Bruker libraries not found
Munchic opened this issue · comments
Hello! I'm trying to run MSFragger inside a Docker container based on Ubuntu 16.04. The command I'm running:
java -Xmx16g -jar /MSFragger-3.4/MSFragger-3.4.jar /MSFragger-3.4/closed_fragger.params /data/20180924_50ngHeLa_1.0.25.1_Hystar5.0SR1_S2-A1_1_2042.d
The error that I get:
ERROR Timsdata - The ext folder with timsdata-2-8-7-1.dll (Win) or libtimsdata-2-8-7-1.so (Linux) is needed. If you are using an old ext folder, please upgrade.
I am aware that there was a similar ticket before and that the ext folder should be at the same level with the .jar executable which is what I have:
root@293ff0d813a4:/MSFragger-3.4# ls
MSFragger-3.4.jar MSFragger-LICENSE.pdf RawFileRdr_License_Agreement_RevA.pdf closed_fragger.params nonspecific_fragger.params redist.txt
MSFragger-LICENSE-3RD-PARTY.txt Nglyco-HCD_fragger.params THIRD-PARTY-LICENSE-README.txt ext open_fragger.params version.txt
Inside ext/bruker folder it looks like this:
root@293ff0d813a4:/MSFragger-3.4/ext/bruker# ls
THIRD-PARTY-LICENSE-README.txt libtimsdata-2-7-0.so libtimsdata-2-8-7-1.so redist.txt timsdata-2-8-7-1.dll timsdata-2-8-7-1.lib
The file libtimsdata-2-8-7-1.so is just a duplicate of libtimsdata-2-7-0.so I made in case that's the version that's checked, with or without it I still get the same error. I also tried to duplicate and name libtimsdata.so (which is what redist.txt seems to be asking for). Please let me know if I am doing something wrong.
In the future, do you think it's possible to configure the location of ext folder from within fragger.params? I feel like that would eradicate issues with finding path to the libraries. Thank you so much for your help!
Do you have mono installed?
Best,
Fengchao