Merge pull request #89 from cnobles/v1.1.1

v1.1.1

README.md

@@ -1,5 +1,4 @@
 ## iGUIDE - improved Genome-wide Unbiased Identification of Double-strand DNA break Events
-[![Build Status](https://travis-ci.org/cnobles/iGUIDE.svg?branch=master)](https://travis-ci.org/cnobles/iGUIDE)
 [![CircleCI](https://circleci.com/gh/cnobles/iGUIDE.svg?style=svg)](https://circleci.com/gh/cnobles/iGUIDE)
 [![Documentation Status](https://readthedocs.org/projects/iguide/badge/?version=latest)](http://iguide.readthedocs.io/en/latest/?badge=latest)
 [![DOI](https://zenodo.org/badge/88088016.svg)](https://zenodo.org/badge/latestdoi/88088016)
@@ -14,6 +13,14 @@ To get started, checkout the iGUIDE documentation at [iGUIDE.ReadTheDocs.io](htt
 
 ### Changelog:
 
+**v1.1.1 (December 16th, 2024)**
+
+* Added reference gene lists to `./genomes` directory, as well as updated versions.
+* Resolved bug associated with recovering multihit sites during analysis.
+* Added option for Anaconda testing in test script to support custom installs. Try: `bash etc/tests/test.sh iguide 1 anaconda` with an anaconda install.
+* Added functionality for more compatible gene lists between reference gene sets used for enrichment analysis.
+* Updated sections of the documentation.
+
 **v1.1.0 (March 8th, 2020)**
 
 * Modified how samples designated as Mock are treated during the analysis

configs/simulation.config.yml

@@ -138,10 +138,10 @@ refGenes :
     file : "genomes/hg38.refSeq.ext.nomodel.rds"
     symbolCol : "name2"
 oncoGeneList : 
-    file : "http://bushmanlab.org/assets/doc/allOnco_Feb2017.tsv"
+    file : "genomes/allOnco_Feb2017.tsv"
     symbolCol : "symbol"
 specialGeneList : 
-    file : "http://bushmanlab.org/assets/doc/humanLymph.tsv"
+    file : "genomes/humanLymph.tsv"
     symbolCol : "symbol"
 maxTargetMismatch : 6
 upstreamDist : 100

docs/changelog.rst

@@ -3,6 +3,14 @@
 ChangeLog
 =========
 
+**v1.1.1 (December 16th, 2024)**
+
+- Added reference gene lists to `./genomes` directory, as well as updated versions.
+- Resolved bug associated with recovering multihit sites during analysis.
+- Added option for Anaconda testing in test script to support custom installs. Try: `bash etc/tests/test.sh iguide 1 anaconda` with an anaconda install.
+- Added functionality for more compatible gene lists between reference gene sets used for enrichment analysis.
+- Updated sections of the documentation.
+
 **v1.1.0 (March 8th, 2020)**
 
 - Modified how samples designated as Mock are treated during the analysis

docs/conf.py

@@ -20,13 +20,13 @@
 # -- Project information -----------------------------------------------------
 
 project = 'iGUIDE'
-copyright = '2019, Christopher Nobles, Ph.D.'
+copyright = '2024, Christopher Nobles, Ph.D.'
 author = 'Christopher Nobles, Ph.D.'
 
 # The short X.Y version
 version = ''
 # The full version, including alpha/beta/rc tags
-release = 'v1.0.0'
+release = 'v1.1.1'
 
