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dev-java/htsjdk

Java API for high-throughput sequencing data (HTS) formats

Screenshots

  • htsjdk-9999
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    Overlay: science (layman)
  • htsjdk-2.19.0
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  • htsjdk-2.3.0
    ~amd64 ~x86
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ChangeLog

commit a12a2d7f3f65eb66e44d3fc907f4b24e85ef201a
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Mon Mar 25 12:50:28 2019 +0100

dev-java/htsjdk: drop old 2.1.0 version

commit 6d3f8d736bf1a9653f516c3e959a97948c61f843
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Mon Mar 25 12:08:21 2019 +0100

dev-java/htsjdk: 2.3.0 which was the last using Apache ant

Bump to EAPI7

Building does not work since sandbox has now no network access.

Downloading https://services.gradle.org/distributions/gradle-5.2.1-bin.zip

Exception in thread "main" java.net.SocketException: Network
is unreachable (connect failed)

htsjdk calls some `gradlew` wrapper so the recent ebuilds
need more work to use dev-java/gradle-bin package.

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

commit aef6b7cc29677f3720adb39bebdc124ab6f64aa7
Author: Justin Lecher <jlec@gentoo.org>
Date: Sat Oct 27 20:45:04 2018 +0100

Sort keywords

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 3072d10e6c4f21185d53e4728d0fa0fad58537e7
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Dec 10 22:20:38 2017 +0000

Update Manifests to new hashes

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit bce61aa3e4fe85fe411df858eb30ebe72a3a8f88
Author: Justin Lecher <jlec@gentoo.org>
Date: Sat Nov 18 20:39:44 2017 +0000

Consistently ident with tabs

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 3199ec7737e923dc19479e5de7b31bb583071931
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Apr 30 11:12:48 2017 +0100

Cleanup remote IDs

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 61094665a0622c77dea66a04ec74b5e4fd71bb46
Author: Justin Lecher <jlec@gentoo.org>
Date: Sat Apr 29 10:50:07 2017 +0100

Update remote ids

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit f69e73182fc7cdc6c600a72fceb88ae1626db25d
Author: Justin Lecher <jlec@gentoo.org>
Date: Sat Feb 25 16:50:59 2017 +0000

Drop leftover from CVS in HEADER

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit d656b6d1ca11a70c8c47fb326e16bd3564006518
Author: Justin Lecher <jlec@gentoo.org>
Date: Fri Feb 3 17:05:17 2017 +0000

Drop quoting form EAPI

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 5a564879dd68bd1fba0d1a3229bbe76d3fbdc124
Author: Justin Lecher <jlec@gentoo.org>
Date: Fri Feb 3 16:29:09 2017 +0000

Drop "." from DESCRIPTION

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 6e6616f8521d20074bbca6522e2a5570718d5736
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Jan 12 00:26:50 2017 +0100

dev-java/htsjdk: add a live ebuild, add a note

Not sure if current build system still creates $HOME/.git but from
reading github Issues it seem it is still needed: users are even asked
to run 'git clone' to work around the issue when gradle fails to do that.

Package-Manager: Portage-2.3.3, Repoman-2.3.1

commit d0811884dba63b23093aa0cf580171e4ba51a36f
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Tue Jul 12 23:42:07 2016 +0200

dev-java/htsjdk: make gradle use relocated $HOME/.gradle/ inside sanbox paths

This dies later because .git/ directory does not exist (probably $HOME/.git/ was
looked up).

Package-Manager: portage-2.2.28

commit 691de03a081a82665985b69eb879c6be3ecd7f7e
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Tue Jul 12 18:31:39 2016 +0200

dev-java/htsjdk: added 2.1.0 version needed=bundled so far in cramtools-3.0

Package-Manager: portage-2.2.28

commit 9ce6536356df2dffa9672161ae47b8de609c7682
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Tue Jul 12 18:28:58 2016 +0200

dev-java/htsjdk: re-added back 2.2.2 version due to picard-2

Package-Manager: portage-2.2.28

commit 091fd4549ad2edd83419e0f645cc902a2f71ae23
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Tue Jul 12 17:53:53 2016 +0200

dev-java/htsjdk: version bump, moved from ant to gradle, SANDBOX VIOLATION

Package-Manager: portage-2.2.28

commit f14032b578bf9d6b6bd840a05ad00f47867207f8
Author: Johann Schmitz <ercpe@gentoo.org>
Date: Sun Apr 24 08:13:12 2016 +0200

dev-java/htsjdk: Fixed error with EAPI=6

Package-Manager: portage-2.2.26

commit c3ab7823c9462b681b308ab69346acc77cea683f
Author: Johann Schmitz <ercpe@gentoo.org>
Date: Sun Apr 24 08:08:19 2016 +0200

dev-java/htsjdk: New ebuild (dependency of picard-2)

Package-Manager: portage-2.2.26