I created a 'config' directory at project base and moved three original files to 'config/upsala': globalConfig.sh globalConfig.xml uppmax_global_config.xml. I then modified setup.sh file to allow this syntax:
An example command is like this: ./setup.sh /space/system/piper afmd /space/system/lib nogatk
Which means:
To install piper to /space/system/piper
To pickup config files under config/afmd directory. Current possible choices are afmd and upsala, but more subdirectory for any new institution can be added.
Register /space/system/lib to piper so it can look for additional library dependencies (If they are put there, of course)
The fourth argument, whenever none-empty, will tell setup.sh not to download and compile GATK. This is nicer than commenting/uncommenting the function call.
Commit 704a1ac9d26cc686d
This is an additional commit to remove dependency on GenomeAnalysisTK.jar. This is because Queue.jar already includes content of GenomeAnalysisTK.jar. Putting both of them together in lib causes warning about redundant packages found, such as the one about org.slf4j bindings.
I would like to suggest merging of the following two commits:
Commit aac74bce7e22
https://github.com/biocyberman/piper/commit/aac74bce7e22137e6fb7a539f21102c7ef5ebf3e
I created a 'config' directory at project base and moved three original files to 'config/upsala':
globalConfig.sh globalConfig.xml uppmax_global_config.xml. I then modifiedsetup.shfile to allow this syntax:./setup.sh /path/to/install/piper institution /path/to/otherlibraries/lib NoGATKCompileAn example command is like this:
./setup.sh /space/system/piper afmd /space/system/lib nogatkWhich means:
/space/system/piperconfig/afmddirectory. Current possible choices areafmdandupsala, but more subdirectory for any new institution can be added.setup.shnot to download and compile GATK. This is nicer than commenting/uncommenting the function call.Commit 704a1ac9d26cc686d This is an additional commit to remove dependency on
GenomeAnalysisTK.jar. This is becauseQueue.jaralready includes content ofGenomeAnalysisTK.jar. Putting both of them together inlibcauses warning about redundant packages found, such as the one aboutorg.slf4jbindings.https://github.com/biocyberman/piper/commit/704a1ac9d26cc686d460fd93dc9b551f6ced77f5
My commit tree looks a bit messy, I will try to keep them in good order from now on :)