From d27e52855d1aa442cebce7901815a673cf34f8b8 Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Wed, 3 Jul 2013 23:03:49 +0000
Subject: Updated notes and created requirements.txt file

---
 misc/gn_installation_notes.txt                   | 38 ++++++++++++++++-
 misc/notes.txt                                   | 11 ++++-
 misc/requirements.txt                            | 53 ++++++++++++++++++++++++
 wqflask/wqflask/correlation/show_corr_results.py |  2 -
 4 files changed, 100 insertions(+), 4 deletions(-)
 create mode 100644 misc/requirements.txt

diff --git a/misc/gn_installation_notes.txt b/misc/gn_installation_notes.txt
index bad21226..565cf9f5 100644
--- a/misc/gn_installation_notes.txt
+++ b/misc/gn_installation_notes.txt
@@ -1,6 +1,37 @@
+UFW - default firewall confirguation tool for Ubuntu; eases iptables firewall configuration
+
+Enable UFW:
+sudo ufw enable
+Check status of UFW:
+sudo ufw status verbose
+
+Limit ssh:
+sudo ufw limit ssh
+
+Enable http, https:
+sudo ufw allow http
+sudo ufw allow https
+
+===========================================
+
+http://evilrouters.net/2011/02/18/using-etckeeper-with-git-on-ubuntu/
+
+Install etckeeper:
+sudo apt-get install etckeeper
+
+Edit /etc/etckeeper/etckeeper.conf to comment out VCS="bzr" and comment in VCS="git"
+
+Initialize repository:
+sudo etckeeper init
+
+Do initial commit:
+sudo etckeeper commit "Initial commit."
+
+===========================================
+
 Get git:
 
-sudo apt-get install git-core
+sudo apt-get install git
 
 ===========================================
 
@@ -16,6 +47,11 @@ git pull origin flask(or whatever the branch is)
 Search for package with a specified file that can be installed with apt-get
 apt-file search _______
 
+============================================
+
+Install pip:
+sudo apt-get install python-pip
+
 Install from requirements.txt:
 pip install -r gene/wqflask/requirements.txt -t ve27
 
diff --git a/misc/notes.txt b/misc/notes.txt
index 92ed267b..9da6c4ea 100644
--- a/misc/notes.txt
+++ b/misc/notes.txt
@@ -92,6 +92,15 @@ python runserver.py
 
 ===========================================
 
+UFW - default firewall confirguation tool for Ubuntu; eases iptables firewall configuration
+
+Enable UFW:
+sudo ufw enable
+Check status of UFW:
+sudo ufw status verbose
+
+===========================================
+
 Update user password:
 use mysql;
 UPDATE user SET password=PASSWORD('whatever') WHERE user='webqtl';
@@ -117,7 +126,7 @@ pylint --help
 
 Start screen session:
 
-If "no option -R":
+If "no option -R" or running for first time:
 byobu-select-backend
 2. screen
 
diff --git a/misc/requirements.txt b/misc/requirements.txt
new file mode 100644
index 00000000..bd4e3c2f
--- /dev/null
+++ b/misc/requirements.txt
@@ -0,0 +1,53 @@
+Cheetah==2.4.4
+GnuPGInterface==0.3.2
+Jinja2==2.6
+Landscape-Client==12.05
+M2Crypto==0.21.1
+MarkupSafe==0.15
+PAM==0.4.2
+PyYAML==3.10
+Reaper==1.0
+Twisted-Core==11.1.0
+Twisted-Names==11.1.0
+Twisted-Web==11.1.0
+apache-libcloud==0.12.3
+apt-xapian-index==0.44
+argparse==1.2.1
+boto==2.2.2
+chardet==2.0.1
+cloud-init==0.6.3
+command-not-found==0.2.44
+configobj==4.7.2
+## FIXME: could not find svn URL in dependency_links for this package:
+distribute==0.6.24dev-r0
+euca2ools==2.0.0
+httplib2==0.7.2
+keyring==0.9.2
+language-selector==0.1
+launchpadlib==1.9.12
+lazr.restfulclient==0.12.0
+lazr.uri==1.0.3
+msgpack-python==0.1.10
+numarray==1.5.2
+oauth==1.0.1
+paramiko==1.7.7.1
+pyOpenSSL==0.12
+pycrypto==2.4.1
+pycurl==7.19.0
+pylibacl==0.5.0
+pyserial==2.5
+python-apt==0.8.3ubuntu7.1
+python-debian==0.1.21ubuntu1
+pyxattr==0.5.0
+pyzmq==13.0.0
+rdiff-backup==1.2.8
+redis==2.7.2
+salt-cloud==0.8.0
+simplejson==2.3.2
+ufw==0.31.1-1
+unattended-upgrades==0.1
+virtualenv==1.8.4
+wadllib==1.3.0
+wsgiref==0.1.2
+yolk==0.4.3
+zope.interface==3.6.1
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index f69fe551..4a0937bb 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -203,8 +203,6 @@ class CorrelationResults(object):
                 #        mb = trait_object.mb
                 #    )
 
-            
-
             #trait_list = self.getTissueCorrelationByList( primary_trait_symbol = self.this_trait.symbol,
             #                                            corr_results = self.correlation_results,
             #                                            TissueProbeSetFreezeId = 1,
-- 
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