Colelyman’s gists

Colelyman / gist:4049013

Created November 9, 2012 23:30

Simon 124 Cole Lyman

Colelyman / AndroidManifest.xml

Created April 7, 2016 19:45

Orientation hack for activities.

	<activity android:name=".ui.activities.MainActivity"
	android:configChanges="orientation\|keyboardHidden\|screenSize">
	android:label="Main Activity"
	android:name=".MainActivity"
	<intent-filter>
	<action android:name="android.intent.action.MAIN" />

	<category android:name="android.intent.category.LAUNCHER" />
	</intent-filter>
	</activity>

Colelyman / jupyter.sh

Last active October 24, 2018 11:07

Get Jupyter Notebook Running in SSH Tunnel

	user@server$ jupyter notebook --no-browser --port=8889
	# run client side
	user@client$ ssh -N -f -L localhost:8000:localhost:8889 remote_user@remote_host
	firefox http://localhost:8000
	# source: https://coderwall.com/p/ohk6cg/remote-access-to-ipython-notebooks-via-ssh

Colelyman / View Aligned Reads

Last active October 17, 2018 03:34

This gist is a mini tutorial on how to view aligned reads in the command line using samtools tview.

	# Convert .sam file to .bam file
	$ samtools view -b -S -o [outputted bam file] [inputted sam file]
	# Sort and index the .bam file
	$ samtools sort [inputted bam file] > [output prefix of bam file].sorted
	$ samtools index [inputted bam file].sorted.bam

Colelyman / tibble-dplyr-tricks.R

Last active March 25, 2017 22:02

Useful tricks for manipulating tibbles with dplyr that I have found useful.

	library(tibble)

	# create a tibble with no rows, but defined columns
	tbl <- tibble(name=character(), age=numeric(), gender=factor())

	# add a row to the tibble. The values can even be vectors!!
	tbl <- add_row(tbl, name='Steve', age='24', gender='male')

Colelyman / sbatch_tricks.sh

Created December 9, 2017 07:15

Some tricks for doing cool things with sbatch scripts.

	# start a job after another job succeeds
	JOBID=$(sbatch --parsable job1.sh) && sbatch --dependency=afterok:$JOBID job2.sh

	# start a job after another job fails
	JOBID=$(sbatch --parsable job1.sh) && sbatch --dependency=afternotok:$JOBID job2.sh

	# get the time and memory of a running node
	sstat --format="CPUTime,Elapsed,MaxRSS" -j $SLURM_JOB_ID

Colelyman / install.sh

Created January 2, 2018 21:02

How to link software installed in a custom location using autotools.

	# to be run within your project that is built with autotools (aka has a configure script)
	# replace the text within '<...>' with the respective paths
	export LD_LIBRARY_PATH=<lib directory of the library>:$LD_LIBRARY_PATH

	./configure CPPFLAGS="-I<include directory of the library> -L<lib directory of the library>"

	make CPPFLAGS="-I<include directory of the library> -L<lib directory of the library>" LDFLAGS="-I<include directory of the library> -L<lib directory of the library>"

Colelyman / keybase.md

Created August 23, 2018 23:47

I hereby claim:

To claim this, I am signing this object:

Colelyman / file-defer-close.lisp

Last active October 23, 2018 03:39

A Common Lisp macro that opens a file and closes it after some computation is done.

	(defmacro open-file-defer-close (file-path file-handle &body body)
	"Opens FILE-PATH as FILE-HANDLE, executes BODY and finally closes FILE-HANDLE."
	`(let ((,file-handle ,(open file-path)))
	,@body
	(close ,file-handle)))

Colelyman / genomes.txt

Created April 8, 2019 23:30