Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/vidjil/vidjil into rbx.vidjil.org

doc/format-analysis.org

@@ -20,9 +20,9 @@ present in the =.vidjil= file.
 
 ** =.vidjil= file -- one sample
 
-This is a kind a minimal =.vidjil= file, describing clones in one sample.
+This is a minimal =.vidjil= file, describing clones in one sample.
 The segmentation is here =TRGV5*01 5/CC/0 TRGJ1*02=.
-Note that other elments could be added by some program (such as =tag= or =clusters=).
+Note that other elements could be added by some program (such as =tag= or =clusters=).
 
 #+BEGIN_SRC js
     {
@@ -63,8 +63,11 @@ Note that other elments could be added by some program (such as =tag= or =cluste
 
 ** =.vidjil= file -- several samples
 
-This a =.vidjil= file obtaining by mergin with =fuse.py= two =.vidjil= files corresponding to two samples.
+This a =.vidjil= file obtained by merging with =fuse.py= two =.vidjil= files corresponding to two samples.
 Clones that have a same =id= are gathered.
+It is the responsability of the program generating the initial =.vidjil= files to choose these =id= to
+do a correct gathering ('windows' is used by Vidjil, 'clone sequence' is used by EC-NGS/Brno pipeline, 
+and 'IMGT clonotype (AA) or (nt)' could also be used by some programs).
 
 #+BEGIN_SRC js
     {

server/web2py/applications/vidjil/models/task.py

@@ -94,6 +94,7 @@ def run_vidjil(id_file, id_config, id_data, id_fuse):
     ## execute la commande vidjil
     print "===Vidjil output==="
     print cmd
+    db.commit()
     p = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE, stderr=STDOUT, close_fds=True)
     p.wait()
     print p.stdout.read()
@@ -129,6 +130,7 @@ def run_vidjil(id_file, id_config, id_data, id_fuse):
     
     print "===fuse  output==="
     print cmd
+    db.commit()
     p = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE, stderr=STDOUT, close_fds=True)
     p.wait()
     print p.stdout.read()