seandavi

#!/bin/bash
sudo apt-get install -y libcurl4-gnutls-dev
sudo apt-get install -y libxml2-dev
sudo apt-get install -y texlive

seandavi

#' Generate a DOI for a bioconductor package
#' 
#' This function makes calls out to the EZID API (v2) described
#' here: \url{https://ezid.lib.purdue.edu/doc/apidoc.2.html}. The 
#' function creates a new DOI for a bioc package (cannot already 
#' exist). The target URL for the DOI is the short Bioconductor
#' package URL.
#' 
#' The login information for the "real" Bioconductor account 
#' should be stored in the environment variables "EZID_USERNAME"

seandavi

library(RMySQL)
con = dbConnect(MySQL(),user='sdavis',password='XXXXX',host='127.0.0.1',port=3308,dbname='solexa')
con = dbConnect(MySQL(),user='sdavis',password='mic2222',host='127.0.0.1',port=3308,dbname='solexa')
res = dbGetQuery(con,
                 "select study_id,source.name, sample.name, fcb.type as software, 
                     fcb.dateStamp as basecalldate, fcb.softwareVersion as version, study_id,
                     sr.date as run_date, sr.sequencer as sequencer, ssr.library_id as library_id, 
                     sr.ID as run_id, sample.ID as sample_id, nt.value as sample_source,
                     sample.sample_type, part.value as partitioning_method, ssr.ID as read_group_id
                 from solexa_sample as sample

seandavi

library(dplyr)
library(bigrquery)

db1 = src_bigquery(project = 'bigquery-public-data', dataset = 'hacker_news', billing = 'isb-cgc-04-0020')

comments = tbl(src = db1, 'full')
stories  = tbl(src = db1, 'stories')

sessionInfo()

seandavi

#!/path/2/Rscript

# License: CC0 (just be nice and point others to where you got this)
# Author: Robert M Flight <[email protected]>, github.com/rmflight
#
# This is a post-commit hook that after a successful commit subsequently increments the package version in DESCRIPTION
# and commits that. Analogous to the pre-commit at https://gist.github.com/rmflight/8863882, but useful if you only have
# good reasons for not doing it on the pre-commit.
#
# To install it, simply copy this into the ".git/hooks/post-commit" file of your git repo, change /path/2/Rscript, and make

seandavi

# Note that this will need to be 
# edited to address different google
# project details
library(downloader)
library(readr)
zipname = "Thesaurus.zip"
# change to get the version you like.
download("http://evs.nci.nih.gov/ftp1/NCI_Thesaurus/Thesaurus_17.02d.FLAT.zip",destfile=zipname)
unzip(zipname)
thes = read_tsv("Thesaurus.txt")

seandavi

#!/bin/bash
sudo apt-get install -y libcurl4-openssl-dev libxml2-dev libssl-dev
sudo apt-get install -y r-base r-base-dev
sudo apt-get install -y gdebi-core
wget https://download2.rstudio.org/rstudio-server-1.0.136-amd64.deb
sudo gdebi --non-interactive rstudio-server-1.0.136-amd64.deb
# rstudio will be running on port 8787

seandavi

#!/bin/bash
sudo apt-get install -y \
    apt-transport-https \
    ca-certificates \
    curl \
    software-properties-common
curl -fsSL https://download.docker.com/linux/debian/gpg | sudo apt-key add -
sudo add-apt-repository \
   "deb [arch=amd64] https://download.docker.com/linux/debian \
   $(lsb_release -cs) \

seandavi

---
Software:
  - title: metabox
    languages: 
      - R
    doi: 10.1371/journal.pone.0171046
    manuscript: http://dx.doi.org/10.1371/journal.pone.0171046
    pubmed_id: 28141874
    repository: https://github.com/kwanjeeraw/metabox/
    application_type: web application

seandavi

--- !clarkevans.com/^invoice
invoice: 34843
date   : 2001-01-23
bill-to: &id001
    given  : Chris
    family : Dumars
    address:
        lines: |
            458 Walkman Dr.
            Suite #292