OSX 10.11.5 TOPPAS V2.0.0（66a7739）OPenMS TOPPAS无法找到的Java
我是新来OpenMS和TOPPAS。我正在尝试执行DeMIX TOPPAS工作流程： https://github.com/userbz/DeMix
我相信我的一切都正确配置。我已根据自述更改了.toppas文件，包括更改所有路径。
该工作流使用“MSGFPlus.jar”，该文件在工作流程（.toppas）中显示为正确的路径。然而，当我运行的工作流程，我得到的错误...
Fatal error: Java not found. Java is needed to run MS-GF+. Make sure that it can be executed by calling 'java', e.g. add the directory containing the Java binary to your PATH variable."
我相信TOPP运行我的本地用户，但它似乎没有，如果我作为本地用户或root身份运行到重要。这个错误表明我检查了java是否在我的路径中，这似乎是本地用户和root用户的。
Mikes-MacBook-Pro:~ mikes$ java -version
java version "1.8.0_74"
Java(TM) SE Runtime Environment (build 1.8.0_74-b02)
Java HotSpot(TM) 64-Bit Server VM (build 25.74-b02, mixed mode)
Mikes-MacBook-Pro:~ mikes$
Mikes-MacBook-Pro:~ mikes$ sudo bash
Password:
bash-3.2# java -version
java version "1.8.0_74"
Java(TM) SE Runtime Environment (build 1.8.0_74-b02)
Java HotSpot(TM) 64-Bit Server VM (build 25.74-b02, mixed mode)
bash-3.2#
编辑： 我曾尝试使用 '打开' 命令行打开TOPPAS.app，并增加 '的/ usr/bin中/ JAVA' 到Info.plist中...的建议here，但我仍然会得到相同的错误。
编辑： 有问题的.jar文件并运行在命令行OK ......
Mikes-MacBook-Pro:MSGFPlus mikes$ java -jar ./MSGFPlus.jar -s /Users/.../DeMix-master/Example/20131106_Q2_SDC_120MIN_HELA1.mzML -d /Users/.../2016-21-07_uniprot_sprot.fasta
MS-GF+ Beta (v10089) (7/16/2014)
Loading database files...
Creating the suffix array indexed file... Size: 197666693
AlphabetSize: 28
Suffix creation: 0.00% complete.
Suffix creation: 5.06% complete.
(snip)
Sorting 0.00% complete.
Sorting 5.81% complete.
(snip)
Sorting 98.78% complete.
Loading database finished (elapsed time: 207.38 sec)
Reading spectra...
Ignoring spectrum controllerType=0 controllerNumber=1 scan=20845: spectrum is not centroided.
(snip)
Ignoring spectrum controllerType=0 controllerNumber=1 scan=21339: spectrum is not centroided.
Ignoring 421 profile spectra.
Ignoring 0 spectra having less than 10 peaks.