Hello
Following the instructions for installing EcoFunPrimer and RDPTools, the PrimerDesign.jar is not being created in the PrimerDesign/dist folder as is described in the instructions.
A jar file called EcoFunPrimer.jar is installed in the PrimerDesign/dist folder and libPrimer3.so file with a lib directory.
Separately, installing MetaFunPrimer, a PrimerDesign.jar is created inside the MetaFunPrimer/src directory, not the RDPTools/PrimerDesign/dist directory, so I could test the instruction: java -Xmx8g -jar /path/to/PrimerDesign.jar [--help].
The output is
ERROR: Program needs os type, used default: mac
ERROR: Program needs output file directory to start
ERROR: Program needs sequence input fasta file to start
Exception in thread "main" java.lang.NullPointerException
at edu.msu.cme.rdp.readseq.utils.SeqUtils.guessFileFormat(SeqUtils.java:326)
at edu.msu.cme.rdp.readseq.utils.SeqUtils.getSeqReaderCore(SeqUtils.java:261)
at edu.msu.cme.rdp.readseq.readers.SequenceReader.(SequenceReader.java:38)
at edu.msu.cme.rdp.readseq.readers.SequenceReader.readFully(SequenceReader.java:75)
at edu.msu.cme.rdp.primerdesign.selectprimers.SelectPrimerPipeline.main(SelectPrimerPipeline.java:68)
at edu.msu.cme.rdp.primerdesign.selectprimers.PrimerDesign.main(PrimerDesign.java:233)
In contract, the installed EcoFunPrimer.jar out put is
java -Xmx8g -jar EcoFunPrimer.jar [--help]
USAGE: java -jar EcoFunPrimer.jar
screen - Screen for primer regions with for the best coverage at each position
select - Select primer pairs using slidescale or user defined fwd and rev primer positions
Hello Following the instructions for installing EcoFunPrimer and RDPTools, the PrimerDesign.jar is not being created in the PrimerDesign/dist folder as is described in the instructions.
A jar file called EcoFunPrimer.jar is installed in the PrimerDesign/dist folder and libPrimer3.so file with a lib directory.
Separately, installing MetaFunPrimer, a PrimerDesign.jar is created inside the MetaFunPrimer/src directory, not the RDPTools/PrimerDesign/dist directory, so I could test the instruction: java -Xmx8g -jar /path/to/PrimerDesign.jar [--help].
The output is
ERROR: Program needs os type, used default: mac ERROR: Program needs output file directory to start ERROR: Program needs sequence input fasta file to start Exception in thread "main" java.lang.NullPointerException at edu.msu.cme.rdp.readseq.utils.SeqUtils.guessFileFormat(SeqUtils.java:326) at edu.msu.cme.rdp.readseq.utils.SeqUtils.getSeqReaderCore(SeqUtils.java:261) at edu.msu.cme.rdp.readseq.readers.SequenceReader.(SequenceReader.java:38)
at edu.msu.cme.rdp.readseq.readers.SequenceReader.readFully(SequenceReader.java:75)
at edu.msu.cme.rdp.primerdesign.selectprimers.SelectPrimerPipeline.main(SelectPrimerPipeline.java:68)
at edu.msu.cme.rdp.primerdesign.selectprimers.PrimerDesign.main(PrimerDesign.java:233)
In contract, the installed EcoFunPrimer.jar out put is
java -Xmx8g -jar EcoFunPrimer.jar [--help] USAGE: java -jar EcoFunPrimer.jar
screen - Screen for primer regions with for the best coverage at each position
select - Select primer pairs using slidescale or user defined fwd and rev primer positions