0x3bfc’s gists

0x3bfc / vagrant_up.log

Created July 15, 2015 09:28

SSH Vagrant GCE instances

	INFO global: Vagrant version: 1.7.2
	INFO global: Ruby version: 2.0.0
	INFO global: RubyGems version: 2.0.14
	INFO global: VAGRANT_DOTFILE_PATH="/store/VirtualBox VMs/"
	INFO global: VAGRANT_EXECUTABLE="/opt/vagrant/bin/../embedded/gems/gems/vagrant-1.7.2/bin/vagrant"
	INFO global: VAGRANT_INSTALLER_EMBEDDED_DIR="/opt/vagrant/bin/../embedded"
	INFO global: VAGRANT_INSTALLER_VERSION="2"
	INFO global: VAGRANT_HOME="/store/.vagrant.d/"
	INFO global: VAGRANT_DETECTED_OS="Linux"
	INFO global: VAGRANT_INSTALLER_ENV="1"

0x3bfc / Vagrantfile

Last active August 29, 2015 14:25

Vagrant file for Multiple Instances on GCE

	# Customize these global variables
	$GOOGLE_PROJECT_ID = "MYPROJECTID"
	$GOOGLE_CLIENT_EMAIL = "[email protected]"
	$GOOGLE_JSON_KEY_LOCATION = "/home/ubuntu/.ssh/privatekey-gce.json"
	$LOCAL_USER = "ubuntu"
	$LOCAL_SSH_KEY = "/home/ubuntu/.ssh/id_rsa"

	# Example Debian provistion script
	$PROVISION_DEBIAN = <<SCRIPT
	uname=$(uname -a)

0x3bfc / vagrant_up_google.log

Created July 16, 2015 16:17

Vagrant google log

	INFO global: Vagrant version: 1.7.2
	INFO global: Ruby version: 2.0.0
	INFO global: RubyGems version: 2.0.14
	INFO global: VAGRANT_DOTFILE_PATH="/store/VirtualBox VMs/"
	INFO global: VAGRANT_EXECUTABLE="/opt/vagrant/bin/../embedded/gems/gems/vagrant-1.7.2/bin/vagrant"
	INFO global: VAGRANT_INSTALLER_EMBEDDED_DIR="/opt/vagrant/bin/../embedded"
	INFO global: VAGRANT_INSTALLER_VERSION="2"
	INFO global: VAGRANT_HOME="/store/.vagrant.d/"
	INFO global: VAGRANT_DETECTED_OS="Linux"
	INFO global: VAGRANT_INSTALLER_ENV="1"

0x3bfc / vcfmerger.py

Created January 14, 2016 15:47

	#!/usr/bin/python
	import os
	import sys
	import subprocess

	"""
	This method is inspired from this issue on stackoverflow
	http://stackoverflow.com/questions/23091077/get-all-nested-directories-in-a-folder-python
	"""
	def list_dirs(path):

0x3bfc / frodock.output-Docker container

Created January 30, 2016 21:49

	ubuntu@ip-172-31-5-104:~/FRODOCK_v2.0_Linux$ ./run_frodock_tests.sh
	STAGE-1 Creation of receptor vdw potential map
	With hydrogens: no
	Grid voxel: 1.0
	Option: VdW potential. Probe radius: 2.0
	Written output potential (VdW or Electrostatic) map: 3hfl_fv_W.ccp4

	real 0m12.466s
	user 0m12.458s
	sys 0m0.008s

0x3bfc / frodock.output-Native

Created January 31, 2016 13:58

	user@NGS-1:/home/nuser/frodock/FRODOCK_v2.0_Linux$ time ./run_frodock_tests.sh
	STAGE-1 Creation of receptor vdw potential map
	With hydrogens: no
	Grid voxel: 1.0
	Option: VdW potential. Probe radius: 2.0
	Written output potential (VdW or Electrostatic) map: 3hfl_fv_W.ccp4
	STAGE-2 Creation of the receptor electrostatic potential map
	With hydrogens: no
	Grid voxel: 1.0
	Option: Electrostatic potential.

0x3bfc / frodock.vm.1a8m1alu

Created January 31, 2016 16:58

	ubuntu@ip-172-31-5-104:~/frodock/FRODOCK_v2.0_Linux$ time ./run_frodock_tests.sh 1a8m 1alu pdb_data
	STAGE-1 Creation of receptor vdw potential map
	With hydrogens: no
	Grid voxel: 1.0
	Option: VdW potential. Probe radius: 2.0
	Written output potential (VdW or Electrostatic) map: 1a8m_W.ccp4
	STAGE-2 Creation of the receptor electrostatic potential map
	With hydrogens: no
	Grid voxel: 1.0
	Option: Electrostatic potential.

0x3bfc / frodock-native-1a8m_1bj8

Created January 31, 2016 18:00

	nuser@NGS-1:/home/nuser/frodock/FRODOCK_v2.0_Linux$ time ./run_frodock_tests.sh 1a8m 1bj8 pdb_data
	STAGE-1 Creation of receptor vdw potential map
	With hydrogens: no
	Grid voxel: 1.0
	Option: VdW potential. Probe radius: 2.0
	Written output potential (VdW or Electrostatic) map: 1a8m_W.ccp4
	STAGE-2 Creation of the receptor electrostatic potential map
	With hydrogens: no
	Grid voxel: 1.0
	Option: Electrostatic potential.

0x3bfc / galaxy-docker

Created February 22, 2016 14:05


	tavaxy@c863b843f754:/var/www/tavaxy/engines/galaxy$ sh run.sh --reload
	Starting subprocess with file monitor
	python path is: /var/www/tavaxy/engines/galaxy/eggs/numpy-1.3.0-py2.6-linux-x86_64-ucs4.egg, /var/www/tavaxy/engines/galaxy/eggs/pysam-0.1.1_kanwei_90e03180969d-py2.6-linux-x86_64-ucs4.egg, /var/www/tavaxy/engines/galaxy/eggs/Whoosh-0.3.18-py2.6.egg, /var/www/tavaxy/engines/galaxy/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg, /var/www/tavaxy/engines/galaxy/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /var/www/tavaxy/engines/galaxy/eggs/bx_python-0.5.0_dev_f74aec067563-py2.6-linux-x86_64-ucs4.egg, /var/www/tavaxy/engines/galaxy/eggs/amqplib-0.6.1-py2.6.egg, /var/www/tavaxy/engines/galaxy/eggs/pexpect-2.4-py2.6.egg, /var/www/tavaxy/engines/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /var/www/tavaxy/engines/galaxy/eggs/Babel-0.9.4-py2.6.egg, /var/www/tavaxy/engines/galaxy/eggs/Beaker-1.4-py2.6.egg, /var/www/tavaxy/engines/galaxy/eggs/Mako-0.2.5-py2.6.egg, /var/www/tavaxy/engines/

0x3bfc / apache_https_443_paraview_web_wss

Created May 16, 2016 17:13


	<VirtualHost _default_:443>
	SSLEngine on
	SSLCertificateFile "C:\Program Files (x86)\Apache Software Foundation\SSL\apache.crt"
	SSLCertificateKeyFile "C:\Program Files (x86)\Apache Software Foundation\SSL\apache.key"

	ServerName mylocalhost.com
	ServerAdmin [email protected]
	DocumentRoot "C:\Program Files (x86)\ParaView 4.1.0\share\paraview-4.1\www"
	ErrorLog "logs/pv-error_log"

Ahmed 0x3bfc