Subject: use Debian paths
Description: update some paths to use Debian package paths
Last-Updated: 2014-02-01
Author: Olivier Sallou <osallou@debian.org>
Forwarded: no
--- a/run_mapsembler_and_phaser.sh
+++ b/run_mapsembler_and_phaser.sh
@@ -1,8 +1,9 @@
+#!/bin/bash
 #######################################################################
 #################### HEADER, CHANGE VALUES HERE #######################
 #######################################################################
-starters_file="sample_example/fragments.fa"
-read_sets="sample_example/reads.fa" # FOR instance: "read_set1.fa.gz read_set2.fq.gz"
+starters_file="/usr/share/doc/mapsembler2/sample_example/fragments.fa"
+read_sets="/usr/share/doc/mapsembler2/sample_example/reads.fa.gz" # FOR instance: "read_set1.fa.gz read_set2.fq.gz"
 prefix_index="index" # all files used for indexing will be written will start with this prefix
 prefix_results="res" # all final files will be written will start with this prefix
 k=31 # size of kmers
@@ -10,7 +11,7 @@
 d=1 # estimated number of error per read (used by kissreads only)
 g=10000000 # estimated genome size. Used only to control kissnp2 memory usage. e.g. 3 billion (3000000000) uses 4Gb of RAM.
 t=0
-PATH_TOOLS="./tools/" # path were executables kissnp2 and kissreads are. Leave blank if they are located in a directory located in the PATH environnement variable
+PATH_TOOLS="/usr/bin/" # path were executables kissnp2 and kissreads are. Leave blank if they are located in a directory located in the PATH environnement variable
 #######################################################################
 #################### END HEADER                 #######################
 #######################################################################
