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srividya22 / interproscan

Automatically exported from code.google.com/p/interproscan
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results written to install directory #8

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Run interproscan.sh from different directory (e.g. user's home)
2. Use default or relative basename
3.

What is the expected output? What do you see instead?

Expected: results will be written to same directory as input file
Observed: results are written to install directory (same dir as interproscan.sh)

What version of the product are you using? On what operating system?

interproscan 5RC1 64-bit
Debian 6.0

Please provide any additional information below.

By default or when giving relative names to '-b', the results are written to 
the same directory as interproscan.sh. This is unexpected and problematic when 
users do not have write permissions on this directory tree. The workaround is 
to give '-b' an absolute pathname to the desired output directory, but this 
seems like a bug in the software.

Thanks.

Original issue reported on code.google.com by jvolken...@biotech.wisc.edu on 6 Jun 2012 at 4:45

GoogleCodeExporter commented 9 years ago 
A similar bug is with the input parameter: 
If you give in the input a relative name (and not an absolute path), it will 
use the installation directory as the base name prefix for the file.
So, for instance, you can run the command "<install dir>/interproscan.sh -i 
test_proteins.fasta -f tsv" from any directory, and it will take the file 
("test_proteins.fasta", in this case) from the installation directory (and even 
if you don't have the file "test_proteins.fasta" in the current directory).
Of course, in this case as well, the output is being tried to be written to the 
installation directory

Original comment by rosen...@gmail.com on 13 Jan 2013 at 2:03

GoogleCodeExporter commented 9 years ago 
Hi all,

Sorry for the long delay in replying to your request.
We will have a look into that and will come back as soon as we fixed that. 
Unfortunately I can not write anything helpful, before we had a look into that.

Thanks for reporting that issue.
Kind Regards,
Maxim

Original comment by Maxim.Sc...@gmail.com on 17 Jan 2013 at 10:51

GoogleCodeExporter commented 9 years ago 
Dear InterProScan users,

We did reproduce your reported issue and yes this is a bug or at least a weird 
behaviour you wouldn't expect.
We've put that on our TODO list and we will fix that most likely in the next 
release after InterProScan RC5.

Kind Regards,
Maxim

Original comment by Maxim.Sc...@gmail.com on 27 Feb 2013 at 12:38

GoogleCodeExporter commented 9 years ago 
Dear InterProScan users,

We have updated the code now so that the next InterProScan release will behave 
the way you suggested. It definitely makes more sense for it to work this way.

Kind regards,
Craig

Original comment by newboycr...@gmail.com on 27 Mar 2013 at 2:05

GoogleCodeExporter commented 9 years ago 
[deleted comment]
GoogleCodeExporter commented 9 years ago 
Hi all,
I did another code commitment related to this, which should fix now all the 
possible use cases. It should work for options -i (FASTA input file), -b 
(multiple output files), -o (single output file), -T (temp directory).
I would also like to mention that it will be part of the new InterProScan 5 
release version RC6.

Many Thanks,
Maxim

Original comment by Maxim.Sc...@gmail.com on 9 Apr 2013 at 11:25