--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smalt/instructions.sh	Tue Mar 08 11:43:08 2022 +0000
@@ -0,0 +1,34 @@
+# Run docker image 'debian/wheezy' in interactive mode
+sudo docker run -i -t debian:wheezy
+
+# Run the below in this image
+
+apt-get update
+apt-get install python
+apt-get install wget
+apt-get install mercurial
+
+mkdir tool
+cd tool
+
+wget ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-0.7.3.tgz
+tar -xvvzf smalt-0.7.3.tgz
+
+# because the smalt_wrapper.py finds the binary name based on `uname -i` which is unknown in docker
+mv smalt-0.7.3/smalt_x86_64 smalt_unknown
+
+hg clone https://toolshed.g2.bx.psu.edu/repos/cjav/smalt smalt_deps
+cp smalt_deps/smalt_wrapper.py .
+
+# add smalt tools to PATH (probably different ways to do this)
+ln -s /tool/smalt_unknown /usr/bin 
+ln -s /tool/smalt_wrapper.py /usr/bin
+
+# make smalt_wrapper executable
+chmod a+x /tool/smalt_wrapper.py
+
+# exit out of docker image and run the below to commit to new container.  replace the number '07b...' with container id for the above docker container.
+sudo docker commit -m "make smalt_wrapper executable" -a "Aaron Petkau" 07b937918961 apetkau/smalt:v3
+
+# push to dockerhub
+# please see instructions at http://docs.docker.com/userguide/dockerimages/#push-an-image-to-docker-hub