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sanger-pathogens / SnpEffWrapper

Takes a VCF and applies annotations from a GFF using SnpEff
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openjdk support? #12

Open peterjc opened 5 years ago

peterjc commented 5 years ago

We have this version of Java installed,

$ java -version
openjdk version "1.8.0_92"
OpenJDK Runtime Environment (Zulu 8.15.0.1-linux64) (build 1.8.0_92-b15)
OpenJDK 64-Bit Server VM (Zulu 8.15.0.1-linux64) (build 25.92-b15, mixed mode)

Hacking the regular expression match = re.match('^java version "1\.7\.[^"]+"$', first_line) to read match = re.match('^openjdk version "1\.8\.[^"]+"$', first_line) in snpEffWrapper/wrapper.py seems to be enough to run the tool.

Is there good reason not to accept openjdk and versions after 1.7.x?

peterjc commented 5 years ago

Also the README file says Java (>= 1.7), yet the code requires Java 1.7.x only