LBMC » MyLabStocks

# Makefile for Sphinx documentation

#

# You can set these variables from the command line.

SPHINXOPTS    =

SPHINXBUILD   = sphinx-build-2.7

PAPER         =

BUILDDIR      = build

SOURCE=.

# Internal variables.

PAPEROPT_a4     = -D latex_paper_size=a4

PAPEROPT_letter = -D latex_paper_size=letter

ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) $(SOURCE)

# the i18n builder cannot share the environment and doctrees with the others

I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source

.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext

help:

	@echo "Please use \`make <target>' where <target> is one of"

	@echo "  html       to make standalone HTML files"

	@echo "  dirhtml    to make HTML files named index.html in directories"

	@echo "  singlehtml to make a single large HTML file"

	@echo "  pickle     to make pickle files"

	@echo "  json       to make JSON files"

	@echo "  htmlhelp   to make HTML files and a HTML help project"

	@echo "  qthelp     to make HTML files and a qthelp project"

	@echo "  devhelp    to make HTML files and a Devhelp project"

	@echo "  epub       to make an epub"

	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"

	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"

	@echo "  text       to make text files"

	@echo "  man        to make manual pages"

	@echo "  texinfo    to make Texinfo files"

	@echo "  info       to make Texinfo files and run them through makeinfo"

	@echo "  gettext    to make PO message catalogs"

	@echo "  changes    to make an overview of all changed/added/deprecated items"

	@echo "  linkcheck  to check all external links for integrity"

	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"

clean:

	-rm -rf $(BUILDDIR)/*

html:

	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html

	@echo

	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."

dirhtml:

	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml

	@echo

	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."

singlehtml:

	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml

	@echo

	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."

pickle:

	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle

	@echo

	@echo "Build finished; now you can process the pickle files."

json:

	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json

	@echo

	@echo "Build finished; now you can process the JSON files."

htmlhelp:

	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp

	@echo

	@echo "Build finished; now you can run HTML Help Workshop with the" \

	      ".hhp project file in $(BUILDDIR)/htmlhelp."

qthelp:

	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp

	@echo

	@echo "Build finished; now you can run "qcollectiongenerator" with the" \

	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"

	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/seqtl.qhcp"

	@echo "To view the help file:"

	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/seqtl.qhc"

devhelp:

	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp

	@echo

	@echo "Build finished."

	@echo "To view the help file:"

	@echo "# mkdir -p $$HOME/.local/share/devhelp/seqtl"

	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/seqtl"

	@echo "# devhelp"

epub:

	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub

	@echo

	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."

latex:

	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex

	@echo

	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."

	@echo "Run \`make' in that directory to run these through (pdf)latex" \

	      "(use \`make latexpdf' here to do that automatically)."

latexpdf:

	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex

	@echo "Running LaTeX files through pdflatex..."

	$(MAKE) -C $(BUILDDIR)/latex all-pdf

	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."

text:

	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text

	@echo

	@echo "Build finished. The text files are in $(BUILDDIR)/text."

man:

	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man

	@echo

	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."

texinfo:

	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo

	@echo

	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."

	@echo "Run \`make' in that directory to run these through makeinfo" \

	      "(use \`make info' here to do that automatically)."

info:

	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo

	@echo "Running Texinfo files through makeinfo..."

	make -C $(BUILDDIR)/texinfo info

	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."

gettext:

	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale

	@echo

	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."

changes:

	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes

	@echo

	@echo "The overview file is in $(BUILDDIR)/changes."

linkcheck:

	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck

	@echo

	@echo "Link check complete; look for any errors in the above output " \

	      "or in $(BUILDDIR)/linkcheck/output.txt."

doctest:

	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest

	@echo "Testing of doctests in the sources finished, look at the " \

	      "results in $(BUILDDIR)/doctest/output.txt."

