I'm going through the instructions page on https://gatkforums.broadinstitute.org/gatk/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference
Specifically, the command I don't see how to do is:
java -jar CreateSequenceDictionary.jar R= Homo_sapiens_assembly18.fasta O= Homo_sapiens_assembly18.dict [Fri Jun 19 14:09:11 EDT 2009] net.sf.picard.sam.CreateSequenceDictionary R= Homo_sapiens_assembly18.fasta O= Homo_sapiens_assembly18.dict [Fri Jun 19 14:09:58 EDT 2009] net.sf.picard.sam.CreateSequenceDictionary done. Runtime.totalMemory()=2112487424 44.922u 2.308s 0:47.09 100.2% 0+0k 0+0io 2pf+0w
I think that
CreateSequenceDictionary.jar comes from Picard, so I downloaded that from https://broadinstitute.github.io/picard/, but I don't see
CreateSequenceDictionary.jar anywhere in the directory. However, I do see
I assume that
.jar files are analogous to C executables, and
.java files are analogous to
.c human-readable code.
Going through the Picard readme file, I see that I should execute
./gradlew shadowJar but this build fails on two different computers that I'm on.
So I can't make/get
I'm at a loss, how do I generate this dict file?