I wanted to use gatk but it turned out the version 2.4 is too old and commandline arguments changed meanwhile. Current version is 3.3. Second, the gatk-9999.ebuild does not work because upstream at about version 3.1 or 3.2 moved from ant to maven. Three, there are two repositories for gatk and I propose gatk and gatk-protected packages are introduced in portage tree. The latter should use a different REPO: https://github.com/broadgsa/gatk-protected/ (it has some extra apps for non-commercial use only). See https://www.broadinstitute.org/gatk/download/ .
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=07bea2652d449ecfd5bae8ca97e28e66272d902d commit 07bea2652d449ecfd5bae8ca97e28e66272d902d Author: David Seifert <soap@gentoo.org> AuthorDate: 2021-04-05 16:48:21 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2021-04-05 16:48:21 +0000 package.mask: last-rite sci-biology/gatk Bug: https://bugs.gentoo.org/418625 Bug: https://bugs.gentoo.org/431644 Bug: https://bugs.gentoo.org/515816 Bug: https://bugs.gentoo.org/542940 Bug: https://bugs.gentoo.org/574632 Bug: https://bugs.gentoo.org/780396 Signed-off-by: David Seifert <soap@gentoo.org> profiles/package.mask | 6 ++++++ 1 file changed, 6 insertions(+)
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=92cb6e9daf7c9865bfc003d4968b56501d5d00c6 commit 92cb6e9daf7c9865bfc003d4968b56501d5d00c6 Author: Jakov Smolic <jakov.smolic@sartura.hr> AuthorDate: 2021-05-04 21:57:13 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2021-05-04 22:29:36 +0000 sci-biology/gatk: Remove last-rited pkg Closes: https://bugs.gentoo.org/780396 Closes: https://bugs.gentoo.org/574632 Closes: https://bugs.gentoo.org/542940 Closes: https://bugs.gentoo.org/515816 Closes: https://bugs.gentoo.org/431644 Closes: https://bugs.gentoo.org/418625 Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr> Closes: https://github.com/gentoo/gentoo/pull/20667 Signed-off-by: Sam James <sam@gentoo.org> profiles/package.mask | 6 ------ sci-biology/gatk/Manifest | 1 - sci-biology/gatk/gatk-2.4.ebuild | 32 -------------------------------- sci-biology/gatk/metadata.xml | 11 ----------- 4 files changed, 50 deletions(-)
