IGV provides functionality that allows a user to create a script to take screenshots of regions of interest.
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#!/bin/bash | |
#--- config | |
SERVICE_NAME=galaxy | |
RUN_AS=galaxy | |
RUN_IN=/your/galaxy/directory | |
#--- main actions |
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#!perl | |
# Copyright 2012 Jeffrey Kegler | |
# This file is part of Marpa::R2. Marpa::R2 is free software: you can | |
# redistribute it and/or modify it under the terms of the GNU Lesser | |
# General Public License as published by the Free Software Foundation, | |
# either version 3 of the License, or (at your option) any later version. | |
# | |
# Marpa::R2 is distributed in the hope that it will be useful, | |
# but WITHOUT ANY WARRANTY; without even the implied warranty of | |
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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#!/usr/bin/env perl | |
use v5.10; | |
use strict; | |
use warnings; | |
use Carp; | |
use IO::Prompt::Tiny 'prompt'; | |
use Net::GitHub; | |
use Path::Tiny; | |
use RT::Client::REST::Ticket; | |
use RT::Client::REST; |
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REF=/path/to/ref.fasta | |
.PHONY:all | |
all: align/variants.vcf | |
align/variants.vcf: align/Sample1_sorted.bam align/Sample2_sorted.bam align/Sample3_sorted.bam | |
/path/to/samtools mpileup -uf ${REF} $^ |\ | |
/path/to/bcftools view -vcg - >$@ | |
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# install Homebrew | |
$ su ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" | |
# show brew commands | |
$ brew help | |
# check current user | |
$ echo $(whoami) | |
# grant access to the folders |
NCBI blastp seems to have a bug where it reports different top hits when -max_target_seqs is changed. This is a serious problem because the first 20 hits (for example) should be the same whether -max_target_seqs 100 or -max_target_seqs 500 is used.
The bug is reproducible on the command line when searching NCBI's nr blast database (dated 25-Nov-2015) using NCBI 2.2.28+, 2.2.30+ and 2.2.31+.
At first I thought it was something to do with my local exe/blastdb, but the same problem is also apparent on the NCBI blastp web interface (as of 30-Nov-2015)
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$ ./universal-greetings.p6 | |
Hello from the Perl Universe!!! |
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#!/usr/bin/env python | |
""" | |
Script for generating collaborators in a csv file from a bibtex, for easy | |
insertion into the new NSF format. | |
""" | |
from __future__ import division | |
import datetime |
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library(phyloseq) | |
library(pheatmap) | |
library(vegan) | |
library(ggplot2) | |
library(corrplot)#for cor.mtest | |
library(psych)#corr.test | |
library(matrixStats)#rowSds | |
library(metagenomeSeq)#differential abundance testing | |
library(randomForest) | |
library(dplyr) |
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