Fix MacOS issue for FASTA

seppinho commented 6 years ago

MacOS requires a different jbwa library.
Check OS and then load correct library.

nuin commented 6 years ago

I am having this exact error on a Mac

Exception in thread "main" java.lang.UnsatisfiedLinkError: /private/var/folders/gn/8t3hpbvx63qd3lfn5pnhqx880000gp/T/jbwa-0.7.17/libbwajni.so: dlopen(/private/var/folders/gn/8t3hpbvx63qd3lfn5pnhqx880000gp/T/jbwa-0.7.17/libbwajni.so, 1): no suitable image found.  Did find:
    /private/var/folders/gn/8t3hpbvx63qd3lfn5pnhqx880000gp/T/jbwa-0.7.17/libbwajni.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00
    /private/var/folders/gn/8t3hpbvx63qd3lfn5pnhqx880000gp/T/jbwa-0.7.17/libbwajni.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00
    at java.lang.ClassLoader$NativeLibrary.load(Native Method)
    at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1938)
    at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1821)
    at java.lang.Runtime.load0(Runtime.java:809)
    at java.lang.System.load(System.java:1086)
    at importer.FastaImporter.load(FastaImporter.java:59)
    at genepi.haplogrep.main.Haplogrep.run(Haplogrep.java:153)
    at genepi.base.Tool.start(Tool.java:193)
    at genepi.haplogrep.main.Haplogrep.main(Haplogrep.java:197)

elffuos commented 5 years ago

Hi, What is a Jbwa file and how do I load it? there is no reference page. Please help.

Arslan-Zaidi commented 5 years ago

Hi, is there a fix for this? I'm having the same issue. Thanks

seppinho commented 5 years ago

@Arslan-Zaidi no fix yet, but maybe you or someone else can help me building the native lib (MacOS required):

git clone https://github.com/lindenb/jbwa/
make
send me the jbwa-native.jar

thanks!

nuin commented 5 years ago

@seppinho I have a jbwa.jar here is this what you need?

The jbwa-native is a tar file. I can upload that too.

seppinho commented 5 years ago

Thanks. Can't access the file yet ("file is uploading"). One more thing, can you also send me the folder src/main/native?

best

seppinho commented 5 years ago

@nuin awesome! the tar file would be great and also the files from src/main/native as a tar.

nuin commented 5 years ago

@seppinho I will send you an email with the whole folder in a tar ball.

nuin commented 5 years ago

It bounced

@seppinho Sent to your UIBK address

nuin commented 5 years ago

@seppinho Correct address now, I had your UIBK address in my contacts, didn't notice you moved. Let me know of any issues.

seppinho commented 5 years ago

Thanks! library (*.jnilib) is included. I think I have everything to build a new version. Thanks for your quick help

nuin commented 5 years ago

Great, let me know if you need any other Mac stuff.

seppinho commented 5 years ago

@nuin. Thanks, I just build a pre-release. Can you let me know if it works? https://github.com/seppinho/haplogrep-cmd/releases/download/v2.1.20/haplogrep-2.1.20.jar

nuin commented 5 years ago

It works fine now. Tested with a couple of FASTA files.

seppinho commented 5 years ago

Awesome. Thanks for your time. I'll close this issue and create a new release

seppinho / haplogrep-cmd

Fix MacOS issue for FASTA #18