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Update documentation re sybilSBML #143
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Spoke too soon. It's x86 only so while installation works it doesn't actually load later on on my ARM mac. Sorry for the noise. Will update if I find a solution that works on both architectures. |
Don't think an issue is the best place to put this info, but for reference this is how I got sybilSBML installed and working on an M1 Mac: First, build and install libSBML with fbc and group extensions:
Then, download sybilSBML 3.1.3 source tarball from https://www.cs.hhu.de/fileadmin/redaktion/Oeffentliche_Medien/Fakultaeten/Mathematisch-Naturwissenschaftliche_Fakultaet/Informatik/Bioinformatik/sybilSBML_3.1.3.tar.gz Build and install it:
The |
Thank you so much! We appreciate any help to get sybilSBML running on different platforms. I'll add a link to this issue in the documentation. |
Perfect, happy to help! |
Hello, wanted to post an update on this. On MacOS Sequoia, libSBML-5.19.0 does not compile anymore, the latest release libSBML 5.20.4 does. Now for sybilSBML 3.1.3 to correctly compile, I needed to do two things in addition to the instructions above from @jonasho:
After this, sybilSBML 3.1.3 compiles still with warnings but the XML output test from Note: On Linux (Oracle Linux 9), with conda install libsbml 5.20.4, step 2) was of course also needed for sybilSBML 3.1.3 and furthermore a more permissive global CFLAGS in ~/.R/Makevars was also needed:
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On recent versions of MacOS, the sybilSBML package can't be easily installed due to it linking dynamically to libSBML. An updated version of the package which is statically linked is available at https://www.cs.hhu.de/en/research-groups/computational-cell-biology/software-contributions/sybil.
Updating the installation instructions to reflect this would greatly aid Mac users (and also simplify the whole SBML section – I assume installation is similarly facilitated on other systems as well when libsbml is no longer a dependency).
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