# -*- coding: utf-8 -*-

#

# mylabstocks documentation build configuration file, created by

# sphinx-quickstart on Thu Dec 13 16:44:18 2012.

#

# This file is execfile()d with the current directory set to its containing dir.

#

# Note that not all possible configuration values are present in this

# autogenerated file.

#

# All configuration values have a default; values that are commented out

# serve to show the default.

import sys, os

# If extensions (or modules to document with autodoc) are in another directory,

# add these directories to sys.path here. If the directory is relative to the

# documentation root, use os.path.abspath to make it absolute, like shown here.

#sys.path.insert(0, os.path.abspath('.'))

sys.path.insert(0, os.path.abspath('../../src/'))

# -- General configuration -----------------------------------------------------

# If your documentation needs a minimal Sphinx version, state it here.

#needs_sphinx = '1.0'

# Add any Sphinx extension module names here, as strings. They can be extensions

# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.

# extensions = []

extensions = ['sphinx.ext.autodoc']#, 'sphinx.ext.doctest']# , 'sphinx.ext.coverage', 'sphinx.ext.inheritance_diagram']

# Add any paths that contain templates here, relative to this directory.

templates_path = ['_templates']

# The suffix of source filenames.

source_suffix = '.rst'

# The encoding of source files.

#source_encoding = 'utf-8-sig'

# The master toctree document.

master_doc = 'index'

# General information about the project.

project = u'MyLabStocks'

copyright = u' since 2007, Florent CHUFFART, Gael YVERT'

# The version info for the project you're documenting, acts as replacement for

# |version| and |release|, also used in various other places throughout the

# built documents.

#

# The short X.Y version.

version = '0.1'

# The full version, including alpha/beta/rc tags.

release = '0.1.0'

# The language for content autogenerated by Sphinx. Refer to documentation

# for a list of supported languages.

#language = None

# There are two options for replacing |today|: either, you set today to some

# non-false value, then it is used:

#today = ''

# Else, today_fmt is used as the format for a strftime call.

#today_fmt = '%B %d, %Y'

# List of patterns, relative to source directory, that match files and

# directories to ignore when looking for source files.

exclude_patterns = []

# The reST default role (used for this markup: `text`) to use for all documents.

#default_role = None

# If true, '()' will be appended to :func: etc. cross-reference text.

#add_function_parentheses = True

# If true, the current module name will be prepended to all description

# unit titles (such as .. function::).

#add_module_names = True

# If true, sectionauthor and moduleauthor directives will be shown in the

# output. They are ignored by default.

#show_authors = False

# The name of the Pygments (syntax highlighting) style to use.

pygments_style = 'sphinx'

# A list of ignored prefixes for module index sorting.

#modindex_common_prefix = []

# -- Options for HTML output ---------------------------------------------------

# The theme to use for HTML and HTML Help pages.  See the documentation for

# a list of builtin themes.

html_theme = 'default'

# Theme options are theme-specific and customize the look and feel of a theme

# further.  For a list of options available for each theme, see the

# documentation.

#html_theme_options = {}

# Add any paths that contain custom themes here, relative to this directory.

#html_theme_path = []

# The name for this set of Sphinx documents.  If None, it defaults to

# "<project> v<release> documentation".

#html_title = None

# A shorter title for the navigation bar.  Default is the same as html_title.

#html_short_title = None

# The name of an image file (relative to this directory) to place at the top

# of the sidebar.

#html_logo = None

# The name of an image file (within the static path) to use as favicon of the

# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32

# pixels large.

#html_favicon = None

# Add any paths that contain custom static files (such as style sheets) here,

# relative to this directory. They are copied after the builtin static files,

# so a file named "default.css" will overwrite the builtin "default.css".

html_static_path = ['_static']

# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,

# using the given strftime format.

#html_last_updated_fmt = '%b %d, %Y'

# If true, SmartyPants will be used to convert quotes and dashes to

# typographically correct entities.

#html_use_smartypants = True

# Custom sidebar templates, maps document names to template names.

#html_sidebars = {}

# Additional templates that should be rendered to pages, maps page names to

# template names.

#html_additional_pages = {}

# If false, no module index is generated.

#html_domain_indices = True

# If false, no index is generated.

#html_use_index = True

# If true, the index is split into individual pages for each letter.

#html_split_index = False

# If true, links to the reST sources are added to the pages.

#html_show_sourcelink = True

# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.

