David Chin prehensilecode

HOWTO build NCI-GDC/gdc_client

Notes on building https://github.com/NCI-GDC/gdc-client

Issue

Following their instructions, get error in building lxml Python package:

Building wheels for collected packages: lxml
  Building wheel for lxml (setup.py): started

Assume
- OpenBLAS installation location given by environment variable OPENBLAS_DIR
  - $OPENBLAS_DIR/include
  - $OPENBLAS_DIR/lib
- OpenBLAS copiled with dynamic arch, i.e. architecture determined at runtime:
  - Edit Makefile.rule to set: DYNAMIC_ARCH=1
  - Or just do make DYNAMIC_ARCH=1 to build
Configure line

./configure --prefix=/my/local/opt/R/$version \

Random Grid Engine tips and tricks

The following work with Son of Grid Engine (SGE) 8.1.9 as configured on the University of Sheffield's ShARC and Iceberg clusters.

Jobs with dependancies

You can use the -hold_jid <<job-name or job-name>> option to make jobs run only when other jobs have finished, rather than having jobs start and sit waiting for other tasks to complete.

	#!/usr/bin/env python3
	import sys
	import os
	import re
	import pwd

	# some of the User_Aliases lines contain buggy usernames
	# which have "a" at the end of the username

	broken_usernames = set()

	#! /usr/bin/nft -f

	### localhost
	define LOCALHOST = { 127.0.0.1 }
	define LOCALHOST6 = { ::1 }

	table inet filter {
	chain input {
	type filter hook input priority 0; policy drop;
	ct state invalid counter drop comment "early drop of invalid packets"

	python-lsp-server
	importmagic
	epc
	pycodestyle
	mccabe
	pyflakes
	pylint
	rope
	yapf
	ipython

	#!/usr/bin/env python
	import sys
	import os
	import numpy as np

	text = [[4, 3, 8, 9, 5, 1, 2, 7, 6], [8, 3, 4, 1, 5, 9, 6, 7, 2],
	[6, 1, 8, 7, 5, 3, 2, 9, 4], [6, 9, 8, 7, 5, 3, 2, 1, 4],
	[6, 1, 8, 7, 5, 3, 2, 1, 4], [6, 1, 3, 2, 9, 4, 8, 7, 5]]

	text = np.array(text)

	mkdir bin
	find . -not -type d -and -not -path '/\.git/' -exec git mv {} bin \;

	TIL
	- tree [dirname] : shows an ASCII-formatted tree of directory dirname