enh: docker support + basic usage doc

Dockerfile

@@ -0,0 +1,43 @@
+FROM neurodebian:stretch
+
+ARG DEBIAN_FRONTEND="noninteractive"
+
+RUN apt-get update -qq && apt-get install -y --no-install-recommends less \
+                                                                     ca-certificates \
+                                                                     wget \
+                                                                     unzip \
+                                                                     octave \
+                                                                     octave-general \
+                                                                     octave-signal \
+                                                                     octave-image \
+                                                                     liboctave-dev \
+                       && apt-get clean \
+                       && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# download HCP workbench (1.3.0) for CIFTI support
+WORKDIR /opt
+RUN wget -q https://ftp.humanconnectome.org/workbench/workbench-linux64-v1.3.0.zip -O wb.zip \
+    && unzip wb.zip \
+    && rm wb.zip
+
+# copy repo into /opt/palm
+WORKDIR palm
+COPY . .
+
+# recompile mex files to be compatible with our system
+WORKDIR fileio
+RUN cd \@gifti/private \
+    && mkoctfile --mex zstream.c \ 
+    && mkoctfile --mex miniz.c \
+    && cd ../../\@xmltree/private \
+    && mkoctfile --mex xml_findstr.c \
+    && cd ../../\@file_array/private \
+    && mkoctfile --mex file2mat.c \
+    && mkoctfile --mex mat2file.c
+
+# add palm and workbench to our PATH
+ENV PATH=/opt/palm:/opt/workbench/bin_linux64:$PATH
+
+# enter with call to palm executable
+WORKDIR /working
+ENTRYPOINT ["palm"]

README.md

@@ -1,3 +1,23 @@
 To learn about PALM, please visit **http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM**
 
 On the link above there is no history about the package itself, so here it goes some. In one way or another, work on a permutation tool has been ongoing for a while, with some of the functions having been loosely written back in 2008, if not earlier. These functions began to be assembled and integrated by mid-2013. Between Oct/2013 and Mar/2014, Git was used locally for version control, but eventually PALM went on without it. Various early alpha versions circulated to collaborators, with the first public release in late Feb/2015 in the FSL website. These releases were, and continue to be, in the form of tarballs. Since all were kept, it was easy to retroactively apply the commits to the same local repository that had been neglected, and finally make it public on GitHub today, 04/Jul/2015.
+
+
+----
+
+### Docker usage
+
+[Docker](https://www.docker.com/get-started) is an application that allows encapsulation of software environments. These environments are referred to as `containers` and `images`. [Click here](https://docs.docker.com/get-started/#containers-and-virtual-machines) for more information on Docker.
+
+##### Build
+PALM includes a `Dockerfile` with instructions to build the image.
+
+1) Clone (`git clone`) or download this repository.
+2) `cd` into this repo and run `docker build --rm -t mypalm .`
+
+##### Usage
+Once you have built (or pulled) the image, you can run it with local data. You can pass local directories into docker containers using the `-v` flag. Here's an example command for running PALM:
+
+```bash
+docker run --rm -it -v /path/to/my/data:/data mypalm -i /data/mydata.nii -d /data/design.mat -t /data/design.con
+```