From 2b5d86e93b12517f439e990df6f5b14aa7172355 Mon Sep 17 00:00:00 2001
From: Moritz Schaefer <mail@moritzs.de>
Date: Sun, 15 Nov 2020 01:19:15 +0100
Subject: [PATCH 1/3] add support for conda

---
 README.md  | 12 ++++++++++++
 conda.yaml | 18 ++++++++++++++++++
 2 files changed, 30 insertions(+)
 create mode 100644 conda.yaml

diff --git a/README.md b/README.md
index cc8dbba..112cb20 100644
--- a/README.md
+++ b/README.md
@@ -65,6 +65,18 @@ Details on the models are provided in the respective subfolders as well as in th
 Here, we provide a brief description on the core funtionality of TEPIC, the computation of TF-gene scores. 
 
 ## Installing TEPIC
+
+### Using conda
+
+If you use conda, create the required environment by running
+
+    conda env create tepic -f conda.yaml
+
+Then, in the Code/ directory, compile TRAPmulti.cpp
+
+    g++ TRAPmulti.cpp -O3 -fopenmp -o TRAPmulti
+
+### Manual installation
 To run *TEPIC* the following packages/software must be installed:
 * Python (minimum version 2.7)
 * [bedtools](https://github.com/arq5x/bedtools2): Installation instructions for bedtools can be found [here](http://bedtools.readthedocs.io/en/latest/content/installation.html). Please make sure to add
diff --git a/conda.yaml b/conda.yaml
new file mode 100644
index 0000000..496a09d
--- /dev/null
+++ b/conda.yaml
@@ -0,0 +1,18 @@
+name: TEPIC
+channels: 
+  - bioconda
+  - conda-forge
+  - r
+dependencies:
+  - compilers
+  - bedtools
+  - numpy
+  - scipy
+  - twobitreader
+  - r-gplots
+  - r-ggplot2
+  - r-glmnet
+  - r-domc
+  - r-reshape2
+  - r-gridextra
+

From 781df86495e2b608e7bc331ffb15fe8043c954e1 Mon Sep 17 00:00:00 2001
From: Moritz Schaefer <mail@moritzs.de>
Date: Sun, 15 Nov 2020 01:22:27 +0100
Subject: [PATCH 2/3] extend documentation

---
 README.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/README.md b/README.md
index 112cb20..1026f4b 100644
--- a/README.md
+++ b/README.md
@@ -71,10 +71,16 @@ Here, we provide a brief description on the core funtionality of TEPIC, the comp
 If you use conda, create the required environment by running
 
     conda env create tepic -f conda.yaml
+    
+Activate the environment using
+
+    conda activate tepic
 
 Then, in the Code/ directory, compile TRAPmulti.cpp
 
     g++ TRAPmulti.cpp -O3 -fopenmp -o TRAPmulti
+    
+You can now use TEPIC.sh
 
 ### Manual installation
 To run *TEPIC* the following packages/software must be installed:

From 8c828f4a67623968b8fd2a86dc1bea1bd9995f20 Mon Sep 17 00:00:00 2001
From: Moritz <mail@moritzs.de>
Date: Tue, 16 Feb 2021 22:30:31 +0100
Subject: [PATCH 3/3] Add missing data table depenency

---
 conda.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conda.yaml b/conda.yaml
index 496a09d..6baa1a3 100644
--- a/conda.yaml
+++ b/conda.yaml
@@ -15,4 +15,4 @@ dependencies:
   - r-domc
   - r-reshape2
   - r-gridextra
-
+  - r-data.table