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| 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" |
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| # Customize these global variables | |
| $GOOGLE_PROJECT_ID = "MYPROJECTID" | |
| $GOOGLE_CLIENT_EMAIL = "ahmedaabdulwahed@gmail.com" | |
| $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) |
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| 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
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| #!/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
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| 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
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| 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
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| 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
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| 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
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| 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
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| <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 admin@mylocalhost.com | |
| DocumentRoot "C:\Program Files (x86)\ParaView 4.1.0\share\paraview-4.1\www" | |
| ErrorLog "logs/pv-error_log" |
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