annotate rDiff/examples/get_data.sh @ 2:233c30f91d66

updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
author vipints <vipin@cbio.mskcc.org>
date Tue, 08 Oct 2013 07:15:44 -0400
parents 0f80a5141704
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
1 #!/bin/bash
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
2
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
3 set -e
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
4
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
5 echo %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
6 echo % rDiff examples: get_data.sh %
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
7 echo %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
8 echo
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
9 echo This script gets reads and the genome sequence
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
10 echo for one A.thaliana example.
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
11 echo
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
12
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
13 export DATA_DIR=data
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
14
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
15 if [ -d $DATA_DIR ]
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
16 then
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
17 echo Data directory ./$DATA_DIR already exists
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
18 echo \(remove it to run this script again\)
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
19 exit -1
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
20 fi
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
21
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
22 echo Downloading rDiff example data from FTP server ...
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
23 wget -c http://cbio.mskcc.org/public/raetschlab/user/drewe/rdiff/example_data.tar.gz
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
24 echo uncompressing ...
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
25 tar -xzf example_data.tar.gz
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
26 mv example_data $DATA_DIR
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
27 echo
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
28 echo -n Done.
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
29 echo