Edits on output.rst with new Output filenames

CHANGES

@@ -1,5 +1,7 @@
 ## 1.0.1 (2017-01-27)
 
+- Edit pysam.TabixFile (Error :attribute doesn't exist)  -> pysam.Tabixfile 
+- add flag "-p gff" in run_tabix call (overlaps.py)
 - updated summary script for new gridExtra requirements (rows=NULL instead of show.rownames=FALSE)
 - fixed log file bug 
 - fixed internals feature to work for distances larger than default distance

README.md

@@ -35,51 +35,64 @@ Installation and Command-line usage
 Make sure all prerequisites are met:
 
 - [R/Rscript](http://www.r-project.org/) (v3.3.0 or higher, follow instructions on url)
-- [Python](http://continuum.io/downloads) (v2.7.8-anaconda-2.1.0, install with ```bash Anaconda2-4.2.0-Linux-x86_64.sh``` and ```PATH=dir/to/python_anaconda:$PATH```)
-- [htslib](http://www.htslib.org/download/) (1.3.2 or higher, follow instructions on url)
 
+- [Python](https://repo.continuum.io/archive/) (v2.7.8-anaconda-2.1.0)
+	* Choose Anaconda2-4.2.0-Linux-x86 (for 32bit) or -x86_64 (for 64bit),
+	* Install with ```bash Anaconda2-4.2.0-Linux-x86_64.sh```, 
+	* Follow instructions and type 'yes' to prepend Anaconda to PATH in your .bashrc file,
+	* or type after installation: ``` $export PATH=/home/<user>/anaconda2/bin:$PATH ```
+
+- [htslib](http://www.htslib.org/download/) (1.3.2 or higher) 
+	Follow instructions : 
+	* ```cd htslib-1.3.2/```
+	* ```./configure```
+	* ```make```
+	* ```sudo make install ``` (will be installed to /usr/local/bin/) 
+	* or ```sudo make prefix=/home/<user>/htslib install```
+	Further information given in [url](https://github.com/samtools/htslib/blob/develop/INSTALL)
 
 Install required packages for R:
 ```bash
 install.packages(c("ggplot2", "devtools", "gplots", "gridExtra", "jsonlite", "VennDiagram"))
 source("https://bioconductor.org/biocLite.R")
 biocLite(c("RBGL","graph"))
-# to install the last required package, devtools has to be loaded to use the install from github function
+
+# To install the last required package-Vennerable, devtools has to be loaded to use the install from github function
 # if you copy this and want to use it in once, 
 # make sure the library loading is not interrupted by the question if present packages should be updated
+
 library(devtools)
 install_github("jenzopr/Vennerable")
 ```
 
-
-### Install UROPA locally 
+Install UROPA locally by running:
 
 ```bash
 git clone https://github.molgen.mpg.de/loosolab/UROPA.git
-export PATH=$PATH:dir/to/uropa
+export PATH=$PATH:dir/to/uropa/uropa.py 
 ```
 
-```bash                        
-Usage: uropa [options]          
+```python                         
+Usage: uropa.py [options]          
 
 Available options:
 
