update of documentation according to repo's new name

doc/dependencies.rst

@@ -2,7 +2,7 @@ Dependencies
 ================================================================
 
 These manuals aim at helping you install programs and
-dependencies used in the Gene-regulation library. 
+dependencies used in the SnakeChunks library. 
 
 Some of them are mandatory, and some are optional, depending 
 on the Snakemake workflows you need to run. 
@@ -225,7 +225,7 @@ It is the first system to support the use of automatically inferred multiple nam
 -  `Forum <https://groups.google.com/forum/#!forum/snakemake>`__
 -  See also Snakemake section for tutorials. 
 
-NB: Python 3 and pip3 are required (see `this section <http://gene-regulation.readthedocs.io/en/latest/dependencies.html#python>`__). 
+NB: Python 3 and pip3 are required (see `this section <http://SnakeChunks.readthedocs.io/en/latest/dependencies.html#python>`__). 
 
 ::
 
@@ -328,7 +328,7 @@ We recommend installing it manually:
     ln -s -f $HOME/app_sources/FastQC/fastqc $HOME/bin/fastqc
 
 NB: FastQC requires to have Java installed (even for commandline use). 
-See dedicated `section <http://gene-regulation.readthedocs.io/en/latest/dependencies.html#java>`__ to install it.
+See dedicated `section <http://SnakeChunks.readthedocs.io/en/latest/dependencies.html#java>`__ to install it.
 
 Check installation:
 
@@ -614,7 +614,7 @@ The following tools can be used to perform ChIP-seq peak-calling.
 Homer
 ****************************************************************
 
-Required in order to run the `tutorials <http://gene-regulation.readthedocs.io/en/latest/tutorials.html#>`__. 
+Required in order to run the `tutorials <http://SnakeChunks.readthedocs.io/en/latest/tutorials.html#>`__. 
 
 `Web page <http://homer.salk.edu/>`__
 
@@ -641,7 +641,7 @@ To install packages, simply use the -install option and the name(s) of
 the package(s).
 
 However, Homer can also work with custom genomes in FASTA format and gene
-annotations in GTF format. Thus the Gene-regulation workflows don't require to install any genome. 
+annotations in GTF format. Thus the SnakeChunks workflows don't require to install any genome. 
 
 Check installation: 
 
@@ -652,7 +652,7 @@ Check installation:
 MACS 1.4
 ****************************************************************
 
-Required in order to run the demo workflow "ChIP-seq" on dataset GSE20870 (in the  `tutorials <http://gene-regulation.readthedocs.io/en/latest/tutorials.html#>`__ section). 
+Required in order to run the demo workflow "ChIP-seq" on dataset GSE20870 (in the  `tutorials <http://SnakeChunks.readthedocs.io/en/latest/tutorials.html#>`__ section). 
 
 
 -  `Documentation <http://liulab.dfci.harvard.edu/MACS/00README.html>`__
@@ -676,7 +676,7 @@ Check installaiton:
 MACS 2
 ****************************************************************
 
-Required in order to run the `tutorials <http://gene-regulation.readthedocs.io/en/latest/tutorials.html#>`__. 
+Required in order to run the `tutorials <http://SnakeChunks.readthedocs.io/en/latest/tutorials.html#>`__. 
 
 -  `Webpage <https://github.com/taoliu/MACS/>`__
 
@@ -1012,12 +1012,12 @@ Other
 Makefile
 ----------------------------------------------------------------
 
-The Gene-regulation library comprises a makefile that can install most of the 
+The SnakeChunks library comprises a makefile that can install most of the 
 dependencies described in the previous section. It is recommended when you're setting up a virtual environments, 
-as described in `these tutorials <http://gene-regulation.readthedocs.io/en/latest/environments.html>`_. 
+as described in `these tutorials <http://SnakeChunks.readthedocs.io/en/latest/environments.html>`_. 
 
 If you want to run the workflows on your personal computer or on a server, you should follow the `manual installation 
-<http://gene-regulation.readthedocs.io/en/latest/dependencies.html#manual-installation>`_, or contact a sysadmin. 
+<http://SnakeChunks.readthedocs.io/en/latest/dependencies.html#manual-installation>`_, or contact a sysadmin. 
 
 The makefile currently allows running the following workflows:
 
@@ -1029,15 +1029,15 @@ It is not yet handling al the RNA-seq dependencies.
 
