sbml2sbml

[paul....@gmail.com]

Hi, 

I am new to SBML format. I was trying to convert an sbml file of  level="1" version="2" to level "3" version "1" using the online facillity: https://www.ebi.ac.uk/biomodels/tools/converters/ but it seems that in the outputfile there is no change in the level. 

With the standalone version, I am getting the the following error:

guest-8d46b42c:sbfc-1.3.7 debdaspaul$ ./sbml2sbml.sh  model-b.xml L3V1 

readlink: illegal option -- f

usage: readlink [-n] [file ...]

usage: dirname path

./sbml2sbml.sh: line 12: /sbfConverter.sh: No such file or directory

Many thanks 

Sincerely 

Debdas

[Nicolas Rodriguez]

Hi,

On 5 June 2018 at 10:37, <paul....@gmail.com> wrote:

Hi, 

I am new to SBML format. I was trying to convert an sbml file of  level="1" version="2" to level "3" version "1" using the online facillity: https://www.ebi.ac.uk/biomodels/tools/converters/ but it seems that in the outputfile there is no change in the level. 

That probably mean that there was an error during the conversion. But unfortunately, the way the converter is build at the moment, it does return the original model instead of reporting the conversion errors. We already noticed this problem and have it on our todo list.

 

With the standalone version, I am getting the the following error:

On which system are you trying to run the script ? It seems that the option we use for the 'readlink' program does not exist there.

Note that when running it locally you will need to have a local version of libsbml installed.

 

guest-8d46b42c:sbfc-1.3.7 debdaspaul$ ./sbml2sbml.sh  model-b.xml L3V1 

readlink: illegal option -- f

usage: readlink [-n] [file ...]

usage: dirname path

./sbml2sbml.sh: line 12: /sbfConverter.sh: No such file or directory

 

If you can provide me with the file to converter, I could have a look at it and try to find why the conversion did not work.

Thanks,

Nico