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Automatically exported from code.google.com/p/yabi
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Unable to pass directory parameters. #71

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
I am trying to setup a pair of tools; velveth, which sets up a directory, which 
is the input for velvetg. Often a user will want totry multiple velvetg runs on 
the velveth output.

There are two parts to this
1) Unable to select a directory with 'select file' - it just opens.
2) When designating a directory ('myAssembly') as an output from velveth, then 
selecting it as an input to velvetg, the parameter that gets passed to velvetg 
includes one of the subfiles/dirs ('myAssembly/Log' - the log subdir that 
velveth writes.)
e.g. (https://bioflow.qfab.org/yabiadmin/admin/yabiengine/syslog/4984/)
Submitting to ssh+pbspro://sarah.williams@bora.qfab.org:22/ command: velvetg 
"/home/sarah.williams/bioflow/abf3ba27-fc62-4fe9-82c1-4d68be17757b/input/assembl
ydir/Log" -amos_file "no" -cov_cutoff "5" -read_trkg "no"

Part (1) is perhaps the more important, as velveth shoudln't need to be rerun 
when trialling velvetg options. Is there a way (other than free text)?

Using firefox.

Thanks.

Original issue reported on code.google.com by s.willi...@qfab.org on 26 Aug 2011 at 2:19

GoogleCodeExporter commented 9 years ago 
Should be answered by this: 
http://code.google.com/p/yabi/wiki/FAQ?ts=1314677830&updated=FAQ#I'm_trying_to_a
dd_a_tool_that_takes_an_input_directory_whic

Original comment by amacgregor on 30 Aug 2011 at 4:18