SnpEff PKGBUILD rewritten to compile from source

[kbipinkumar]

Involved packages

• snpeff and snpsift

Involved issue

Close #85

Details

• Tested in the local machine (largest 16G RAM) and it is passed without any issue
• Fix the Packages
  • PKGBUILD
  • lilac.yaml
  • lilac.py
• Would like to continue to work with us

Additional Note

i have closed the previous pull request as it was too cumbersome to squash all commits. this version of PKGBUILD does compile from source successfully. i have also tested the resulting binaries for functionality and those seem to work as expected (similar to existing package in AUR repo).

in line with AUR repo package i have also added binary wrappers for jar executables so that users can call up the jar files using snpeff and snpsift instead of typing the whole java -jar '/usr/share/java/snpEff/snpEff.jar' everytime they want to run the tool.

[hubutui]

Cool, could you update lilac.yaml to use LF line terminators?
Then you could:

git add lilac.yaml
git commit --amend
git push -f

without creating another commit.

[hubutui]

You change the line terminators according to this link. Or use some editor, like vs code.

[kbipinkumar]

Cool, could you update lilac.yaml to use LF line terminators? Then you could:

git add lilac.yaml
git commit --amend
git push -f

without creating another commit.

i am using vscode. anyways i have double checked for using LF line terminators. please check now

[hubutui]

install the MIT license file to /usr/share/licenses/$pkgname, since MIT is not listed in licenses.

[kbipinkumar]

you mean copying license file from source folder like this

install -Dm644 ${srcdir}/$_pkgname-$pkgver/LICENSE.md "${pkgdir}"/usr/share/licenses/$pkgname/LICENSE

should be changed to

install -Dm644 ${srcdir}/$_pkgname-$pkgver/LICENSE.md "${pkgdir}"/usr/share/licenses/$pkgname/MIT

?