RNAfold is OK but RNAduplex cannot be executed in miRdup process

Question

[beauchemin.david.3]

Hello,

I got an issue regarding miRdup execution when I execute it RNAfold seems to work well but the problem rather comes from subsequent RNAduplex processing. (OS : W10). I'm beginner and I'm not really used to all this but maybe the whole problem comes from Windows?

I paste RNAfold, RNAduplex and .dll in miRdup folder, I also tried to execute from Vienna Tool folder directly. My infiles are in fasta.

cl = ['java','-jar','miRdup_1.4/miRdup.jar','-predict','-i', 'output1/pre_seq_map.fasta','-m', 'output1/miRNA_map.fasta', '-r','miRdup_1.4']
subprocess.call(cl) #also tried directly on windows command line

____________________________
checking RNAfold... OK
**checking RNAduplex... FAIL**
Vienna tools cannot be executed
Process finished with exit code 0
____________________________

ls miRdup_1.4

.local
lib
libgcc_s_seh-1.dll
libgomp-1.dll
libgsl-0.dll
libgslcblas-0.dll
libwinpthread-1.dll
miRdup.jar
readme.txt
RNAduplex.exe
RNAfold.exe
src
testFiles

So I'm wondering why is this happening. Thank you

[GenoMax]

I assume you have taken this note for Windows into consideration?

The Windows installer will not change the PATH variable of your system. In order to omit the path to the binaries while using the programs of the ViennaRNA Package, please add the path of your ViennaRNA Package installation directory to your PATH variable manually.

Changing PATH in Windows.

Edit: Are you running this directly in windows or in cygwin/unix environment?

[beauchemin.david.3]

I did it yes

I run it directly on windows 10 I should figure out to change environment..

Answer 1

[mickael.leclercq]

You put RNAfold.exe, RNAduplex.exe and dlls in miRdup folder, good, but you should execute the command within the folder itself.

java -jar miRdup.jar -predict -i output1/pre_seq_map.fasta -m output1/miRNA_map.fasta

-r option is not recognized on windows