From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 63030138334 for ; Mon, 25 Mar 2019 11:56:40 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 63B7EE0907; Mon, 25 Mar 2019 11:56:39 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 31D8DE0907 for ; Mon, 25 Mar 2019 11:56:38 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 62DA4335D48 for ; Mon, 25 Mar 2019 11:56:37 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 0BB42326 for ; Mon, 25 Mar 2019 11:56:36 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1553514988.b7426d8f1df55eb09a50815dc95882363bb44895.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/tablet/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/tablet/tablet-1.17.08.17.ebuild sci-biology/tablet/tablet-9999.ebuild X-VCS-Directories: sci-biology/tablet/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: b7426d8f1df55eb09a50815dc95882363bb44895 X-VCS-Branch: master Date: Mon, 25 Mar 2019 11:56:36 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: af4addd9-733b-4eb1-baae-5f9c4992585e X-Archives-Hash: 3097e222c2a5f351c31df3305fc42824 commit: b7426d8f1df55eb09a50815dc95882363bb44895 Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Mon Mar 25 11:56:28 2019 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Mon Mar 25 11:56:28 2019 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b7426d8f sci-biology/tablet: still installs a mix of our and bundled jars We have only dev-java/htdjdk-2.3.0 in the tree as newer versions use gradle. The tablet-1.17.08.17 lacks the lib/htsjdk-2.0.11.jar so we cannot install it. Use sci-biology/tablet-bin instead. https://github.com/cropgeeks/tablet/issues/6 Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs fold.natur.cuni.cz> sci-biology/tablet/tablet-1.17.08.17.ebuild | 29 +++++++++++++++++++++-------- sci-biology/tablet/tablet-9999.ebuild | 17 ++++++++++++++--- 2 files changed, 35 insertions(+), 11 deletions(-) diff --git a/sci-biology/tablet/tablet-1.17.08.17.ebuild b/sci-biology/tablet/tablet-1.17.08.17.ebuild index 08a272961..158caba78 100644 --- a/sci-biology/tablet/tablet-1.17.08.17.ebuild +++ b/sci-biology/tablet/tablet-1.17.08.17.ebuild @@ -16,7 +16,7 @@ if [ "$PV" == "9999" ]; then KEYWORDS="" else SRC_URI="https://github.com/cropgeeks/tablet/archive/${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="" + KEYWORDS="" # lacks lib/htsjdk-2.0.11.jar fi LICENSE="BSD-2" @@ -29,11 +29,17 @@ DEPEND="${PYTHON_DEPS} >=virtual/jdk-1.8:*" RDEPEND="${PYTHON_DEPS} >=virtual/jre-1.8:* - >=dev-java/commons-compress-1.4.1" -# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, htsjdk-2.11.0.jar -# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not sci-biology/samtools either - -S="${WORKDIR}" + >=dev-java/commons-compress-1.4.1 + dev-java/htsjdk" +# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar +# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 +# samtools-linux64.jar is not sci-biology/samtools but 0.1.12a (r862) +# needs htsjdk-2.0.11.jar + +src_compile(){ + mkdir -p classes || die + ant jar || die +} src_install() { java-pkg_dojar lib/tablet.jar @@ -41,8 +47,15 @@ src_install() { java-pkg_dojar lib/tablet-resources.jar java-pkg_dojar lib/flamingo.jar java-pkg_dojar lib/scri-commons.jar - java-pkg_dojar lib/samtools*.jar - java-pkg_dojar lib/htsjdk*.jar # is htsjdk-2.11.0 in tablet-1.17.08.17 + java-pkg_dojar lib/samtools-all.jar + if [ "${ABI}" == "amd64" ]; then + java-pkg_dojar lib/samtools-linux64.jar + fi + if [ "${ABI}" == "x86" ]; then + java-pkg_dojar lib/samtools-linux32.jar + fi + # is the tar.gz tarball missing by mistake lib/htsjdk*.jar ? + # java-pkg_dojar lib/htsjdk*.jar # is htsjdk-2.11.0 in tablet-1.17.08.17 java-pkg_dojar lib/sqlite-jdbc*.jar echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet diff --git a/sci-biology/tablet/tablet-9999.ebuild b/sci-biology/tablet/tablet-9999.ebuild index 01759c6b4..5cebde785 100644 --- a/sci-biology/tablet/tablet-9999.ebuild +++ b/sci-biology/tablet/tablet-9999.ebuild @@ -31,9 +31,14 @@ RDEPEND="${PYTHON_DEPS} >=virtual/jre-1.8:* >=dev-java/commons-compress-1.4.1" # contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, htsjdk-2.11.0.jar -# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not sci-biology/samtools +# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 +# samtools-linux64.jar is not sci-biology/samtools but 0.1.12a (r862) #S="${WORKDIR}" +src_compile(){ + mkdir -p classes || die + ant jar || die +} src_install() { java-pkg_dojar lib/tablet.jar @@ -41,8 +46,14 @@ src_install() { java-pkg_dojar lib/tablet-resources.jar java-pkg_dojar lib/flamingo.jar java-pkg_dojar lib/scri-commons.jar - java-pkg_dojar lib/samtools*.jar - java-pkg_dojar lib/htsjdk*.jar + java-pkg_dojar lib/samtools-all.jar + if [ "${ABI}" == "amd64" ]; then + java-pkg_dojar lib/samtools-linux64.jar + fi + if [ "${ABI}" == "x86" ]; then + java-pkg_dojar lib/samtools-linux32.jar + fi + java-pkg_dojar lib/htsjdk*.jar # is htsjdk-2.11.0 in tablet-1.17.08.17 java-pkg_dojar lib/sqlite-jdbc*.jar echo "PATH=${EPREFIX}/usr/share/${PN}" > 99Tablet