Added SGE information for alanine scanning

hpc/sge/alanine-scanning/README.rst

@@ -0,0 +1,46 @@
+==============================
+Sun Grid Engine job submission
+==============================
+
+The execution/run script generated by alanine_scanning functions as both a submission script for a workstation and for an SGE cluster
+engine.
+
+In the documentation below, we only describe the changes needed to run the script on the default dataset on an
+SGE cluster; the user is referred to the documentation in protocols/alanine-scanning/README.rst for a more detailed
+explanation of what the script does and how to change the input parameters.
+
+In particular, the *Configuration* section of protocols/alanine-scanning/README.rst should be followed for the commands below
+to work.
+
+----------------------------
+Paths and extensions
+----------------------------
+
+The command lines below use placeholders for paths and extensons. Please change these appropriately *e.g.*:
+
+::
+
+  WORKING_DIRECTORY=.
+  BENCHMARK_PATH=<path/to/alanine-scanning>
+  OUTPUT_DIRECTORY=<directory created by the setup_alanine_scanning.py script>
+
+The output directory will be named according the the current date and username *e.g.* *15-02-02-12-00_username_alanine_scanning*.
+
+-----------------------------
+How to run the full benchmark
+-----------------------------
+
+These commands run the full benchmark for the Kortemme & Baker dataset.
+
+::
+
+  cd ${BENCHMARK_PATH}/protocols/alanine-scanning
+  python setup_alanine_scanning.py
+  cd ${BENCHMARK_PATH}/protocols/alanine-scanning/job_output/${OUTPUT_DIRECTORY}/
+  qsub alascan_run.py
+
+  # if execution is successful
+  cd ${BENCHMARK_PATH}/protocols/alanine_scanning
+  python analyze.py ${BENCHMARK_PATH}/protocols/alanine-scanning/job_output/${OUTPUT_DIRECTORY}
+
+

hpc/sge/ddg_monomer_16/README.rst

@@ -19,7 +19,7 @@ The command lines below use placeholders for paths and extensons. Please change
 ::
 
   WORKING_DIRECTORY=.
-  BENCHMARK_PATH=<path/to/sequence-tolerance>
+  BENCHMARK_PATH=<path/to/ddg_monomer_16>
   OUTPUT_DIRECTORY=<directory created by the preminimization step>
 
 The output directory will be named according the the current date and username *e.g.* 15-02-02-12-00_username_ddg_monomer_16.
@@ -37,13 +37,13 @@ These commands run the full benchmark for the different datasets.
   cd ${BENCHMARK_PATH}/protocols/ddg_monomer_16
   python run_preminimization.py
   cd ${BENCHMARK_PATH}/protocols/ddg_monomer_16/job_output/${OUTPUT_DIRECTORY}/
-  python preminimization_step.py
+  qsub preminimization_step.py
 
   # if execution is successful
   cd ${BENCHMARK_PATH}/protocols/ddg_monomer_16
   python run_ddg.py --force
   cd ${BENCHMARK_PATH}/protocols/ddg_monomer_16/job_output/${OUTPUT_DIRECTORY}/
-  python ddg_step.py
+  qsub ddg_step.py
 
   # if execution is successful
   cd ${BENCHMARK_PATH}/protocols/ddg_monomer_16
@@ -56,13 +56,13 @@ These commands run the full benchmark for the different datasets.
   cd ${BENCHMARK_PATH}/protocols/ddg_monomer_16
   python run_preminimization.py -d ${BENCHMARK_PATH}/input/json/guerois.json
   cd ${BENCHMARK_PATH}/protocols/ddg_monomer_16/job_output/${OUTPUT_DIRECTORY}/
-  python preminimization_step.py
+  qsub preminimization_step.py
 
   # if execution is successful
   cd ${BENCHMARK_PATH}/protocols/ddg_monomer_16
   python run_ddg.py --force
   cd ${BENCHMARK_PATH}/protocols/ddg_monomer_16/job_output/${OUTPUT_DIRECTORY}/
-  python ddg_step.py
+  qsub ddg_step.py
 
   # if execution is successful
   cd ${BENCHMARK_PATH}/protocols/ddg_monomer_16
@@ -75,13 +75,13 @@ These commands run the full benchmark for the different datasets.
   cd ${BENCHMARK_PATH}/protocols/ddg_monomer_16
   python run_preminimization.py -d ${BENCHMARK_PATH}/input/json/potapov.json
   cd ${BENCHMARK_PATH}/protocols/ddg_monomer_16/job_output/${OUTPUT_DIRECTORY}/
-  python preminimization_step.py
+  qsub preminimization_step.py
 
   # if execution is successful
   cd ${BENCHMARK_PATH}/protocols/ddg_monomer_16
   python run_ddg.py --force
   cd ${BENCHMARK_PATH}/protocols/ddg_monomer_16/job_output/${OUTPUT_DIRECTORY}/
-  python ddg_step.py
+  qsub ddg_step.py
 
   # if execution is successful
   cd ${BENCHMARK_PATH}/protocols/ddg_monomer_16
@@ -94,13 +94,13 @@ These commands run the full benchmark for the different datasets.
   cd ${BENCHMARK_PATH}/protocols/ddg_monomer_16
   python run_preminimization.py -d ${BENCHMARK_PATH}/input/json/curatedprotherm.json
   cd ${BENCHMARK_PATH}/protocols/ddg_monomer_16/job_output/${OUTPUT_DIRECTORY}/
-  python preminimization_step.py
+  qsub preminimization_step.py
 
   # if execution is successful
   cd ${BENCHMARK_PATH}/protocols/ddg_monomer_16
   python run_ddg.py --force
   cd ${BENCHMARK_PATH}/protocols/ddg_monomer_16/job_output/${OUTPUT_DIRECTORY}/
-  python ddg_step.py
+  qsub ddg_step.py
 
   # if execution is successful
   cd ${BENCHMARK_PATH}/protocols/ddg_monomer_16