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indraniel / GitHub
Created Dec 4, 2018 — forked from Integralist/GitHub
Download a single file from a private GitHub repo. You'll need an access token as described in this GitHub Help article:
View GitHub
curl --header 'Authorization: token INSERTACCESSTOKENHERE' \
--header 'Accept: application/vnd.github.v3.raw' \
--remote-name \
# Example...
indraniel /
Created Dec 3, 2018
clj tools version of `lein-try`
# tools-deps equivalent of `lein-try`
# Additionally see:
# -- what user/find-deps links to
# -- clj-based uberjarrer
View Running and Writing Output to console at the same time
p = subprocess.Popen(shlex.split(cmd), stdout=subprocess.PIPE)
# Grab stdout line by line as it becomes available. This will loop until
# p terminates.
while p.poll() is None:
l = p.stdout.readline() # This blocks until it receives a newline.
print l
# When the subprocess terminates there might be unconsumed output
# that still needs to be processed.
indraniel / GenotypeGVCF.wdl
Last active Nov 14, 2018
Example of the internals of a cromwell script (taken from the GenotypeGVCFs task of the GATK4 pipeline_)
View GenotypeGVCF.wdl
task GenotypeGVCFs {
File workspace_tar
String interval
String output_vcf_filename
String gatk_path
File ref_fasta
File ref_fasta_index
indraniel / tramp-gcloud-ssh
Created Sep 8, 2018 — forked from scjody/tramp-gcloud-ssh
EMACS TRAMP setup for "gcloud compute ssh"
View tramp-gcloud-ssh
;; TRAMP gcloud ssh
(add-to-list 'tramp-methods
(tramp-login-program "gssh")
(tramp-login-args (("%h")))
(tramp-async-args (("-q")))
(tramp-remote-shell "/bin/sh")
(tramp-remote-shell-args ("-c"))
(tramp-gw-args (("-o" "GlobalKnownHostsFile=/dev/null")
("-o" "UserKnownHostsFile=/dev/null")
indraniel /
Created Sep 8, 2018 — forked from rnwolf/
Tutorial shows how to make backups to Google Cloud Storage.

Google Cloud Storage backup tutorial


This tutorial shows how to make backups to Google Cloud Storage. The backups are:

  • automatic
  • stored off site
  • incremental
indraniel / gcp-price-list.json
Created Jun 13, 2018
Old style google cloud platform (GCP) JSON price list . Modern times now use the GCP billing API
View gcp-price-list.json
"comment": "If you've gotten here by mistake, this is the JSON data used by our pricing calculator. It is helpful for developers. Go to to get back to our web calculator.",
"version": "v1.13",
"updated": "01-August-2017",
"gcp_price_list": {
"sustained_use_base": 0.25,
"sustained_use_tiers": {
"0.25": 1.0,
"0.50": 0.8,
"0.75": 0.6,
indraniel / Dockerfile-GATK4
Last active Jun 6, 2018
GATK4 Dockerfile (
View Dockerfile-GATK4
# Using OpenJDK 8
FROM broadinstitute/gatk:gatkbase-1.2.3
ADD . /gatk
RUN /gatk/gradlew clean compileTestJava sparkJar localJar createPythonPackageArchive -Drelease=$DRELEASE

Common Lisp Scripting with Roswell

"Roswell Script" is implementation-independent Common Lisp scripting program which uses Roswell. Although Roswell itself is a unified interface to Common Lisp implementations, it also encourages writing scripts with it.

To start writing it, run ros init in your terminal:

$ ros init
Usage: ros init [template] name [options...]