This page was last updated on Saturday, 09-Mar-2019 09:56:27 CST

Installation notes for introgression browser version xxx

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Prerequisites

• docker

Installation

1. $ ver=""
2. $ cd /programinstallers/
3. $ git clone git@github.com:sauloal/introgressionbrowser.git
   Cloning into 'introgressionbrowser'...
   The authenticity of host 'github.com (192.30.253.113)' can't be established.
   RSA key fingerprint is SHA256:nThbg6kXUpJWGl7E1IGOCspRomTxdCARLviKw6E5SY8.
   Are you sure you want to continue connecting (yes/no)? no
4. $ ssh-keyscan github.com >> ~/.ssh/known_hosts
   # github.com:22 SSH-2.0-babeld-9d924d26
   # github.com:22 SSH-2.0-babeld-9d924d26
   # github.com:22 SSH-2.0-babeld-9d924d26
5. $ git clone git@github.com:sauloal/introgressionbrowser.git

   Cloning into 'introgressionbrowser'...
   Warning: Permanently added the RSA host key for IP address '192.30.253.112' to the list of known hosts.
   Permission denied (publickey).
   fatal: Could not read from remote repository.
   
   Please make sure you have the correct access rights
   and the repository exists.

6. $ cd /opt/
7. $ git clone https://github.com/sauloal/introgressionbrowser.git
8. $ cd introgressionbrowser
9. $ sudo docker run -it --rm --volume $PWD:/var/www/ibrowser2/ -w /var/www/ibrowser2 -p 127.0.1.1:7000:7000 --name ibrowser7000 sauloal/introgressionbrowser ./ibrowser.py data/
   …
   data folder /var/www/ibrowser2/data does not exists
10. $ mkdir data
11. $ sudo docker run -it --rm --volume $PWD:/var/www/ibrowser2/ -w /var/www/ibrowser2 -p 127.0.0.1:10000:10000 --name ibrowser sauloal/introgressionbrowser ./ibrowser.py data/
    …
    !!!!!!!!! NO DATABASES GIVEN. PLEASE ADD DATABASES !!!!!!!!!
12. $ cd data

    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/arabidopsis_50k.sqlite
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/arabidopsis_50k.sqlite.nfo
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/config.py
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/RIL.customorder
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/RIL_10k.sqlite
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/RIL_10k.sqlite.nfo
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/RIL_50k.sqlite
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/RIL_50k.sqlite.nfo
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/RIL_50k_mode_ril.sqlite
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/RIL_50k_mode_ril.sqlite.nfo
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/RIL_50k_mode_ril_delete.sqlite
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/RIL_50k_mode_ril_delete.sqlite.nfo
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/RIL_50k_mode_ril_greedy.sqlite
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/RIL_50k_mode_ril_greedy.sqlite.nfo
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/tom84.customorder
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/tom84_10k.sqlite
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/tom84_10k.sqlite.nfo
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/tom84_10k_introgression.sqlite
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/tom84_10k_introgression.sqlite.nfo
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/tom84_50k.sqlite
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/tom84_50k.sqlite.nfo
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/tom84_50k_introgression.sqlite
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/tom84_50k_introgression.sqlite.nfo
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/tom84_genes.sqlite
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/tom84_genes.sqlite.nfo
    wget --no-clobber --continue --progress=bar https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/ibrowser_clean_15.10_empty_1.4.ova
    cd ..

13. …
    docker: Error response from daemon: driver failed programming external connectivity on endpoint ibrowser (a33975dac2be8c3376efbe20c63985cd4eb3e219b483c81a1c3525fff974574b): (COMMAND_FAILED: '/sbin/iptables -w2 -t filter -A DOCKER ! -i docker0 -o docker0 -p tcp -d 172.17.0.2 --dport 10000 -j ACCEPT' failed: iptables: No chain/target/match by that name.).
    I had to add :DOCKER - to /home/admin/scripts/iptables.pickle
14. Change port in data/config.py from 10000 to 7000
15. Open port 7000 in firewall, then try (add -d to detach)
    $ nohup sudo docker run -it --rm -d --volume $PWD:/var/www/ibrowser2/ -w /var/www/ibrowser2 -p 127.0.1.1:7000:7000 --name ibrowser7000 sauloal/introgressionbrowser ./ibrowser.py data/ > log.stdout 2> log.stderr &
    …
    
16. Access from other computers
    $ sudo sysctl -w net.ipv4.conf.all.route_localnet=1
17. $ sudo iptables -t nat -I PREROUTING -p tcp --dport 7000 -j DNAT --to 127.0.1.1:7000
18. List all containers (only IDs) sudo docker ps -aq
    Stop all running containers. sudo docker stop $(sudo docker ps -aq)
    Remove all containers. sudo docker rm $(sudo docker ps -aq)
19. $
20. $
21. $
22. $

Abandoned attempt to install locally

1. $ sudo apt-get install build-essential checkinstall openssl sqlite3 libsqlite3-dev libfreetype6 libfreetype6-dev zlib1g-dev libjpeg62 libjpeg62-dev pkg-config libblas-dev liblapack-dev gfortran zlib1g-dev
2. $ sudo apt-get autoremove
3. $ sudo apt-get install python-setuptools python-dev python-numpy python-scipy python-matplotlib python-pandas python-sympy python-pip python-imaging python-numpy
4. $ sudo pip install --requirement requirements.txt
   …
   ValueError: A 0.7-series setuptools cannot be installed with distribute. Found one at /usr/lib/python2.7/dist-packages
5. $ sudo mv /usr/local/lib/python2.7/dist-packages/distribute-0.6.35-py2.7.egg /tmp/
6. This next step changed version from 20.7.0 to 40.8.0
   $ sudo pip install --upgrade setuptools
7. $ sudo mv /tmp/distribute-0.6.35-py2.7.egg /usr/local/lib/python2.7/dist-packages/
8. $ sudo pip install --requirement requirements.txt
   …
   Installing ETE (A python Environment for Tree Exploration).
   …
   NameError: name 'sys_platform' is not defined
   …
9. $ sudo pip uninstall distribute
   …
   Would remove:
   /usr/local/lib/python2.7/dist-packages/distribute-0.6.35-py2.7.egg
   Proceed (y/n)? y
   Successfully uninstalled distribute-0.6.35
   …
   
10. $ sudo pip install --upgrade --requirement requirements.txt
11. $ sudo apt-get install libapache2-mod-wsgi apache2
12. $ sudo a2enmod wsgi
    Module wsgi already enabled
13. $ sudo ln -s ibrowser.conf /etc/apache2/mods-available/ibrowser.conf
14. $ sudo /etc/init.d/apache2 reload
15. $ sudo apt-get install pypy
16. $ ./ibrowser.py

    IMPORTING BEHAVIOUR
    IMPORTING FUNCTIONS
    importing flask
    importing jinja2
    importing user database
    importing sha3
    Traceback (most recent call last):
      File "./ibrowser.py", line 31, in 
        from behaviour import *
      File "/opt/introgressionbrowser/behaviour.py", line 26, in 
        from routes import *
      File "/opt/introgressionbrowser/routes.py", line 17, in 
        from user_database import *
      File "/opt/introgressionbrowser/user_database.py", line 12, in 
        from flask.ext.sqlalchemy import SQLAlchemy
    ImportError: No module named ext.sqlalchemy

17. $
18. $