BrunoGrandePhD

#############################################
pwd
STDOUT
/home/galaxy/galaxy_dist/database/tmp/tmp-toolshed-mtdIAQaet/ensembl-tools-release-77
#############################################

#############################################
pwd
STDERR

BrunoGrandePhD

$ sh galaxy_dist/run_tool_shed.sh -bootstrap_from_tool_shed http://toolshed.g2.bx.psu.edu
Bootstrapping from tool shed at http://toolshed.g2.bx.psu.edu.
Creating database... done.
Creating user 'bgrande' with email address '[email protected]'...Traceback (most recent call last):
  File "lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py", line 152, in <module>
    app = BootstrapApplication( config )
  File "lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py", line 46, in __init__
    create_tables=False )
  File "/home/galaxy/galaxy_dist/lib/galaxy/webapps/tool_shed/model/mapping.py", line 330, in init
    result.shed_counter = shed_statistics.ShedCounter( result )

BrunoGrandePhD

#!/usr/bin/env python

"""
detect_gifs.py
==============
This script tries to automatically detect
GIF opportunities within a batch of photos.
"""

from __future__ import print_function

BrunoGrandePhD

suppressPackageStartupMessages({
  library(readr)
  library(dplyr)
})

maf_cols <- c(
  "Hugo_Symbol","Entrez_Gene_Id","Center","NCBI_Build","Chromosome","Start_Position",
  "End_Position","Strand","Variant_Classification","Variant_Type","Reference_Allele",
  "Tumor_Seq_Allele1","Tumor_Seq_Allele2","dbSNP_RS","dbSNP_Val_Status","Tumor_Sample_Barcode",
  "Matched_Norm_Sample_Barcode","Match_Norm_Seq_Allele1","Match_Norm_Seq_Allele2",

BrunoGrandePhD

# Ensure that fonts are embedded in a PDF file for correct printing
# Credit: http://stackoverflow.com/a/4234150
function fixpdf {
	# Print usage is no arguments are given
	if [ "$#" -eq 0 ]; then
		echo "Usage: fixpdf PDF_FILE [PDF_FILE ...]"
	fi
	# Check if ghostscript is installed
	if ! type gs >/dev/null 2>&1; then
		echo 'Error: ghostscript is either not installed or not in your PATH.'

BrunoGrandePhD

# Input:
# - exons.bed: Exons BED file with the fourth column containing the gene name for gene coverage summarizing
# - sample.bam: BAM file using the same genome build (aka chromosome names and coordinate system) as exons.bed
# Output:
# - Tab-delimited file with two columns: gene name and average coverage

samtools bedcov exons.bed sample.bam \
    | awk ' \
        BEGIN { \
            FS=OFS="\t"} \

BrunoGrandePhD

git branch new-master  # Assumption: HEAD is pointing to the new commits
git checkout master
git branch before-revert 
git revert --no-edit commit_X..master  # Revert the commits you want to discard
git rebase -i before-revert  # Optional: squash all commits except top one to create one revert commit
git checkout new-master
git rebase master
git checkout master
git merge new-master
git branch -D new-master before-revert

BrunoGrandePhD

## GGplot2 workshop Sciprog October 24 2016
# Author: Michelle Jones

library(ggplot2)
#install the packages for the workshop
#install.packages(c("tidyverse","ggthemes","cowplot"))
#install.packages("gapminder")
#Load packages
library(tidyverse)
library(ggthemes)

BrunoGrandePhD

# The commands below are a guide to remove a large file that has been
# accidentally committed to a Git repository's history. If the file is
# larger than 100 MB, GitHub will prevent you from pushing your latest
# commits. The annotated steps below should help you remove the large
# file from your commit history, even if you've made new commit since.


# Some Git users advise against rebasing. You can safely use it here
# because you haven't published your changes yet.
# So, you first need to rebase your current branch onto the point that

BrunoGrandePhD

FROM ubuntu:latest
RUN apt-get update
RUN apt-get install -y vim wget git htop tmux
RUN apt-get install -y openssh-client default-jre default-jdk
RUN apt-get install -y python2.7
RUN ln -s /usr/bin/python2.7 /usr/bin/python
RUN wget https://bootstrap.pypa.io/get-pip.py
RUN python get-pip.py
RUN pip2.7 install numpy
RUN pip2.7 install pandas