Update Dockerfile

Dockerfile

@@ -1,6 +1,7 @@
-# This build container image ends up about 3GB
 FROM ubuntu:22.04 AS build-container
 
+RUN rm /bin/sh && ln -s /bin/bash /bin/sh
+
 # libboost-python on Ubuntu 22.04 is python 3.10
 # liboost-python-dev includes python3.10-dev with it
 # We don't need intel-mkl or any other specific BLAS lib because carvaIBD only uses Armadillo headers
@@ -10,13 +11,18 @@ RUN apt-get update &&  \
     DEBIAN_FRONTEND=noninteractive apt-get install -y \
     build-essential \
     cmake \
+    git \
     libarmadillo-dev \
     libboost-iostreams-dev \
     libboost-numpy-dev \
     libboost-python-dev
 
 WORKDIR /app
 COPY . .
+# Add this step to fetch the submodule content
+
+RUN git submodule update --init --recursive
+# Make sure their is no previous build directory
 RUN rm -rf build
 
 RUN mkdir build
@@ -27,7 +33,7 @@ RUN make -j4
 
 # Make a leaner run container without build dependencies
 # How much leaner is it? It's about 170MB
-FROM ubuntu:22.04 as run-container
+FROM ubuntu:22.04 AS run-container
 
 # We seem to not need libboost-numpy at runtime?!
 RUN apt-get update &&  \
@@ -36,10 +42,11 @@ RUN apt-get update &&  \
     libboost-iostreams1.74.0 \
     libboost-numpy1.74.0 \
     libboost-python1.74.0 \
+    liblapack3 \
     libpython3.10
 
 WORKDIR /app
-COPY --from=build-container /app/build/carvaIBD carvaIBD
+COPY --from=build-container /app/build/ibdmap ibdmap
 COPY --from=build-container /app/build/*.so .
 
-ENTRYPOINT ["./carvaIBD"]
+ENV PATH="/app:$PATH"

README.md

@@ -1,7 +1,5 @@
 # IBDMap
 
----
-
 IBDMap is a multithreaded scalable application for IBD (Identity By Descent) mapping of binary traits. IBDMap implements a test statistic developed by Browning & Thompson et al., 2012 [cite] that detects regions where IBD sharing is statistically enriched among case-case pairs than among case-control pairs.
 
 IBDMap addresses key challenges in IBD mapping by using a map-reduce approach to analyze genome-wide relative IBD segment enrichment, making it tractable for biobank-scale analysis. IBDMap’s computational flexibility enables execution in a wide array of compute environments.
@@ -16,8 +14,6 @@ The seed should be specified and different for each job on a chromosome. However
 
 ## Key features of IBDMap
 
----
-
 - Implements flexible multiple testing correction options (FWER and FDR approaches)
 - Includes supplementary statistical assessments, such as:
     - Likelihood ratio test for signal localization
@@ -183,7 +179,15 @@ If you are in a compute environment that prevents you from running containers as
 singularity pull ibdmap.sif docker:jtb114/ibdmap:latest
 ```
 
-This command will create a new singularity image called `ibdmap.sif`
+This command will create a new singularity image called `ibdmap.sif`. The tool can then be run using the following command to view the help menu:
+
+```bash
+# Docker image
+docker run --rm {image ID/tag} ibdmap -h
+
+# Singularity image
+singularity exec ibdmap.sif ibdmap -h
+```
 
 ## Data Formatting