Simulator temporary folder

sivarajankumar / fluxcapacitor

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Simulator temporary folder #34

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago

For which program(s) you want a new feature?
Simulator

Which build of the program(s)?
20100423

What steps will reproduce the problem?
specify as TMP_DIR in the .PAR file a different location than the system
default temporary directory

What is the expected output? What do you see instead?
Temporary files should all be written to the folder specified by TMP_DIR.
However, at least some temporary files are still written in the system
default directory for temporary files.

Original issue reported on code.google.com by gmicha@gmail.com on 12 May 2010 at 11:40

GoogleCodeExporter commented 8 years ago

Original comment by gmicha@gmail.com on 14 May 2010 at 7:21

Changed state: Accepted

GoogleCodeExporter commented 8 years ago

Original comment by gmicha@gmail.com on 14 May 2010 at 7:22

Changed state: Started

GoogleCodeExporter commented 8 years ago

From build 20100514 onward, temporary directory gets correctly set when read in 
with
parameter file.

http://code.google.com/p/fluxcapacitor/downloads/detail?name=FluxSimulator-20100
514.tar.gz

Original comment by gmicha@gmail.com on 14 May 2010 at 7:34

Changed state: Fixed

GoogleCodeExporter commented 8 years ago

[Forum thread:
http://fluxcapacitor.wikidot.com/forum/t-240675/change-the-temporary-folder#post
-793923]

(1) The simulator cannot be used from command line anymore. I generated 
finished the
annotation, expression and library stage from the GUI and tried to start the
sequencing from CL without success:

weese@sequoia:~/pipeline/software/FluxSimulator/bin$ ./sim.sh -sp
~/pipeline/simulated/paired/human_all.par
[HELLO] I am the Flux Simulator (build 20100514), nice to meet you!

[INIT] I am collecting information on the run.
initializing profiler *

initializing library **
weese@sequoia:~/pipeline/software/FluxSimulator/bin$

When I open the same par file in the GUI and press play in the sequencing tab
everything works fine.

(2) After the sequencing the par file is overwritten by the GUI and the TMP_DIR 
entry
which I manually inserted before disappears.

Original comment by gmicha@gmail.com on 26 May 2010 at 2:14

Changed state: Reopened

GoogleCodeExporter commented 8 years ago

[deleted comment]

GoogleCodeExporter commented 8 years ago

Could reproduce both problems:

(1) is related to an abort of the command line if no sequence error file is 
read. The
corresponding change happened during concurrent code modifications in the 
process of
handling  Issue 31  respectively  Issue 33 .

(2) writing out the temporary file was suppressed iff it corresponds to the 
system
temp dir. As in the process of solving the original issue in this thread the 
system
temp dir was overwritten by the user specified folder, output in the .PAR file 
is
currently supressed.

Original comment by gmicha@gmail.com on 26 May 2010 at 2:49

GoogleCodeExporter commented 8 years ago

Fixed both issues in Simulator 20100526

http://code.google.com/p/fluxcapacitor/downloads/detail?name=FluxSimulator-20100
526.tar.gz&can=2&q=#makechanges

Original comment by gmicha@gmail.com on 26 May 2010 at 2:58

Changed state: Fixed