initial commit for pipeline only including model and prediction

src/pipeline/submit_pipeline_model.sh

+#!/bin/bash
+
+# ------------------------------------------------------------------------------
+# config
+# ------------------------------------------------------------------------------
+
+
+# here somehow write the prefix depending on what we are testing
+JOB_NAME_PREFIX=ppln_ae10m_50
+
+INPUT_PATH='/work/voigtma/ppln_ae_50_new-2017-02-07T13-46-33'
+NAME=$JOB_NAME_PREFIX-$(date +%FT%H-%M-%S)
+
+OUTPUT_PATH=/work/$USER/$NAME
+
+# qsub -v means that OUTPUT_PATH goes into environment (normally export, but with qsub different)
+QSUB="qsub -terse -v OUTPUT_PATH=$OUTPUT_PATH -o /work/$USER/$NAME.log -j y"
+
+
+# ------------------------------------------------------------------------------
+# model-fitting & prediction 
+# ------------------------------------------------------------------------------
+
+
+  MODEL_JOB_ID_FITTING=$($QSUB  \
+    -N ${JOB_NAME_PREFIX}_fitting \
+    $HOME/orangutan_density_distribution/src/model_fitting/submit_abundance_model.sh \
+    -i $INPUT_PATH \
+    --ESW-aerial 0.025 \
+    --stability \
+    --include-aerial)
+
+
+  # prediction submitten
+ MODEL_JOB_ID_PRED=$($QSUB \
+    -N ${JOB_NAME_PREFIX}_prediction \
+    -hold_jid $MODEL_JOB_ID_FITTING \
+    -t 1999:2015 \
+    $HOME/orangutan_density_distribution/src/prediction/submit_abundance_pred.sh \
+    -i $OUTPUT_PATH \
+    --predictor-input-directory $INPUT_PATH \
+    -q)
+