 ::
 
-    # it is assumed that you have defined a global variable with the path to the Gene-regulation library
-    cd ${GENE_REG_PATH}
+    # it is assumed that you have defined a global variable with the path to the SnakeChunks library
+    cd ${SNAKECHUNKS_PATH}
     make -f scripts/makefiles/install_tools_and_libs.mk all
     source ~/.bashrc
 
 ..
 Conda
 ----------------------------------------------------------------
-A number of dependencies of Gene-regulation can be installed through a Conda environment. 
+A number of dependencies of SnakeChunks can be installed through a Conda environment. 
 This list is not exhaustive. 
     conda install -c bioconda sickle=0.5 
     conda install -c bioconda bowtie=1.2.0 

doc/environments.rst

@@ -1,7 +1,7 @@
 Virtual environments
 ================================================================
 
-Tutorials on how to run Gene-regulation workflows in virtual environments 
+Tutorials on how to run SnakeChunks workflows in virtual environments 
 or virtual machines (VM).
 
 These protocols were developed on a Unix computer, with the OS
@@ -56,8 +56,8 @@ useful links:
 The first parts of this tutorial will explain you how to use the IFB cloud 
 for general purposes. 
 
-For a specific use of the Gene-regulation appliance, you should refer yourself to 
-`this section <http://gene-regulation.readthedocs.io/en/latest/environments.html#using-the-gene-regulation-appliance>`__.
+For a specific use of the SnakeChunks appliance, you should refer yourself to 
+`this section <http://SnakeChunks.readthedocs.io/en/latest/environments.html#using-the-SnakeChunks-appliance>`__.
 
 User account creation & configuration
 ****************************************************************
@@ -171,7 +171,7 @@ existing one. You just need to chose a "base" to build it on.
        ssh -A -p 22 root@192.54.201.XXX
 
 Once you're connected to your appliance, you can install all the programs 
-that you want. You can check out `this section <http://gene-regulation.readthedocs.io/en/latest/dependencies.html#>`__ for a manual on how to install NGS tools. 
+that you want. You can check out `this section <http://SnakeChunks.readthedocs.io/en/latest/dependencies.html#>`__ for a manual on how to install NGS tools. 
 Beware that the amount of disk space of the appliance itself 
 is limited!
 
@@ -214,7 +214,7 @@ Software installation
 
 Once you're connected to the VM through ``ssh``, you can install any
 program just the way you would do it locally (see tutorials in `this
-directory <http://gene-regulation.readthedocs.io/en/latest/dependencies.html#>`__
+directory <http://SnakeChunks.readthedocs.io/en/latest/dependencies.html#>`__
 for instance).
 
 Configuration
@@ -247,7 +247,7 @@ Fetch following paragraph and uncomment command ``force-color``.
     source ~/.bashrc
 
 
-Using the Gene-regulation appliance
+Using the SnakeChunks appliance
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Requirements
@@ -274,7 +274,7 @@ Appliances usually have a limited amount of disk space (up to 10 or 20Go).
 If the instance to be run necessitates disk space, you have to create a
 virtual disk (vDisk) prior to launching it.
 
-Check out `this section <http://gene-regulation.readthedocs.io/en/latest/environments.html#virtual-disk-creation>`__ 
+Check out `this section <http://SnakeChunks.readthedocs.io/en/latest/environments.html#virtual-disk-creation>`__ 
 for details.
 
 1. Click *New vDisk* button.
@@ -323,14 +323,14 @@ default under ``/root/mydisk``, or ``~/mydisk``.
 Here we create a folder to store the source data files and the files 
 that will results from the execution of our workflow. 
 
-We also create a link to the gene-regulation library. 
+We also create a link to the SnakeChunks library. 
 
 ::
 
     ANALYSIS_DIR=${HOME}/mydisk/ChIP-seq_SE_GSE20870
     mkdir -p ${ANALYSIS_DIR}
     cd ${ANALYSIS_DIR}
-    ln -s ${HOME}/gene-regulation-4.0 gene-regulation
+    ln -s ${HOME}/SnakeChunks-4.0 SnakeChunks
 
 Download data
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -372,18 +372,18 @@ You can use the option ``-n`` to make a dry run.
 ::
 
     cd  ${ANALYSIS_DIR}
-    snakemake -p -s gene-regulation/scripts/snakefiles/workflows/import_from_sra.wf --configfile gene-regulation/examples/ChIP-seq_SE_GSE20870/config.yml -n
+    snakemake -p -s SnakeChunks/scripts/snakefiles/workflows/import_from_sra.wf --configfile SnakeChunks/examples/ChIP-seq_SE_GSE20870/config.yml -n
 
