Use bin and data directory heirarchy

wtsi-npg · Jun 6, 2014 · 76329c4 · 76329c4
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Showing 5 changed files with 5 additions and 5 deletions.
diff --git a/README.vtfp b/README.vtfp
@@ -58,14 +58,14 @@ vtfp.pl
 
      kl2@sf2-farm-srv1:~/projects/viv$ grep -v "^#" examples/example_06.vtf | tr -d "\n\t" > example_06_vtf.json
 
-     kl2@sf2-farm-srv1:~/projects/viv$ vtfp.pl -l ex06.log -q example_06_vtf.json
+     kl2@sf2-farm-srv1:~/projects/viv$ bin/vtfp.pl -l ex06.log -q example_06_vtf.json
      KeyID	Req	Id	RawAttrib
      greetings_file	required	greetings_file	name
      intercept_file	not_required	intercept_file	name
 
   Preprocessing this, specifying only the required KeyID "greetings_file" gives:
 
-     kl2@sf2-farm-srv1:~/projects/viv$ vtfp.pl -l ex06.log -keys greetings_file -vals Hello.txt example_06_vtf.json
+     kl2@sf2-farm-srv1:~/projects/viv$ bin/vtfp.pl -l ex06.log -keys greetings_file -vals Hello.txt example_06_vtf.json
 
      {
      'nodes' => [
@@ -112,9 +112,9 @@ vtfp.pl
 
   Preprocessing this, both substitutable parameters gives:
 
-     kl2@sf2-farm-srv1:~/projects/viv$ vtfp.pl -l ex06.log -keys greetings_file -vals Hello.txt -keys intercept_file -vals intercept.txt example_06_vtf.json
+     kl2@sf2-farm-srv1:~/projects/viv$ bin/vtfp.pl -l ex06.log -keys greetings_file -vals Hello.txt -keys intercept_file -vals intercept.txt example_06_vtf.json
   or:
-     kl2@sf2-farm-srv1:~/projects/viv$ vtfp.pl -l ex06.log -keys greetings_file,intercept_file -vals Hello.txt,intercept.txt example_06_vtf.json
+     kl2@sf2-farm-srv1:~/projects/viv$ bin/vtfp.pl -l ex06.log -keys greetings_file,intercept_file -vals Hello.txt,intercept.txt example_06_vtf.json
 
      {
      'nodes' => [

diff --git a/viv.pl → bin/viv.pl b/viv.pl → bin/viv.pl
diff --git a/vtfp.pl → bin/vtfp.pl b/vtfp.pl → bin/vtfp.pl
diff --git a/examples/tophat2_sample_template.vtf → data/tophat2_sample_template.vtf b/examples/tophat2_sample_template.vtf → data/tophat2_sample_template.vtf
diff --git a/examples/README.examples b/examples/README.examples
@@ -7,6 +7,6 @@ For example:
   grep -v "^#" example_01.cfg | tr -d "\n\t" > example_01_cfg.json
 
 You can then use the viv script with this JSON file (if you are working from the examples directory):
-  ../viv.pl -s -x -v 3 -o example_01.log example_01_cfg.json
+  ../bin/viv.pl -s -x -v 3 -o example_01.log example_01_cfg.json
 
 The resulting log file is verbose - you may want to reduce the verbosity level (the value supplied to the -v flag).