list of target pairs: 'starting_position,target_length starting_p |
| $path = $args[0] | |
| [Reflection.Assembly]::LoadWithPartialName("System.Windows.Forms"); | |
| $i = new-object System.Drawing.Bitmap $path | |
| $i.RotateFlip("Rotate90FlipNone") | |
| $i.Save($args[1],"png") |
| #!/bin/bash -v | |
| # Define these according to the run | |
| N=5000 | |
| NCPUS=4 | |
| # Use wildcards or specify an exact input fasta filename below (should be in your current working directory) | |
| INPUT_FASTA="input.fasta" | |
| DATE=`date +%d_%m_%Y` | |
| REFDB="nt" | |
| #CMD=`printf "hmmscan --cpu %s --domtblout \%s/\%s.pfam.domtblout ~/.hmmer-3.1/Pfam/Pfam-A.hmm \%s > \%s/\%s_pfam.log",$NCPUS` |
| #!/bin/bash | |
| # installs plenv, perl, carton, cpanminus, sets up environment in .bash_profile or .profile | |
| # from https://github.com/tokuhirom/plenv#readme | |
| MY_PROFILE_FILE="$HOME/.profile" | |
| if [[ -n "$PERL_MB_OPT" ]]; then | |
| echo "You must unset your local::lib environment variables first" | |
| echo "Edit your ~/.bash_profile or ~/.bashrc and remove any references" | |
| echo "to local::lib or export PERL*..." |
| # util.R: | |
| # Utilities to make R a happier place | |
| # Originally created by Brendan O'Connor, brenocon.com/code | |
| # Edited by Ido Bar. | |
| # Source the file directly from this gist using `devtools::source_gist("7f63547158ecdbacf31b54a58af0d1cc", filename = "util.R")` | |
| ######################################## | |
| ## Put everything into an environment, to not pollute global namespace | |
| util = new.env() |
| # If loading in an environment that doesn't respect my RPATH environment | |
| # variable, set it here | |
| sourceDir <- file.path(path.expand("~"), "R", "source") | |
| if (Sys.getenv("RPATH") == "") { | |
| if (!file.exists(sourceDir)) dir.create(sourceDir) | |
| Sys.setenv(RPATH=sourceDir) | |
| } | |
| # Load commonly used functions and packages |
| #!/bin/bash | |
| _usage() { | |
| cat <<EOF | |
| $* | |
| Usage: $0 <[options]> | |
| Options: | |
| -i --in input fasta file. If not specified will defaults to stdin [-] | |
| -o --out output combined results file. If not specified will defaults to stdout [-] | |
| -p --parts how many parts to break to input fasta into [default:5000] |
Follow these instructions to setup a new computer with commonly used tools and software for scientific data analysis (with emphasis on bioinformatics)
Download the uniref90 xml file first (warning - this is ~15 GB, will take a while)