#html_show_sphinx = True

# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.

#html_show_copyright = True

# If true, an OpenSearch description file will be output, and all pages will

# contain a <link> tag referring to it.  The value of this option must be the

# base URL from which the finished HTML is served.

#html_use_opensearch = ''

# This is the file name suffix for HTML files (e.g. ".xhtml").

#html_file_suffix = None

# Output file base name for HTML help builder.

htmlhelp_basename = 'mylabstocksdoc'

# -- Options for LaTeX output --------------------------------------------------

latex_elements = {

# The paper size ('letterpaper' or 'a4paper').

#'papersize': 'letterpaper',

# The font size ('10pt', '11pt' or '12pt').

#'pointsize': '10pt',

# Additional stuff for the LaTeX preamble.

#'preamble': '',

}

# Grouping the document tree into LaTeX files. List of tuples

# (source start file, target name, title, author, documentclass [howto/manual]).

latex_documents = [

  ('index', 'mylabstocks.tex', u'MyLabStocks Documentation',

   u'Florent CHUFFART, Gael YVERT', 'manual'),

]

# The name of an image file (relative to this directory) to place at the top of

# the title page.

#latex_logo = None

# For "manual" documents, if this is true, then toplevel headings are parts,

# not chapters.

#latex_use_parts = False

# If true, show page references after internal links.

#latex_show_pagerefs = False

# If true, show URL addresses after external links.

#latex_show_urls = False

# Documents to append as an appendix to all manuals.

#latex_appendices = []

# If false, no module index is generated.

#latex_domain_indices = True

# -- Options for manual page output --------------------------------------------

# One entry per manual page. List of tuples

# (source start file, name, description, authors, manual section).

man_pages = [

    ('index', 'MyLabStocks', u'MyLabStocks Documentation',

     [u'Florent CHUFFART, Gael YVERT'], 1)

]

# If true, show URL addresses after external links.

#man_show_urls = False

# -- Options for Texinfo output ------------------------------------------------

# Grouping the document tree into Texinfo files. List of tuples

# (source start file, target name, title, author,

#  dir menu entry, description, category)

texinfo_documents = [

  ('index', 'MyLabStocks', u'MyLabStocks Documentation',

   u'Florent CHUFFART, Gael YVERT', 'MyLabStocks', 'One line description of project.',

   'Miscellaneous'),

]

# Documents to append as an appendix to all manuals.

#texinfo_appendices = []

# If false, no module index is generated.

#texinfo_domain_indices = True

# How to display URL addresses: 'footnote', 'no', or 'inline'.

#texinfo_show_urls = 'footnote'

*****************************************

Readme / Documentation for `MyLabStocks`

*****************************************

`MyLabStocks` is a web application allowing to easily store, share and retrieve 

information about molecular biology materials stored in a laboratory. 

License

=======

Copyright CNRS 2012-2013                                                 

- Florent CHUFFART                                                         

- Gael YVERT                                                               

This software is a computer program which purpose is to perform quantitative analysis of epigenetic marks at single nucleosome resolution.     

The Software is provided “as is” without warranty of any kind, either express or implied, including without limitation any implied warranties of condition, uninterrupted use, merchantability, fitness for a particular purpose, or non-infringement. You use this software at your own risk.

This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software.  You can  use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info".                                                

As a counterpart to the access to the source code and  rights to copy, modify and redistribute granted by the license, users are provided only  with a limited warranty  and the software's author,  the holder of the economic rights,  and the successive licensors  have only  limited liability.                                                               

In this respect, the user's attention is drawn to the risks associated with loading,  using,  modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean  that it is complicated to manipulate,  and  that  also therefore means  that it is reserved for developers  and  experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and,  more generally, to use and operate it in the same conditions as regards security.                                     