 If there is no error, you can procede with the analysis:
 
 ::
 
     # This workflow extracts .fastq files from the .sra archives
-    snakemake -p -s gene-regulation/scripts/snakefiles/workflows/import_from_sra.wf --configfile gene-regulation/examples/ChIP-seq_SE_GSE20870/config.yml
+    snakemake -p -s SnakeChunks/scripts/snakefiles/workflows/import_from_sra.wf --configfile SnakeChunks/examples/ChIP-seq_SE_GSE20870/config.yml
     # This workflow performs quality check and trimming on the raw data
-    snakemake -p -s gene-regulation/scripts/snakefiles/workflows/quality_control.wf --configfile gene-regulation/examples/ChIP-seq_SE_GSE20870/config.yml
+    snakemake -p -s SnakeChunks/scripts/snakefiles/workflows/quality_control.wf --configfile SnakeChunks/examples/ChIP-seq_SE_GSE20870/config.yml
     # This workflow perform a classic ChIP-seq analysis, including mapping, peak-calling and motif search
-    snakemake -p -s gene-regulation/scripts/snakefiles/workflows/ChIP-seq.wf --configfile gene-regulation/examples/ChIP-seq_SE_GSE20870/config.yml
+    snakemake -p -s SnakeChunks/scripts/snakefiles/workflows/ChIP-seq.wf --configfile SnakeChunks/examples/ChIP-seq_SE_GSE20870/config.yml
 
 Using 4CPU & 8Go of RAM, the workflow should take about 12mn to complete.
 
@@ -500,13 +500,13 @@ You can visualize the peaks by running IGV from the terminal.
 .. figure:: ../img/igv.png
    :alt: 
 
-Create your own Gene-regulation appliance
+Create your own SnakeChunks appliance
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Creating a new appliance from scratch is very similar to using one. You
-have to satisfy the requirements described `here <http://gene-regulation.readthedocs.io/en/latest/environments.html#ifb-cloud-utilities>`__.
+have to satisfy the requirements described `here <http://SnakeChunks.readthedocs.io/en/latest/environments.html#ifb-cloud-utilities>`__.
 
-If you want to manipulate data, you should also create a vDisk following `these instructions <http://gene-regulation.readthedocs.io/en/latest/environments.html#virtual-disk-creation>`__.
+If you want to manipulate data, you should also create a vDisk following `these instructions <http://SnakeChunks.readthedocs.io/en/latest/environments.html#virtual-disk-creation>`__.
 
 Creation of an *appliance*
 ****************************************************************
@@ -533,37 +533,37 @@ The new instance should appear in orange bold fonts in the dashboard.
 
 You can connect to the instance through ``ssh`` as shown in previous sections.
 
-Get the ``gene-regulation`` repository
+Get the ``SnakeChunks`` repository
 ****************************************************************
 
 ::
 
-    wget -nc https://github.com/rioualen/gene-regulation/archive/4.0.tar.gz
+    wget -nc https://github.com/rioualen/SnakeChunks/archive/4.0.tar.gz
     tar zvxf 4.0.tar.gz
 
 Run makefile to install the dependencies
 ****************************************************************
 
-The Gene-regulation library contains a makefile that installs most of the dependencies required to execute the snakemake workflows. 
-You can also install tools manually, following `these instructions <http://gene-regulation.readthedocs.io/en/latest/dependencies.html#manual-installation>`__. 
+The SnakeChunks library contains a makefile that installs most of the dependencies required to execute the snakemake workflows. 
+You can also install tools manually, following `these instructions <http://SnakeChunks.readthedocs.io/en/latest/dependencies.html#manual-installation>`__. 
 
 The execution of the makefile may take a while (up to 30mn-1h), mostly because of the python libraries that are necessary to several NGS tools. 
 
 Then you should source the ``.bashrc`` in order to update the ``$PATH`` accordingly.
 
