diff options
| -rw-r--r-- | misc/gn_installation_notes.txt | 38 | ||||
| -rw-r--r-- | misc/notes.txt | 18 |
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 |