The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms.           

Installation Instructions

=========================

This installation has been fully tested on:

  -  Debian 7.2.0 amd64 netinst [1], running on virtual machine using Oracle VM VirtualBox [2] for macosx (dev)

  -  Ubuntu Server 12.04.3 LTSUbuntu server LTS [3], running on physical machine (prod)

[1] http://cdimage.debian.org/debian-cd/7.2.0/amd64/iso-cd/debian-7.2.0-amd64-netinst.iso

[2] https://www.virtualbox.org

[3] http://www.ubuntu.com/download/server

Prerequisites

-------------

.. code:: bash

  sudo apt-get install git mysql-server apache2 php5 phpmyadmin php5-curl csh blast2 tomcat6 ant openjdk-6-jdk 

..

Get MyLabStocks Sources

------------------------

.. code:: bash

  git clone http://forge.cbp.ens-lyon.fr/git/mylabstocks

..

Install wwwBlast

----------------

MyLabStocks is distributed with wwwblast working on a x64 architecture.

For other architectures refer to the NCBI repositories

http://mirrors.vbi.vt.edu/mirrors/ftp.ncbi.nih.gov/blast/executables/release/LATEST

.. code:: bash

  cd mylabstocks/opts/

  tar xfvz wwwblast-2.2.26-x64-linux.tar.gz

  sudo cp -r blast /var/www/.

  sudo chown www-data:www-data /var/www/blast/TmpGifs /var/www/blast/*.log /var/www/blast/db/

  echo "<Directory /var/www/blast/>" > /tmp/blast.conf 

  echo "   Options +ExecCGI" >> /tmp/blast.conf 

  echo "</Directory>" >> /tmp/blast.conf 

  echo "AddHandler cgi-script .cgi" >> /tmp/blast.conf 

  sudo cp /tmp/blast.conf /etc/apache2/conf.d/blast.conf 

  rm /tmp/blast.conf

  sudo /etc/init.d/apache2 restart

  sudo sed -i 's/<option VALUE.*test_na_db/<option VALUE=oligostock_db>oligostock_db<option VALUE=plasmidstock_db>plasmidstock_db<option VALUE=plfeatstock_db>plfeatstock_db/g' /var/www/blast/blast.html

  sudo sed -i 's/<option VALUE.*test_aa_db//g' /var/www/blast/blast.html

  cat /var/www/blast/blast.rc > /tmp/blast.rc

  echo "blastn oligostock_db" >> /tmp/blast.rc

  echo "tblastn oligostock_db" >> /tmp/blast.rc

  echo "tblastx oligostock_db" >> /tmp/blast.rc

  echo "blastn plasmidstock_db" >> /tmp/blast.rc

  echo "tblastn plasmidstock_db" >> /tmp/blast.rc

  echo "tblastx plasmidstock_db" >> /tmp/blast.rc

  echo "blastn plfeatstock_db" >> /tmp/blast.rc

  echo "tblastn plfeatstock_db" >> /tmp/blast.rc

  echo "tblastx plfeatstock_db" >> /tmp/blast.rc

  sudo cp /tmp/blast.rc /var/www/blast/blast.rc

  rm /tmp/blast.rc

  cd ../..

..

Install PlasMapper

------------------

.. code:: bash

  cd mylabstocks/opts/

  tar xfvz PlasMapper_download.tar.gz

  cd PlasMapper

  # modify installdir as /var/lib/tomcat6

  sed -i 's/\/home\/tomcat/\/var\/lib\/tomcat6/g' build.xml 

  # modify servletjar as /usr/share/tomcat6/lib/servlet-api.jar

  sed -i 's/${installdir}\/common\/lib\/servlet-api.jar/\/usr\/share\/tomcat6\/lib\/servlet-api.jar/g' build.xml 

  # change /home/tomcat for /var/lib/tomcat6

  sed -i 's/\/home\/tomcat/\/var\/lib\/tomcat6/g' src/ca/ualberta/xdong/plasMapper/annotate/plasMapConfiguration_en_CA.properties

