Add license document and license text to code. Add simple README file.

README.md

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+# A Simple SGE Template Preprocessor Engine
+
+
+`qsubsec` is a template language for generating script files for submission using the [SGE grid system](https://arc.liv.ac.uk/trac/SGE). By using this system, you can separate the logic of your qsub jobs from the data required for a specific run.
+
+## Overview
+
+The qsubsec utility processes qsubsec-formatted template files to generate code sections that can be submitted for execution (for example through the SGE scheduler). Before processing, template files are checked for token placeholders and these are filled in. The resulting Python code is then executed to generate a set of sections.
+
+The stages in template processing are:
+
+* The template file and token file(s) are read;
+* Any token placeholders found in the template file are filled in using the tokens file(s) read;
+* The resulting Python code is executed to yield a set of sections;
+* Each section is output in turn
+
+Processed sections can be output in multiple formats (currently `bash` and `qsub`), allowing the same templates to be run on multiple different systems.
+
+For more information on the TFF token definition syntax and the qsubsec template syntax, see the documentation directory.
+
+
+## Installation
+
+Installation should be as simple as:
+
+~~~bash
+git clone https://github.com/alastair-droop/qsubsec3.git
+cd qsubsec3
+python setup.py install
+~~~
+
+Although `qsubsec` can be run on most machines, the qsub executable must be available and functional for automatic qsub submission to work (using the `-s` argument with the qsub format).
+
+## Licence
+
+These tools are released under the [GNU General Public License version 3](http://www.gnu.org/licenses/gpl.html).

parseTFF.py

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-#!/usr/bin/env python3
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 import tokens
 import os.path

qsubsec.py

@@ -1,4 +1,15 @@
-#!/usr/bin/env python3
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 import tokens as qstokens
 from sections import SectionList, Limits, CommandType

sectionFormatter.py

@@ -1,4 +1,15 @@
-#!/usr/bin/env python
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 from sections import Requirement, CommandType
 from os import remove

sections.py

@@ -1,4 +1,15 @@
-#!/usr/bin/env python3
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 import logging as log
 import json

templates.py

@@ -1,4 +1,15 @@
-#!/usr/bin/env python
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 import tokens as qstokens
 from sections import Option, CommandType, Section, SectionList

tokens.py

@@ -1,4 +1,16 @@
-#!/usr/bin/env python
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 from collections import OrderedDict
 from string import Formatter
 from itertools import product