 ::
 
-    make -f gene-regulation-4.0/scripts/makefiles/install_tools_and_libs.mk all
+    make -f SnakeChunks-4.0/scripts/makefiles/install_tools_and_libs.mk all
     source ~/.bashrc
 
-If you want to install the x2go server on the VM for visualization purposes, as shown `here <http://gene-regulation.readthedocs.io/en/latest/environments.html#visualizing-results>`__, 
+If you want to install the x2go server on the VM for visualization purposes, as shown `here <http://SnakeChunks.readthedocs.io/en/latest/environments.html#visualizing-results>`__, 
 you can also execute this rule:
 
 ::
 
-    make -f gene-regulation-4.0/scripts/makefiles/install_tools_and_libs.mk add_repos desktop_and_x2go
+    make -f SnakeChunks-4.0/scripts/makefiles/install_tools_and_libs.mk add_repos desktop_and_x2go
 
-You should now be able to execute the example workflow by following instructions from `here <http://gene-regulation.readthedocs.io/en/latest/environments.html#download-source-data>`__. 
+You should now be able to execute the example workflow by following instructions from `here <http://SnakeChunks.readthedocs.io/en/latest/environments.html#download-source-data>`__. 
 
 In order for your appliance to remain persistant and be available to
 other users on the IFB cloud, you should contact an admin. 
@@ -635,9 +635,11 @@ Switch back to azerty:
 -->
 
 
-Gene-regulation with Docker
+SnakeChunks with Docker
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
+*This section is not up to date*
+
 Create shared repositories and download source data
 ****************************************************************
 

doc/gene-regulation_library.rst

@@ -1,4 +1,4 @@
-Gene-regulation library
+SnakeChunks library
 ================================================================
 
 The library contains a variety of files, including scripts and 

doc/getting_started.rst

@@ -4,28 +4,28 @@ Getting started
 The commands and tutorials below are designed for a Unix environment, 
 and were tested under the OS Linux Mint Debian Edition (LMDE). 
 
-They assume that the gene-regulation library is downloaded or cloned 
+They assume that the SnakeChunks library is downloaded or cloned 
 into your home directory. You can specify any other preferred directory.
 
-Download Gene-regulation
+Download SnakeChunks
 ----------------------------------------------------------------
 
 ::
 
     cd ${HOME}
-    wget --no-clobber https://github.com/rioualen/gene-regulation/archive/4.0.tar.gz 
+    wget --no-clobber https://github.com/SnakeChunks/SnakeChunks/archive/4.0.tar.gz
     tar xvzf 4.0.tar.gz
-    GENE_REG_PATH=${HOME}/gene-regulation-4.0
+    SNAKECHUNKS_PATH=${HOME}/SnakeChunks-4.0
 
-Clone Gene-regulation
+Clone SnakeChunks
 ----------------------------------------------------------------
 
 ::
 
     cd ${HOME}
-    git clone https://github.com/rioualen/gene-regulation.git
+    git clone https://github.com/SnakeChunks/SnakeChunks.git
 
-Run Gene-regulation
+Run SnakeChunks
 ----------------------------------------------------------------
 
-Please refer yourself to the `Tutorials section <http://gene-regulation.readthedocs.io/en/latest/tutorials.html#>`__. 
+Please refer yourself to the `Tutorials section <http://SnakeChunks.readthedocs.io/en/latest/tutorials.html#>`__. 

doc/index.rst

@@ -1,10 +1,10 @@
-.. GeneRegulation documentation master file, created by
+.. SnakeChunks documentation master file, created by
    sphinx-quickstart on Tue Mar 14 14:04:28 2017.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
    
    
-Gene Regulation
+SnakeChunks
 ================================================================
 
 This git repository holds shared code for the analysis of Next

doc/snakemake.rst

@@ -46,9 +46,9 @@ Tuto material
 
 ::
 
-    wget https://github.com/rioualen/gene-regulation/archive/1.0.tar.gz
+    wget https://github.com/rioualen/SnakeChunks/archive/1.0.tar.gz
     tar xvzf 1.0.tar.gz
-    cd gene-regulation-1.0/doc/snakemake_tutorial
+    cd SnakeChunks-1.0/doc/snakemake_tutorial
 
 Samtools
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -61,7 +61,7 @@ Samtools
     cd samtools-1.3
     make
     sudo make install
-    cd gene-regulation-1.0/doc/snakemake_tutorial
+    cd SnakeChunks-1.0/doc/snakemake_tutorial
 
 Rsamtools
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -243,7 +243,7 @@ Workflow 5: Configuration file
 
     # file: config.yml   
     samples: "GSM521934 GSM521935"    
-    outdir: "gene-regulation-1.0/doc/snakemake_tutorial/results/"
+    outdir: "SnakeChunks-1.0/doc/snakemake_tutorial/results/"
     samtools:     
         threads: "2"