search

OpenMS / THIRDPARTY

External binary dependencies (e.g. search engine binaries) packaged in installers
2 stars 12 forks source link

[FIX] sirius script #30

Closed lukaszimmermann closed 7 years ago

lukaszimmermann commented 7 years ago

realpath did not work with spaces in path Use absolute path for executables in this script

oliveralka commented 7 years ago

Did work with the current build & this script in KNIME.

jpfeuffer commented 7 years ago

Ah nice. You installed the current RC plugin and replaced the script there?

oliveralka commented 7 years ago

Yes.

jpfeuffer commented 7 years ago

Hm okay but note that the current solution now requires a bash (which is not standard on every linux). To be honest it feels like this whole script is more complex than it would have to be. The question is, which cases we want to cover with this?

jpfeuffer commented 7 years ago

But in theory we can merge this for the release and think about it another time. Should work in 99% of the cases.

oliveralka commented 7 years ago

Then merge for the release and let's think about it further. The most important is that APP_Home is set correctly.

The bottom part of the script is from the guys in Jena, so I'm not sure what is really needed for Sirius. In our case we need the Home, Lib (flat & non-flat), Java. In case of Sirius you can specify if you want to use GUROBI.

jpfeuffer commented 7 years ago

Yes. This is kind of what I mean. Ok I will merge.

lukaszimmermann commented 7 years ago

I think that the shell script should be replaced by a Python script to ensure portability.

jpfeuffer commented 7 years ago

This PR made the nightlies fail: https://abibuilder.informatik.uni-tuebingen.de/jenkins/view/OpenMS/job/openms_nightly_packaging/compiler=g++-4.8,os_label=ubuntu_1404/95/testReport/junit/projectroot.src.tests/topp/TOPP_SiriusAdapter_1/