 
 # -- General configuration ---------------------------------------------------

docs/usage.rst

@@ -436,6 +436,97 @@ used::
   rm -r path/to/miniconda3
 
 
+Manual Install
+--------------
+
+**Installing miniconda**
+Skip to installing iGUIDE if you already have miniconda or anaconda installed. 
+These can be executed in your home directory.
+
+Get the latest version of miniconda install script.::
+
+  __conda_url=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+  wget -q ${__conda_url} -O miniconda.sh
+
+Installing miniconda through downloaded script. You can choose a different path 
+for the install, here it is installed into the home directory.::
+
+  __conda_path="~/miniconda3"
+  bash miniconda.sh -b -p ${__conda_path}
+
+Source conda to activate the installation for use.::
+  
+  source ${__conda_path}/etc/profile.d/conda.sh
+
+**Installing iGUIDE**
+The following commands should be called from within the iGUIDE directory 
+(`/path/to/iGUIDE/`) after the repository is cloned.
+
+Install the conda environment from the requirements file. The name field here 
+can be changed to what you would like to call the environment, default for the 
+install script is 'iguide'.::
+
+  conda create --name=iguide --quiet --yes --file etc/build.b1.0.1.txt
+
+After successful creation of the environment, activate the iguide environment (or what 
+you've named it).::
+
+  conda activate iguide
+
+Install the supporting R-package into the environment.::
+
+  R CMD INSTALL tools/iguideSupport 
+
+Setup your environmental variables.::
+
+  __iguide_dir=$(pwd)
+
+  echo -ne "#/bin/sh\nexport IGUIDE_DIR=${__iguide_dir}" > \
+      ${CONDA_PREFIX}/etc/conda/activate.d/env_vars.sh
+
+  mkdir -p ${CONDA_PREFIX}/etc/conda/deactivate.d/
+
+  echo -ne "#/bin/sh\nunset IGUIDE_DIR" > \
+      ${CONDA_PREFIX}/etc/conda/deactivate.d/env_vars.sh
+
+You should now deactivate and reactivate the environment to initiate the environmental 
+variables.::
+
+  conda deactivate
+  conda activate iguide
+
+Lastely, install the command line interface for iGUIDE using pip.::
+  
+  pip install --upgrade tools/iguidelib/
+
+**Testing**
+Test to make sure the components were installed correctly.
+
+Test for required R-packages installed.::
+
+  $(Rscript tools/rscripts/check_for_required_packages.R &> /dev/null) && echo true || echo false
+
+Check to make sure iguideSupport was installed correctly.::
+
+  $(Rscript tools/rscripts/check_pkgs.R iguideSupport &> /dev/null) && echo true || echo false
+
+Run unit tests for iguideSupport.::
+
+  `$(Rscript tools/rscripts/check_iguideSupport.R &> /dev/null) && echo true || echo false'
+
+Check to make sure the pip install of the CLI was successful.::
+
+  command -v iguide &> /dev/null && echo true || echo false
+
+Run tests for iGUIDE, this step will take a little bit to complete if it starts processing 
+the test case. Go grab a coffee, you deserve it getting to this point. :) The test will 
+activate the environment as part of the test, so you should deactivate your environment 
+first and then initiate the test.::
+
+  conda deactivate
+  bash etc/tests/test.sh iguide
+
+
 Config Files
 ************
 
@@ -733,10 +824,10 @@ Demultiplexing parameters
 
 ``skipDemultiplexing``
   Logical (either TRUE or FALSE) to indicate if demultiplexing should be carried
-  out. If TRUE, sequence files (\*.fastq.gz) need to be placed or linked in the 
+  out. If FALSE, sequence files (\*.fastq.gz) need to be placed or linked in the 
   input_data directory of an existing project directory (as with 
   ``iguide setup``), one sequence file for each type (R1, R2, I1, I2). These 
-  need to be identified in the "Run" portion of the config file. If FALSE, then 
+  need to be identified in the "Run" portion of the config file. If TRUE, then 
   demultiplexed files need to be included in the input_data directory of an 
   existing project directory. The files need to be appropriately named, in the 
   format of ``{sampleName}.{readtype}.fastq.gz``, where ``sampleName`` matches 

etc/tests/test.sh

@@ -4,12 +4,21 @@ set -e
 # Input arguments
 __IGUIDE_ENV=${1-iguide}
 __CORES=${2-1}
+__INSTALL=${3-miniconda3}  # Options include: miniconda3 (default) or anaconda
 
 # Clear test directory
 rm -rf analysis/simulation
 
 # Activate conda environment
-source ${HOME}/miniconda3/etc/profile.d/conda.sh
+if [[ ${__INSTALL} = "miniconda3" ]]; then
+    source ${HOME}/miniconda3/etc/profile.d/conda.sh
+elif [[ ${__INSTALL} = "anaconda" ]]; then
+    source ${HOME}/anaconda/etc/profile.d/conda.sh
+else
+    echo "Please use either 'miniconda3' or 'anaconda' for managing conda environments."
+    exit 1
+fi
+
 conda activate ${__IGUIDE_ENV}
 
 # Create test analysis directory