bensutherland

Keybase proof

I hereby claim:

• I am bensutherland on github.
• I am ben_sutherland (https://keybase.io/ben_sutherland) on keybase.
• I have a public key ASBwZ-0DSHJ-Ymizr8VHjHzhQ64r8cTqD53wD9_9V42iHgo

To claim this, I am signing this object:

bensutherland

Render a markdown document to a PDF

How to go from a markdown document, for example a README.md file to a PDF document.

Use grip to display markdown

pip install grip
grip your_markdown.md --export your_markdown.html

Insights from: https://superuser.com/questions/689056/how-can-i-convert-github-flavored-markdown-to-a-pdf

bensutherland

Backup Documents folder to Archive at MGL

How to backup your 'My Documents' folder to the network drive using robocopy.
Note: this instruction comes with absolutely no guarantees and is generally for the author only. That being said, hopefully it is useful for you, and if you see any issues, please let me know.

robocopy should already be on your machine with standard Windows installation
robocopy https://docs.microsoft.com/en-us/windows-server/administration/windows-commands/robocopy

0. Prepare data

Make sure that all files within your My Documents folder are those that you want to back up (i.e. no confidential or personal information).

bensutherland

Install colony on Linux

The following are instructions for installation of colony on linux, specifically for the user, with no guarantees of usefulness or correctness.

This allowed the current version of colony (downloaded 2019-05-21) to be installed with mpi for parallelization on Linux.

Installation instructions

1. Download colony from https://www.zsl.org/science/software/colony

2. Download mpich 3.2.1 source code here: https://www.mpich.org/downloads/

bensutherland

Archive or Restore data from the Ion Torrent at MGL

How to archive sequencing runs from the file system to the archive, and then how to restore the files back from the archive onto the file system.
Note: exercise caution while doing the following!

1. Archive Run

Go to the Data / Data Management page on the Torrent browser. Scroll down to Disk Space Management, and go to the table. This shows details as to whether the files are 'Deleted', 'Archived', or 'Local'.
For the run of interest, select the run's cog at the far right. Select 'Actions' to open a prompt window.
Select the Basecalling Input and Output Files, then click Archive Selected. Under 'Archive Directory', leave the default (i.e. 'Use Configured Archive Directories').
This will put the run into the archive queue.

bensutherland

Offload fastq data from the Ion Torrent at MGL

How to obtain fastq data from the Ion Torrent server at MGL. Requires that the plugin FileExporter has been run.

1. Mount USB on system

Plug in the USB drive into the system.
Use sudo fdisk -l to find where your drive is mounted.
Mount via: sudo mount /dev/sde1 /media/<your_drive> (where /dev/sde1 is the location of drive found above, your_media is your drive name).

2. Find the output files

If data is still on the system drive, the plugin results are here:

bensutherland

Update R

install.packages("installr")
library("installr")
updateR()

Go through prompts, but don't copy over all packages into the new library
as this can result in many packages needing to be manually updated as they do not
work with the current version of R.

bensutherland

Setup GitHub on Windows

Download GitHub Desktop

Go to a git repo that you would like to clone, for example, https://github.com/bensutherland/fasta_SNP_extraction
Click the green button 'Clone or download', and click 'Open in Desktop' This will open https://desktop.github.com/

Click the button 'Download for Windows (64 Bit)'

This will download a setup exe file to your Downloads folder 'GitHubDesktopSetup.exe'