Repo cleanup

.gitignore

@@ -0,0 +1,15 @@
+*.swp
+*.pyc
+**/__pycache__/
+
+/anarci.egg-info/
+/dist/
+/build/
+/build_pipeline/IMGT_sequence_files/
+/build_pipeline/curated_alignments/
+/build_pipeline/muscle_alignments/
+/build_pipeline/HMMs/
+
+/lib/python/anarci/germlines.py
+/lib/python/anarci/dat/
+

.hgignore

@@ -0,0 +1,15 @@
+\.swp$
+\.pyc$
+__pycache__
+
+^anarci.egg-info/
+^dist/
+^build/
+^build_pipeline/IMGT_sequence_files/
+^build_pipeline/curated_alignments/
+^build_pipeline/muscle_alignments/
+^build_pipeline/HMMs/
+
+^lib/python/anarci/germlines.py
+^lib/python/anarci/dat/
+

INSTALL

@@ -4,19 +4,41 @@
 
 Requirements:
     -  HMMER3 version 3.1 or higher - http://hmmer.janelia.org/ 
-
-To install as root run:
+    -  muscle v3 - http://www.drive5.com/muscle/
 
-python setup.py install
+# Build
 
-for users without root access install locally using:
+    bash build.sh
+
+# Installing
+## With `pip`
+Either as root or as user, with:
+
+    pip3 install .
+
+## Without `pip`
+As root:
+
+    python3 setup.py install
+
+As user:
+
+    python3 setup.py install --user
 
-python setup.py install --user
 or
-python setup.py install --home="~"
 
-For more information about installing python programs see:
-https://docs.python.org/2/install/#alternate-installation-the-user-scheme
+    python3 setup.py install --home="~"
+
+# Uninstalling
+## With `pip`
+
+    pip3 uninstall anarci
+
+## Without `pip`
+Manually remove the installed files. Find the executable and python module with
+
+	which ANARCI
+	python3 -c 'import importlib; print(importlib.util.find_spec("anarci").submodule_search_locations)'
 
 For help see README or run:
 $ ANARCI -h

build.sh

@@ -0,0 +1,32 @@
+clean ()
+{
+	rm -rf anarci.egg-info/
+	rm -rf dist/
+	rm -rf build/
+	rm -rf build_pipeline/IMGT_sequence_files/
+	rm -rf build_pipeline/muscle_alignments/
+	rm -rf build_pipeline/curated_alignments/
+	rm -rf build_pipeline/HMMs/
+
+	rm -f lib/python/anarci/germlines.py
+	rm -rf lib/python/anarci/dat
+}
+
+if ! [ -z $1 ]; then
+	if [ $1 = "clean" ]; then
+		clean
+	else
+		echo "Unknown action. Use no argument to build and 'clean' to remove built files. Exiting."
+	fi
+
+	exit 0
+fi
+
+cd build_pipeline/
+echo "Downloading germlines from IMGT and building HMMs..."
+bash RUN_pipeline.sh
+
+cp curated_alignments/germlines.py ../lib/python/anarci/
+mkdir -p ../lib/python/anarci/dat
+cp -r HMMs ../lib/python/anarci/dat
+