  # and set blastallDir=/usr/bin/

  sed -i 's/\/usr\/local\/bin\//\/usr\/bin\//g' src/ca/ualberta/xdong/plasMapper/annotate/plasMapConfiguration_en_CA.properties

  # Here PlasMapper is ready to be configured

  ant clean

  ant build 

  sudo ant install 

  sudo rm -Rf /var/lib/tomcat6/webapps/PlasMapper/tmp

  sudo ln -s /tmp/tomcat6-tomcat6-tmp/ /var/lib/tomcat6/webapps/PlasMapper/tmp

  echo '<?xml version="1.0" encoding="UTF-8"?><Context path="/myapp" allowLinking="true"></Context>' > context.xml

  sudo mv context.xml /var/lib/tomcat6/webapps/PlasMapper/META-INF/

  sudo /etc/init.d/tomcat6 restart

  # Here PlasMapper works on your server at the url http://myserver:8080/PlasMapper

  sudo chown root:www-data /var/lib/tomcat6/webapps/PlasMapper/dataBase/db_vectorFeature/*.*

  sudo chmod 664 /var/lib/tomcat6/webapps/PlasMapper/dataBase/db_vectorFeature/*.*

  sudo chown root:www-data /var/lib/tomcat6/webapps/PlasMapper/dataBase/db_vectorFeature/

  sudo chmod 775 /var/lib/tomcat6/webapps/PlasMapper/dataBase/db_vectorFeature/

  sudo chown root:www-data /var/lib/tomcat6/webapps/PlasMapper/html/feature.html

  sudo chmod 664 /var/lib/tomcat6/webapps/PlasMapper/html/feature.html

  # Here plasmids feature could be blasted by MyLabStock

  cd ../../..

..

Install MyLabStocks

-------------------

.. code:: bash

  sudo cp -r mylabstocks/src /var/www/labstocks

  sudo rm /var/www/labstocks/

  sudo touch /var/www/labstocks/formatdb.log

  sudo chmod 440 /var/www/labstocks/connect_entry.php 

  sudo mkdir /var/www/labstocks/plasmid_files 

  sudo mkdir /var/www/labstocks/raw_dirs

  sudo mkdir /var/www/labstocks/collections

  sudo chown -R www-data:www-data /var/www/labstocks/connect_entry.php /var/www/labstocks/formatdb.log  /var/www/labstocks/plasmid_files /var/www/labstocks/raw_dirs

..

Configurate MyLabStocks

-----------------------

Now you have to update connexion params in /var/www/labstocks/connect_entry.php

.. code:: bash

  sudo vi /var/www/labstocks/connect_entry.php 

..

finally run the following script to  define passwords and instantiate db.

.. code:: bash

  php mylabstocks/src/install_db.phpsh 

..

Congratulation your LabStocks instance is available on the url http://your_server/labstocks.

Links

-----

`MyLabStocks` home, repository and documentation: http://forge.cbp.ens-lyon.fr/redmine/projects/mylabstocks

Gael Yvert lab: http://www.ens-lyon.fr/LBMC/gisv/

Usage

=====

Advanced Search

---------------

In the strain section, the form `Search in genotype` filters strains where the 

fields `locus1`, `locus2`, `locus3`, `locus4`, `locus5`, `ADE2`, `HIS3`, `LEU2`, 

`LYS2`, `MET15`, `TRP1`, `URA3`, `HO_`, `Cytoplasmic_Character` or 

`extrachromosomal_plasmid` contain the given expression. This filter is case 

insensitive.

Plasmids Sequences Management

-----------------------------

Even in edit mode, users are not granted permission to directly edit a plasmid 

sequence, nor the URL to the plasmid sequence file. If a new sequence must be 

entered instead of the current one, users must upload a new sequence file, in 

.gb or .gb.gz format. MyLabStocks then automatically reads the file and update 

the sequence field and the URL. This ensures consistency between URL, sequence 

and the file itself.