-		-h, --help             print this help message and further details on the configuration file
-        -i, --input            filename of configuration file
-        -o, --output           directory for results and prefix of the output file name
-        -r, --reformat         create an additional compact and line-reduced table as result file
-        -s, --summary          filename of additional visualisation of results in graphical format
-        -t n, --threads n      multiprocessed run: n = number of threads to run annotation process
-        -no-comment            do not show comment lines in output files
-        -l, --log              log file name for messages and warnings
-        -d, --debug            print verbose messages (for debugging purposes)
-        -v, --version          print the version and exit
+	- h, --help             print this help message and further details on the configuration file
+        - i, --input            filename of configuration file
+        - o, --output           directory for results and prefix of the output file name
+        - r, --reformat         create an additional compact and line-reduced table as result file
+        - s, --summary          filename of additional visualisation of results in graphical format
+        - t n, --threads n      multiprocessed run: n = number of threads to run annotation process
+        --no-comment            do not show comment lines in output files
+        - l, --log              log file name for messages and warnings
+        - d, --debug            print verbose messages (for debugging purposes)
+        - v, --version          print the version and exit
 ```
 
 How to cite
 -----------
 
-Kondili M, Fust A, Preussner J, Kuenne C, Braun T, and Looso M, UROPA: a tool for Universal RObust Peak Annotation. *(in preparation)*
+Kondili M, Fust A, Preussner J, Kuenne C and Looso M. UROPA: a tool for Universal RObust Peak Annotation. *(in preparation)*
 
 Contribute
 ----------

docs_rst/help.rst

@@ -16,5 +16,6 @@ They will be addressed as soon as possible.
 * **How to annotate with default values?**
 	In order to activate default values, the key itself shouldn't be present in the config file. 
 	If you want to annotate with default values only, do not remove the queries key, but leave it empty like "queries":[] 
-
+* **Why is the summary empty?**
+	It is a problem about gridExtra and ggplot2, the summary starts from page 2
 

docs_rst/index.rst

@@ -17,7 +17,7 @@ annotation.
 -  Utilization of any available GTF files as annotation reference
 -  Multiple queries can be processed in a single run
 -  Graduated annotation due to prioritization
--  Multiple output tables (AllHits, FinalHits, BestperQuery\_Hits)
+-  Multiple output tables (allhits, finalhits, besthits)
 -  Visual summary for annotation evaluation
 -  Preparation of custom annotation files with the UROPA to GTF utility
 
@@ -55,4 +55,4 @@ The project is licensed under the MIT license (see :doc:`/license`)
    custom
    license
    help
-
+

docs_rst/install.rst

@@ -5,61 +5,55 @@ Prerequisites
 -----------------
 For running UROPA locally, the following prerequisites have to be met:
 
-- `Python`_, v2.7 (packages: numpy, sampy)
-- `R/Rscript`_, v3.3.0 or higher (packages: devtools, ggplot2, gplots, gridExtra, jsonlite, RBGL, graph, VennDiagram, Vennerable, snow)
-- `htslib`_ 1.3.2 or higher
-
-Instructions
------------------
-
-Python
-~~~~~~~~~~
-As numpy and sampy packages can be taxing to install in Python, we recommend the usage of the `Anaconda`_ distribution instead (v2.7.8-anaconda-2.1.0 or higher). Install with eg. ``bash Anaconda2-4.2.0-Linux-x86_64.sh`` and include the path in the environment variable ``export PATH=dir/to/python_anaconda:$PATH``.
-
-Using standard Python 2.7, the packages can be installed with ``pip install pysam numpy``.
-
-R
-~~~~~
-The following packages are hosted by CRAN and can be installed from the R console with the syntax ``install.packages("packagename")``.
-
-- `devtools`_
-- `ggplot2`_
-- `gplots`_
-- `gridExtra`_ 
-- `jsonlite`_ 
-- `VennDiagram`_ 
-- `snow`_ 
-
-The RBGL and graph packages are hosted by BioConductor. To install those start R and type ``source("https://bioconductor.org/biocLite.R")`` and ``biocLite(c("RBGL","graph"))``.
-
-Vennerable has to be installed with ``library("devtools")`` followed by ``install_github("jenzopr/Vennerable")``.
-
-HTSlib
-~~~~~
-The HTSlib library is necessary for the indexing of the reference features using Tabix. For installation instructions please refer to the following url: `htslib`_.
-
+- `Python`_, v2.7 
+	- download Anaconda for Linux version Python 2.7 to direction where python should be installed
+
+	- run ``bash Anaconda2-4.3.0-Linux-x86_64.sh``
+
+	- Answer the question "Do you wish the installer to prepend the Anaconda2 install location to PATH in your /home/.../.bashrc ?" with yes OR do ``PATH=dir/to/python_anaconda:$PATH`` after the installation process has finished
+
+	- run ``conda install -c bioconda pysam``
+
+	- if you are NOT using the anaconda version of python 2, the packages `pysam`_ and `numpy`_ can be installed with ``pip install pysam numpy``
+
+- `R/Rscript`_, v3.3.0 or higher (follow the instructions on url)
+
+Load R and install packages:
+
+	- ``install.packages(c("ggplot2", "devtools", "gplots", "gridExtra", "jsonlite", "VennDiagram"))``
+
+	Choose CRAN mirror.
+	- ``source("https://bioconductor.org/biocLite.R")``
+
+	- ``biocLite(c("RBGL","graph"))``
+
+	- ``library(devtools)``
+
+	- ``install_github("jenzopr/Vennerable")``
+
+- `git`_ with ``bash sudo apt-get install git``
 
 UROPA
-~~~~~
-
+-----
 UROPA itself can be installed by simply cloning the Github library and adding the target folder to the system environment variable.
 
 .. code:: bash
 
 	git clone https://github.molgen.mpg.de/loosolab/UROPA
-	export PATH=$PATH:dir/to/uropa
-		
+ 	## Open .bashrc file and create alias name to call <b>uropa<b> in each session easily : 
+	alias uropa='/dir/to/UROPA/uropa.py'
 
 
 .. _R/Rscript: http://www.r-project.org/
 .. _Python: http://continuum.io/downloads
 .. _Anaconda: http://continuum.io/downloads
-.. _htslib: http://www.htslib.org/download/
+.. _git: https://git-scm.com/
 .. _numpy: http://www.numpy.org
 .. _pysam: https://pysam.readthedocs.io/en/latest/index.html
 .. _ggplot2: https://cran.r-project.org/web/packages/ggplot2/index.html
 .. _gplots: https://cran.r-project.org/web/packages/gplots/index.html
 .. _gridExtra: https://cran.r-project.org/web/packages/gridExtra/index.html
+.. _gridExtra: https://cran.r-project.org/web/packages/gridExtra/index.html
 .. _jsonlite: https://cran.r-project.org/web/packages/jsonlite/index.html
 .. _VennDiagram: https://cran.r-project.org/web/packages/VennDiagram/index.html
 .. _snow: https://cran.r-project.org/web/packages/snow/index.html