diff options
Diffstat (limited to 'misc')
| -rw-r--r-- | misc/gn_installation_notes.txt | 149 | ||||
| -rw-r--r-- | misc/notes.txt | 176 |
2 files changed, 321 insertions, 4 deletions
diff --git a/misc/gn_installation_notes.txt b/misc/gn_installation_notes.txt new file mode 100644 index 00000000..bad21226 --- /dev/null +++ b/misc/gn_installation_notes.txt @@ -0,0 +1,149 @@ +Get git: + +sudo apt-get install git-core + +=========================================== + +Clone code from git repository: +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-cache search" searches for text in the description for various packages, while +"apt-file search" searches for files within the packages** + +Search for package with a specified file that can be installed with apt-get +apt-file search _______ + +Install from requirements.txt: +pip install -r gene/wqflask/requirements.txt -t ve27 + + +============================================ + +Using dpkg + +Check which system packages are already installed: +dpkg -l | less + +=========================================== + +Using Yolk + +Install Yolk: +pip install yolk + +Check packages installed in this virtual environment: +yolk -l + +Checks packages that have updates available: +yolk -U + +=========================================== + +Installing virtualenv: +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 + +=========================================== + +Install MySQL Client + +To fix error "mysql_config not found" while installing packages with pip: +sudo apt-get install libmysqlclient-dev + +=========================================== + +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) +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 + +=========================================== + +Installing numarray 1.5.2 + +wget http://downloads.sourceforge.net/project/numpy/Old%20Numarray/1.5.2/numarray-1.5.2.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fnumpy%2Ffiles%2FOld%2520Numarray%2F1.5.2%2Fnumarray-1.5.2.tar.gz%2Fdownload&ts=1358978306&use_mirror=superb-dca2 +mv -v numarray-1.5.2.tar.gz?r=http:%2F%2Fsourceforge.net%2Fprojects%2Fnumpy%2Ffiles%2FOld%20Numarray%2F1.5.2%2Fnumarray-1.5.2.tar.gz%2Fdownload numarray-1.5.2.tar.gz +tar xvf numarray-1.5.2.tar.gz +sudo python setup.py install + +=========================================== + +Installing R + +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 + +========================================== + +Install colordiff (just to make it easier to view differences in files, not necessary for GN) + +sudo apt-get install colordiff + +========================================== + +To get server running: + +!If having seemingly inexplicable problems with imports, make sure I've started the environment! + +Start up virtual environment: +source ~/ve27/bin/activate + +To set WQFLASK_SETTINGS environment variable: +export WQFLASK_SETTINGS=~/gene/wqflask/cfg/zach_settings.py (or wherever file is located) + +To change screen environment variable (if man not working or to get color, for example): +export TERM=screen + +To search for commands in history if necessary: +history | grep "(whatever is being searched for)" + +Run web server: +/usr/local/nginx/sbin/nginx + +Run server: +python runserver.py + +===========================================
\ No newline at end of file diff --git a/misc/notes.txt b/misc/notes.txt index f9834fa3..67133d4a 100644 --- a/misc/notes.txt +++ b/misc/notes.txt @@ -1,17 +1,83 @@ Clone code from git repository: git clone http://github.com/zsloan/genenetwork.git gene +Pull from branch in git repository: +git pull origin flask(or whatever the branch is) + +Add all files in current directory branch to be staged to be committed +git add -A + +Git push to my github repository +git push https://github.com/zsloan/genenetwork.git flask + + +Get the default path being used when a command is typed: +which _______ + +Change default path python looks at when importing +export PYTHONPATH="/home/zas1024/gene/wqflask" + +Get the paths checked when a user types a command: +echo $PATH + +Get all environment variables: +set + + +**** 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 update +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 _______ + +============================================ + +Check which system packages are installed: +dpkg -l | less + +============================================ + +NEVER USE SUDO WITH PIP + +To fix error "mysql_config not found": +sudo apt-get install libmysqlclient-dev + +Create requirements.txt file: +pip freeze > requirements.txt (or whatever filename) + +Install from requirements.txt: +pip install -r gene/wqflask/requirements.txt -t ve27 + ============================================ 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) +export WQFLASK_SETTINGS=~/zach_settings.py (or wherever file is located) + +zach_settings.py is the local config file with the DB_URI +default_settings.py is the config file with the configuration information that would apply +to any running instance of GeneNetwork To change screen environment variable (if man not working or to get color, for example): export TERM=screen @@ -19,15 +85,43 @@ export TERM=screen To search for commands in history if necessary: history | grep "(whatever is being searched for)" -Run web server: -/usr/local/nginx/sbin/nginx +Reload web server: +/usr/sbin/nginx -s reload Run server: python runserver.py =========================================== +Update user password: +use mysql; +UPDATE user SET password=PASSWORD('whatever') WHERE user='webqtl'; +FLUSH PRIVILEGES; + +=========================================== + +Redis things + +Restart redis server: +sudo /etc/init.d/redis_6379 stop +sudo /etc/init.d/redis_6379 start + +=========================================== + +Run pylint: +pylint file_name + +For options: +pylint --help + +=========================================== + Start screen session: + +If "no option -R": +byobu-select-backend +2. screen + byobu -RD (to start) control-a then :multiuser on control-a then :acladd sam @@ -75,20 +169,94 @@ ll h*: Finds items in the directory starting with h =========================================== +du -hms * | sort -n : Gives size used by different directories +-h: human readable +-m: in megabytes (default) +-s: summarize + +=========================================== + +rm -rfv + +=========================================== + +cp -a (archive; copies recursively and doesn't follow symbol links) + -i (interactive, prompts before overwrite) + -v (verbose) + -b (backup) + +mv (same as above, but with no -a) + +=========================================== + +Add user: +sudo adduser +Edit /etc/sudoers to give user root privileges + + +=========================================== + tidyp - Improves/beautifies html code tidyp -m -i -w 100 index_page.html =========================================== -ps -ax - View processes +ps ax - View processes +ps ux (the "u" is for user) kill (process #) =========================================== +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 +tar xvf qtlreaper-1.1.1.tar.gz (to unzip) +python setup.py build +python setup.py install + +=========================================== + +Using Yolk + +Install Yolk: +pip install yolk + +Check packages installed in this virtual environment: +yolk -l + +Checks packages that have updates available: +yolk -U + +=========================================== + 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 + +=========================================== + +Reboot server +sudo reboot + +=========================================== + +Using grep: + +grep -ir (search string) (directory) + +-i ignores case +-r searches recursively through subdirectories of directory you specify + +=========================================== + +MySQL Things - +Create fulltext (MATCH AGAINST syntax) index: +CREATE FULLTEXT INDEX __________ ON Table (Column); |