installation

docs/source/installation.rst

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+MGEScan on Galaxy Installation
+===============================================================================
+
+MGEScan on Galaxy provide local installation and cloud installation. 
+
+Local Installation
+-------------------------------------------------------------------------------
+
+This installation manual is for Ubuntu 14.04+ distribution. Others are not
+tested.
+
+Prerequisite
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Software packages and system packages are requied to run MGEScan.  You need to
+install system packages with ``sudo`` command. An admin ``root`` privilege is
+required.
+
+System Packages
+*******************************************************************************
+
+If you have ``virtualenv``, ``git``, and ``python-dev``, you can skip this
+step.
+
+**Ubuntu**
+
+::
+
+  sudo apt-get update
+  sudo apt-get install python-virtualenv -y
+  sudo apt-get install git -y
+  sudo apt-get install python-dev -y
+
+Environment Variables
+*******************************************************************************
+
+MGEScan will be installed on a default directory ``$HOME/mgescan3``. You can
+change it if you prefer other location to install MGEScan.
+
+::
+
+  export MGESCAN_HOME=$HOME/mgescan3
+  export MGESCAN_SRC=$MGESCAN_HOME/src
+  export GALAXY_HOME=$MGESCAN_HOME/galaxy
+  export TRF_HOME=$MGESCAN_HOME/trf
+  export MGESCAN_VENV=$MGESCAN_HOME/virtualenv/mgescan
+
+
+
+Create a MGESCan start file ``.mgescanrc`` 
+
+::
+
+   cat <<EOF > $HOME/.mgescanrc
+   export MGESCAN_HOME=\$HOME/mgescan3
+   export GALAXY_HOME=\$MGESCAN_HOME/galaxy
+   export TRF_HOME=\$MGESCAN_HOME/trf
+   export MGESCAN_VENV=\$MGESCAN_HOME/virtualenv/mgescan
+   EOF
+
+Then include it to your startup file (i.e. ``.bashrc``).
+
+::
+
+   echo "source ~/.mgescanrc" >> $HOME/.bashrc
+
+
+Software Packages
+*******************************************************************************
+
+Galaxy Workflow, HMMER (3.1b1), EMBOSS Suite and TRF are required.
+
+Galaxy
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+
+.. tip:: Make sure that $MGESCAN_HOME is set by ``echo $MGESCAN_HOME`` command.
+        If you don't see a path similar to ``/home/.../mgescan3/``, you have to
+        define environment variables again.
+
+From Github repository (source code):
+
+::
+
+        cd $MGESCAN_HOME
+        git clone https://github.com/galaxyproject/galaxy/
+        cd galaxy/
+        ./run.sh &
+
+HMMER and EMBOSS
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+
+If you have ``HMMER`` and ``EMBOSS`` on your system, you can skip this step.
+
+**Ubuntu**
+
+::
+
+        sudo apt-get install hmmer -y
+        sudo apt-get install emboss -y
+
+Virtual Environments (virtualenv)
+*******************************************************************************
+
+It is recommended to have an isolated environment for MGEScan Python
+libraries. virtualenv creates a separated space for MGEScan, and issues from
+dependencies and versions of Python libraries can be avoided. Note that you
+have to be in the virtualenv of MGEScan before to run any MGEScan command line
+tools. The following commands create a virtualenv for MGEScan and enable it on
+your account.
+
+::
+
+  mkdir -p $MGESCAN_VENV
+  virtualenv $MGESCAN_VENV
+  source $MGESCAN_VENV/bin/activate
+  echo "source $MGESCAN_VENV/bin/activate" >> ~/.bash_profile
+
+
+Tandem Repeats Finder (trf)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+
+``trf`` is a single binary executable file.
+
+::
+ 
+   mkdir -p $TRF_HOME
+   wget http://tandem.bu.edu/trf/downloads/trf407b.linux64 -P $TRF_HOME
+
+MGEScan Installation
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+From Github repository (source code):
+
+::
+
+  cd $MGESCAN_HOME
+  git clone https://github.com/MGEScan/mgescan.git
+  ln -s mgescan src 
+  cd mgescan
+  python setup.py install
+
+Configuration
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Virtual Environments (virtualenv)
+*******************************************************************************
+
+It is recommended to have an isolated environment for MGEScan Python
+libraries. virtualenv creates a separated space for MGEScan, and issues from
+dependencies and versions of Python libraries can be avoided. Note that you
+have to be in the virtualenv of MGEScan before to run any MGEScan command line
+tools. The following commands create a virtualenv for MGEScan and enable it on
+your account.
+
+::
+
+  source $MGESCAN_VENV/bin/activate
+
+Make sure that you see ``(mgescan)`` label on your prompt.
+
+Galaxy Configurations for MGEScan
+*******************************************************************************
+
+MGEScan github repository contains codes and toolkits for MGEScan on Galaxy.
+Prior to run a Galaxy Workflow web server, the codes and toolkits should be
+installed in the ``galaxy`` main directory.
+
+::
+
+  cp -pr $MGESCAN_SRC/galaxy-modified/* $GALAXY_HOME
+
+trf
+*******************************************************************************
+
+To run ``trf`` anywhere under ``mgescan`` virtualenv, we create a symlink in
+the ``bin`` directory.
+
+::
+
+   ln -s $TRF_HOME/trf407b.linux64 $MGESCAN_VENV/bin/trf
+   chmod 700 $MGESCAN_VENV/bin/trf
+
+
+Start Galaxy
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+::
+
+        cd $GALAXY_HOME
+        nohup sh run.sh &
+
+.. note:: Default port number : 38080 http://[IP ADDRESS]:38080
+
+
+
+
+