fix #9

examples/pipelines/PirusBasic/readme.md

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+# PirusBasic Pipeline
+
+This document explain you how to build a simple pipeline image for Pirus. 
+
+## Requirement
+ * You need LXD on your computer to create it
+ * You should read the official doc of Pirus
+
+##Instructions
+
+    # create a container
+    lxc launch images:ubuntu/xenial pirus
+    # configure it
+    lxc exec pirus -- /bin/bash
+
+    # following directories are mandatory
+    mkdir /pipeline/run
+    mkdir /pipeline/inputs
+    mkdir /pipeline/outputs
+    mkdir /pipeline/logs
+    mkdir /pipeline/db
+
+    # need curl if you want to notify server with the progress of your run
+    apt install curl
+
+    # the script run.sh is the "entry point" of your run
+    echo "curl ${NOTIFY}50" > /pipeline/run/run.sh
+    echo "ls -l /pipeline/database/db > /pipeline/outputs/result.txt" >> /pipeline/run/run.sh
+    chmod +x /pipeline/run/run.sh
+
+    # exit the container
+    exit
+
+    # stop it and create an image
+    lxc stop pirus
+    lxc publish pirus --alias=PirusSimple
+
+    # Your Pipeline is ready to use on your server
+
+
+## TODO : export image as file and edit image conf to create a piruse package installable on any pirus server

examples/pipelines/PirusBasic/run.sh

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+#!/bin/sh
+# coding: utf-8
+
+
+DB="/pipeline/db/"
+OUT="/pipeline/outputs/"
+IN="/pipeline/inputs/"
+LOG="/pipeline/logs/"
+RUN="/pipeline/run/"
+
+
+echo "START Plugin de test"
+echo "===================="
+cd ${RUN}
+pwd
+ls -l
+
+echo "Environment"
+echo "==========="
+env
+
+echo "Inputs files"
+echo "============"
+ls -l ${IN}
+
+
+echo "Loop"
+echo "===="
+for i in `seq 0 100`
+do
+   echo "$i %"
+   curl "$NOTIFY$i"
+   sleep 1
+done
+
+echo "Create output file"
+echo "=================="
+echo "Gene in refGene that have more than 50 exons:" >  ${OUT}refGenAnalysis.txt
+zcat ${DB}refGene.txt.gz | awk '$9 > 50{print $13}' >>  ${OUT}refGenAnalysis.txt
+
+echo "Done"
+echo "===="