From 67c46b8c52dc056a48d87c3dc4bf641b3c5b427f Mon Sep 17 00:00:00 2001 From: Jens Preussner Date: Tue, 5 Sep 2017 16:00:34 +0200 Subject: [PATCH] Bumped version to 1.2.0 --- CHANGES | 6 ++++++ README.md | 16 ++++++++-------- uropa.py | 4 ++-- 3 files changed, 16 insertions(+), 10 deletions(-) diff --git a/CHANGES b/CHANGES index 9c7004c..87f5a78 100644 --- a/CHANGES +++ b/CHANGES @@ -1,3 +1,9 @@ +## 1.2.0 (2017-09-05) + +- Added an UpSetR plot to summary.R to cancel the need for Vennerable R package +- Added proper help to uropa2gtf.R script +- Reflected changes in documentations + ## 1.1.2 (2017-09-04) - Added proper help for auxillary R scripts (exit code 0) diff --git a/README.md b/README.md index c421a29..86551af 100644 --- a/README.md +++ b/README.md @@ -34,23 +34,23 @@ Installation and Command-line usage ------------------------------------ Make sure all prerequisites are met: -- [Python](http://continuum.io/downloads) +- [Python](http://continuum.io/downloads) - 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 + - 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 installation process - run ```conda install -c bioconda pysam``` - [R/Rscript](http://www.r-project.org/) (v3.3.0 or higher; follow instructions on url) - - install required packages step by step: + - install required packages step by step: ```bash - install.packages(c("ggplot2", "devtools", "gplots", "gridExtra", "jsonlite", "VennDiagram", "getopt")) + install.packages(c("ggplot2", "devtools", "gplots", "gridExtra", "jsonlite", "VennDiagram", "getopt", "tidyr", "UpSetR")) 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 + biocLite(c("RBGL", "graph")) + # In order to plot a Chow-Ruskey plot in summary.R, install Vennerable from our modified fork library(devtools) install_github("jenzopr/Vennerable") ``` -- [Git](https://git-scm.com/): run ```bash sudo apt-get install git``` +- [Git](https://git-scm.com/): run ```bash sudo apt-get install git``` ### Install UROPA locally diff --git a/uropa.py b/uropa.py index 8e7c604..679703b 100755 --- a/uropa.py +++ b/uropa.py @@ -4,7 +4,7 @@ @authors: Maria Kondili, Jens Preussner and Annika Fust @license: MIT -@version: 1.1.2 +@version: 1.2.0 @maintainer: Mario Looso @email: mario.looso@mpi-bn.mpg.de """ @@ -95,7 +95,7 @@ "--version", help="prints the version and exits", action="version", - version="%(prog)s 1.1.2") + version="%(prog)s 1.2.0") args = parser.parse_args() config = args.input