First commit to the reproduction pipeline template

Let's start working on this pipeline independently with this first
commit. It is based on my previous experiences, but I had never made a
skeleton of a pipeline before, it was always within a working analysis.

But now that the pipeline has a separate repository for its self, we will
be able to work on it and use it as a base for future work and modify it to
make it even better. Hopefully in time (and with the help of others), it
will grow and become much more robust and useful.

1 files changed, 88 insertions, 0 deletions

diff --git a/configure b/configure
new file mode 100755
index 0000000..be18c25
--- /dev/null
+++ b/configure
@@ -0,0 +1,88 @@
+#! /bin/sh
+#
+# Necessary preparations/configurations for the reproduction pipeline.
+#
+# Original author:
+#     Your name <your@email.address>
+# Contributing author(s):
+# Copyright (C) YYYY, Your Name.
+#
+# This script is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This script is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# General Public License for more details.
+#
+# A copy of the GNU General Public License is available at
+# <http://www.gnu.org/licenses/>.
+
+
+
+
+
+# Location of the settings directory:
+pdir=reproduce/config/pipeline
+
+
+# Message to print for editing
+function msg {
+    echo; echo "Top-level reproduction directories are set.";
+    echo "Please run the following command to start the pipeline:"
+    echo "(Replace '8' with the number of CPU threads available)"
+    echo; echo "    make -j8"
+    echo;
+}
+
+
+# If `DIRECTORIES.mk' is already created, then ignore this step.
+if [ -f $pdir/DIRECTORIES.mk ]; then
+    echo
+    echo "$pdir/DIRECTORIES.mk already exists."
+    echo "To change/correct the top-level directories, please remove/edit it manually."
+    echo
+else
+
+    # Copy the base file to the desired output file.
+    if cp $pdir/DIRECTORIES.mk.in $pdir/DIRECTORIES.mk; then
+
+        # Tell the user to edit the directories.
+        while [ "$userread" != "y" -a "$userread" != "n" ]
+        do
+            echo "Top-level directories..."
+            echo
+            echo "These directories define the input(s) location and the"
+            echo "directory to host the intermediate/processing files."
+            echo
+            echo "To help in your ability to read and manage this pipeline,"
+            echo "it is recommended (but not mandatory) to change them to"
+            echo "a directory outside this reproduction pipeline."
+            echo
+            echo "More descriptions are provided within the file that is"
+            echo "opened if you choose to edit the directories."
+            echo
+            read -p"Edit the default top-level directories (y/n)? " userread
+        done
+
+        # Only continue if the user wants to edit the top level
+        # directories
+        if [ $userread = "y" ]; then
+
+            # Open a text editor to set the given directories
+            if emacs $pdir/DIRECTORIES.mk;   then msg
+            elif gedit $pdir/DIRECTORIES.mk; then msg
+            elif vi $pdir/DIRECTORIES.mk;    then msg
+            else
+                echo
+                echo "No common text editor found on your system."
+                echo "Please set the values in '$pdir/DIRECTORIES.mk' manually."
+                echo
+            fi
+        fi
+    else
+        echo; echo "Couldn't create $pdir/DIRECTORIES.mk"
+    fi
+fi