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authorZachary Sloan2013-01-24 17:46:19 -0600
committerZachary Sloan2013-01-24 17:46:19 -0600
commit7be6c2c94c99148667a05f400ca47df1c472d964 (patch)
tree31bb2bffadeef9826ffc6504c492c9cedb8a49ff /misc
parent2a876f5417625bdfb039a1d885ee0a4ab026498e (diff)
downloadgenenetwork2-7be6c2c94c99148667a05f400ca47df1c472d964.tar.gz
Added a lot to the notes in the process of setting up on the
new server
Diffstat (limited to 'misc')
-rw-r--r--misc/gn_installation_notes.txt38
-rw-r--r--misc/notes.txt18
2 files changed, 54 insertions, 2 deletions
diff --git a/misc/gn_installation_notes.txt b/misc/gn_installation_notes.txt
index 54e8fcee..173f2819 100644
--- a/misc/gn_installation_notes.txt
+++ b/misc/gn_installation_notes.txt
@@ -27,7 +27,18 @@ sudo pip install virtualenv
Tell virtualenv which directory to use:
virtualenv ve27
+Start up virtual environment:
+source ~/ve27/bin/activate
+
+===========================================
+Installing yaml
+
+Install libyaml-dev:
+sudo apt-get install libyaml-dev
+
+Install yaml:
+pip install pyyaml
===========================================
@@ -43,8 +54,11 @@ Installing QTL Reaper
wget http://downloads.sourceforge.net/project/qtlreaper/qtlreaper/1.1.1/qtlreaper-1.1.1.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fqtlreaper%2Ffiles%2Flatest%2Fdownload&ts=1358975786&use_mirror=iweb
mv -v qtlreaper-1.1.1.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fqtlreaper%2Ffiles%2Flatest%2Fdownload&ts=1358975786&use_mirror=iweb qtlreaper-1.1.1.tar.gz
tar xvf qtlreaper-1.1.1.tar.gz (to unzip)
-sudo python setup.py build
-sudo python setup.py install
+python setup.py build
+sudo mkdir /home/zas1024/ve27/include/python2.7/Reaper
+sudo chown /home/zas1024/ve27/include/python2.7/Reaper (or whereever the directory is; the problem
+involved the fact that doing "sudo python setup.py install" doesn't install within the virtualenv)
+python setup.py install
===========================================
@@ -63,6 +77,26 @@ sudo apt-get install r-base-dev
===========================================
+Install Parallel Python (pp)
+
+wget http://www.parallelpython.com/downloads/pp/pp-1.6.3.tar.gz
+tar xvf pp-1.6.3.tar.gz
+python setup.py install
+
+==========================================
+
+Install requests
+
+pip install requests
+
+==========================================
+
+Install logging_tree
+
+pip install logging_tree
+
+==========================================
+
To get server running:
!If having seemingly inexplicable problems with imports, make sure I've started the environment!
diff --git a/misc/notes.txt b/misc/notes.txt
index ab71a99f..e60102fc 100644
--- a/misc/notes.txt
+++ b/misc/notes.txt
@@ -4,9 +4,19 @@ git clone http://github.com/zsloan/genenetwork.git gene
Pull from branch in git repository:
git pull origin flask(or whatever the branch is)
+
+**** apt-get is an Ubuntu system-wide package manager, while pip is a Python-only system
+for python packages ****
+
+Upgrade system packages for security updates, etc:
+apt-get upgrade
+
**"apt-cache search" searches for text in the description for various packages, while
"apt-file search" searches for files within the packages**
+Show information about given result item returned by apt-cache search:
+apt-cache show _______
+
Search for package with a specified file that can be installed with apt-get
apt-file search _______
@@ -25,9 +35,14 @@ To get server running:
!If having seemingly inexplicable problems with imports, make sure I've started the environment!
+Note: Virtual environment is not activated when running as root
+
Start up virtual environment:
source ~/ve27/bin/activate
+Deactivate virtual environment:
+deactivate (just type deactivate)
+
To set WQFLASK_SETTINGS environment variable:
export WQFLASK_SETTINGS=~/gene/wqflask/cfg/zach_settings.py (or wherever file is located)
@@ -128,4 +143,7 @@ Python stuff:
Classes should always inherit "object"
To iterate through dictionary items: for X, Y in MyDictionary.items():
+===========================================
+Create symbolic link:
+ln -s dir_to_link_to linking_dir