leipzig

import tiledb
import tiledbvcf
import numpy as np


cloud_uri = "tiledb://TileDB-Inc/vcf-1kg-dragen-v376"

# This is the config I need to pass
cloud_config = tiledb.Config()
cloud_cfg = tiledbvcf.ReadConfig(tiledb_config=cloud_config)

leipzig

- ABRA2:
  - https://igor.sbgenomics.com/raw/admin/sbg-public-data/abra2-12-germline/5
  - https://igor.sbgenomics.com/raw/admin/sbg-public-data/abra2-12-somatic/2
- Admixture:
  - https://igor.sbgenomics.com/raw/admin/sbg-public-data/admixture-1-3-0/4
- AmpliconQC:
  - https://igor.sbgenomics.com/raw/admin/sbg-public-data/sbg-ampliconqc-amplicon-coverage/1
  - https://igor.sbgenomics.com/raw/admin/sbg-public-data/sbg-ampliconqc-coverage-heatmap/1
  - https://igor.sbgenomics.com/raw/admin/sbg-public-data/sbg-ampliconqc-mark-failed-amplicons/1
  - https://igor.sbgenomics.com/raw/admin/sbg-public-data/sbg-ampliconqc-merge-coverage-beds/1

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#!/usr/bin/expect
set PASSWD "<<yourpass>>"
set timeout 3
spawn /opt/cisco/anyconnect/bin/vpn connect vpn.drexel.edu
expect "Group:"
send -- "0\r"
expect "*Username:*"
send -- "<<yourusername>>\r"
expect "*Password:*"
send -- "$PASSWD\r"

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mz<-c('007','011','017','020','025','046','076','077','090','102','104')
sa<-c('008', '017', '037', '058', '069', '109', '097', '102','028')
jl<-c('075','060','061','106','066','070','104','059','017','001','015','014','038','010','005','039','006','020','031','094')

rn<-str_pad(seq(1,109), 3, pad = "0")
pics<-data.frame(id=rn,mz=FALSE,sa=FALSE,jl=FALSE)

pics[pics$id %in% mz,"mz"]<-TRUE
pics[pics$id %in% sa,"sa"]<-TRUE
pics[pics$id %in% jl,"jl"]<-TRUE

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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"
    }
}

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python -c 'import rpy2.robjects as robjects'

this is almost certainly caused by conda-forge
to fix
conda install -c r r-base

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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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---
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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#!/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'