Couldn't open vcffilterjdk.jar

lindenb / jvarkit

Java utilities for Bioinformatics

https://jvarkit.readthedocs.io/

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Couldn't open vcffilterjdk.jar #168

Closed ASQWZXED closed 3 years ago

ASQWZXED commented 3 years ago

Verify

if you cannot compile/install , read https://github.com/lindenb/jvarkit/wiki/Compilation before submitting a new issue
the version of java

Subject of the issue

I have installed JDK 11 and installed java runtime environment. I installed Jvarkit properly using Git Bash. The vcffilterjdk.jar file has been created, but it couldn't be opened !

Your environment

version of jvarkit: from Git Bash
version of java: JDK 11.0.9
the value of ${JAVA_HOME}: C:\Program Files\Java\jdk-11.0.9
which OS: Windows 10

Steps to reproduce

Tell us how to reproduce this issue. Please provide an example. I installed JDK 11.0.9 and java runtime environment. After that, I setup JAVA_HOME. Next, I downloaded Jvarkit using Git Bash. The vcffilterjdk.jar file has been created. But it couldn't be opened !

Expected behaviour

Couldn't open vcffilterjdk.jar file.

Actual behaviour

Tell us what happens instea. No thing happen

lindenb commented 3 years ago

from the jvarkit directory. What is the output of

ls dist

ASQWZXED commented 3 years ago

dist directory just has this file vcffilterjdk.jar

lindenb commented 3 years ago

so the file is here... what do you mean with Couldn't open vcffilterjdk.jar file. ? how did you try to 'open' the file ? what do you think is 'opening' the file ?

ASQWZXED commented 3 years ago

I thought it is like an exe file that I can inter commands and run it.

How can I run commands like this one. java -jar dist/vcffilterjdk.jar \ -e 'return variant.isSNP() && variant.isBiallelic() && VariantContextUtils.isTransition(variant);' \ input.vcf

lindenb commented 3 years ago

How can I run commands like this one:

I do not understand. Did you only just try to type the command java -jar dist/vcffilterjdk.jar ... ?

and what are those \ ?

ASQWZXED commented 3 years ago

I have a csv file that has SNPs and I want to extract SNP mutations.

I don't know I found it in this website https://www.biostars.org/p/287667/

lindenb commented 3 years ago

I cannot understand your problem if you don't show me the exact commands you're using.

lindenb commented 3 years ago

https://www.biostars.org/p/287667/

\ at the end of line: https://stackoverflow.com/a/3871336/58082

ASQWZXED commented 3 years ago

Okay, where can I found documents on how to use jvarkit?

lindenb commented 3 years ago

Okay, where can I found documents on how to use jvarkit?

http://lindenb.github.io/jvarkit/VcfFilterJdk.html#about-the-script

lindenb commented 3 years ago

Closing. There is no such problem Couldn't open vcffilterjdk.jar.