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#!/usr/bin/perl                                                                                                                                                                                                                                                                                                                                             
use LWP::UserAgent;
use HTTP::Request::Common;

my $userAgent = LWP::UserAgent->new(timeout => 1800); #a half-hour                                                                                                                                                                                                                                                                                          

my $request = POST 'http://mitomaster.mitomap.org/cgi-bin/websrvc.cgi', [
    gb => $ARGV[0],
    fileType => 'id',
    output => 'hsd'

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---

title: "Template for writing scientific papers in R markdown" author: "Petr Keil, pkeil@seznam.cz" date: "11/1/2015" output: pdf_document: fig_caption: yes keep_tex: yes number_sections: yes html_document:

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---
title: "Template for writing scientific papers in R markdown"
author: "Petr Keil, pkeil@seznam.cz"
date: "11/1/2015"
output:
  pdf_document:
    fig_caption: yes
    keep_tex: yes
    number_sections: yes
  html_document:

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#Directories
SOURCEDIR := sources
FASTQDIR := fastq
DECODEDDIR := decoded
BAMDIR := bam
SCRIPTDIR := scripts
TRIMMEDDIR := trimmed

#Parameters
MIN_LENGTH := 15

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library("plyr")
library("XML")
library("ggplot2")

#Concatenate SQL-style
concat<-function(...,sep="",collapse=NULL){
  strings<-list(...)
  #NULL, NA
  if(
    all(unlist(llply(strings,length))>0)

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#!/usr/bin/perl
use strict;
use Getopt::Std;
use LWP::UserAgent;
use HTTP::Request::Common;

my %opt;
my $opt_string = 'hcms';

getopts( "$opt_string", \%opt ) or &usage();

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#!/usr/bin/expect -f
#Upload a file to an Aspera server, filling in the passphrase field
#Usage: ./autopass.sh mybigassfile
set arg1 [lindex $argv 0]
set timeout -1
spawn ascp -i sra-rsakey-putty.ppk -k 1 -Qr -l300M $arg1 user@asperadomain.ncbi.nlm.nih.gov:protected/
expect "Passphrase for key \"rsa-key-blahblah\":"
send "mypassword\r"
expect "Completed"
#add the file you successfully uploaded to a log

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default: vcffilesdone

clean:
        rm disease_loci/*/*vcf
        rm vcffilesdone

#gene cards list of known disease loci
diseaseloci.html:
        curl http://www.genecards.org/cgi-bin/listdiseasecards.pl?type=full > diseaseloci.html
#scrape loci

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#requires 24.4 or higher, just use conda version 
M-x list-packages
C-v to scroll down
hit return on desired packages
C-x o to switch panes
go to [Install] hit return

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{
  "input_file": {
        "class": "File",
        "path": "https://raw.githubusercontent.com/briandoconnor/dockstore-tool-md5sum/master/md5sum.input"
    },
    "output_file": {
        "class": "File",
        "path": "s3://panoramabatch/md5sum.txt"
    }
}