Merge remote-tracking branch 'upstream/master'

.gitignore

@@ -9,6 +9,7 @@ Output/
 .ipynb_checkpoints*
 __pycache__*
 *.egg-info*
+.eggs*
 dist/*
 
 # typical latex tmp files

.travis.yml

@@ -17,18 +17,17 @@ install:
   - conda config --set always_yes yes --set changeps1 no
   - conda update -q conda
 
-  - conda config --add channels bioconda
-  - conda config --add channels conda-forge
-
-  # build package with cond
-  - conda install conda-build
-  - conda build conda.recipe --output-folder=$HOME/build
-  - conda config --add channels "file://${HOME}/build"
-
-  # test package
+  # install dependencies
   - source $HOME/miniconda/etc/profile.d/conda.sh
-  - conda create -q -n drop drop
+  - conda create -q -n drop -c conda-forge -c bioconda python=$TRAVIS_PYTHON_VERSION r-base=4.0.2
   - conda activate drop
+  - conda install -c conda-forge -c bioconda drop
+  - conda remove --force drop wbuild
+  - conda install -c conda-forge -c bioconda wbuild=1.7.1
+  - pip install -r requirements_test.txt
+
+  # install drop
+  - pip install . -vv
 
 script: 
   - conda list 
@@ -37,10 +36,7 @@ script:
   - samtools --version
   - bcftools --version
   - drop --version
+  - wbuild --version
   - python --version
-
-  - mkdir drop_demo
-  - cd drop_demo
-  - drop demo
-  - snakemake -n
-  - snakemake --jobs 2 --cores 2
+
+  - pytest -vv -s

README.md

@@ -1,47 +1,36 @@
 # Detection of RNA Outlier Pipeline
 [![Pipeline status](https://travis-ci.org/gagneurlab/drop.svg?branch=master)](https://travis-ci.org/gagneurlab/drop)
-[![Version](https://img.shields.io/badge/Version-0.9.1-green.svg)](https://github.com/gagneurlab/drop/master)
+[![Version](https://img.shields.io/github/v/release/gagneurlab/drop?include_prereleases)](https://github.com/gagneurlab/drop/releases)
 [![Version](https://readthedocs.org/projects/gagneurlab-drop/badge/?version=latest)](https://gagneurlab-drop.readthedocs.io/en/latest)
 
 The manuscript main file, supplementary figures and table can be found in the manuscript folder or in 
 [protocol exchange](https://protocolexchange.researchsquare.com/article/993ff4a5-38ce-4261-902a-600dbd528ba2/v1).
 
 <img src="drop_sticker.png" alt="drop logo" width="200" class="center"/>
 
-## Installation
-DROP is available on [bioconda](https://anaconda.org/bioconda/drop) for python 3.6 and above.
-We recommend using a dedicated conda environment.
-
+## Quickstart
+DROP is available on [bioconda](https://anaconda.org/bioconda/drop).
+We recommend using a dedicated conda environment. (installation time: ~ 10min)
 ```
-# create environment
-conda create -n drop_env python=3.6
-conda activate drop_env
-
-# install drop
-conda install -c bioconda drop
+conda install -c conda-forge -c bioconda drop
 ```
-Installation time: ~ 10min
-
-Test whether the pipeline runs through by setting up the demo dataset in an empty directory (e.g. ``~/drop_demo``).
 
+Test installation with demo project
 ```
 mkdir ~/drop_demo
 cd ~/drop_demo
-
-# demo will download the necessary data and pipeline files
 drop demo
 ```
 
-The pipeline can be run using `snakemake` commands
-
+The pipeline can be run using [snakemake](https://snakemake.readthedocs.io/) commands
 ```
 snakemake -n # dryrun
-snakemake
+snakemake --cores 1
 ```
 
 Expected runtime: 25 min
 
-For more information on different installation options, check out the 
+For more information on different installation options, refer to the
 [documentation](https://gagneurlab-drop.readthedocs.io/en/latest/installation.html)
 
 ## Set up a custom project
@@ -62,8 +51,13 @@ snakemake aberrantExpression -n
 ```
 
 ## Datasets
-The following publicly-available datasets of gene counts can be used as controls:
+The following publicly-available datasets of gene counts can be used as controls.
+Please cite as instructed for each dataset.
 
 * 119 non-strand specific fibroblasts: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3887451.svg)](https://doi.org/10.5281/zenodo.3887451)
 
+* 139 strand specific fibroblasts: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3963474.svg)](https://doi.org/10.5281/zenodo.3963474)
+
+* 125 strand specific blood: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3963470.svg)](https://doi.org/10.5281/zenodo.3963470)
+
 If you want to contribute with your own count matrices, please contact us: yepez at in.tum.de

docs/source/conf.py

@@ -23,7 +23,7 @@
 author = 'Michaela Müller'
 
 # The full version, including alpha/beta/rc tags
-release = '0.9.1'
+release = '1.0.0'
 
 
 # -- General configuration ---------------------------------------------------

docs/source/index.rst

@@ -3,8 +3,8 @@ DROP - Detection of RNA Outliers Pipeline
 
 DROP is intended to help researchers use RNA-Seq data in order to detect genes with aberrant expression,
 aberrant splicing and mono-allelic expression. It consists of three independent modules for each of those strategies.
-After installing DROP, the user needs to fill in the config file and sample annotation table (:ref:`prepare`).
-Then, DROP can be executed in multiple ways (:ref:`pipeline`).
+After installing DROP, the user needs to fill in the config file and sample annotation table (:doc:`prepare`).
+Then, DROP can be executed in multiple ways (:doc:`pipeline`).
 
 .. toctree::
    :maxdepth: 2
@@ -19,23 +19,28 @@ Then, DROP can be executed in multiple ways (:ref:`pipeline`).
 Quickstart
 -----------
 
-DROP is available on `bioconda <https://anaconda.org/bioconda/drop>`_ for python 3.6 and above.
-We recommend using a dedicated conda environment.
+DROP is available on `bioconda <https://anaconda.org/bioconda/drop>`_.
+We recommend using a dedicated conda environment. (installation time: ~ 10min)
 
 .. code-block:: bash
 
-    conda install -c bioconda drop
+    conda install -c conda-forge -c bioconda drop
 
-Initialize project
+Test installation with demo project
 
 .. code-block:: bash
 
-    cd <path-to-project>
+    mkdir ~/drop_demo
+    cd ~/drop_demo
     drop demo
 
-Call the pipeline
+The pipeline can be run using `snakemake <https://snakemake.readthedocs.io/>`_ commands
 
 .. code-block:: bash
 
-    snakemake
+    snakemake -n # dryrun
+    snakemake --cores 1
 
+Expected runtime: 25 min
+
+For more information on different installation options, refer to :doc:`installation`.