commit: 1a264b0465fa3f8d9bcdf54f8df01d34c4d331e8 Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Sun Jan 10 12:20:39 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Sun Jan 10 12:20:39 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1a264b04
sci-biology/NGSEPcore: cleanup old Package-Manager: Portage-3.0.12, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild | 46 ------------ .../files/NGSEPcore_drop_utf8_chars.patch | 81 ---------------------- 2 files changed, 127 deletions(-) diff --git a/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild b/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild deleted file mode 100644 index 0addb08b8..000000000 --- a/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild +++ /dev/null @@ -1,46 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit java-pkg-2 java-ant-2 - -DESCRIPTION="NGSEP (CNV and indel discovery)" -HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home - https://github.com/NGSEP/NGSEPcore"; -SRC_URI="https://sourceforge.net/projects/ngsep/files/SourceCode/NGSEPcore_${PV}.tar.gz - https://sourceforge.net/projects/ngsep/files/training/UserManualNGSEP_V330.pdf -> ${P}_UserManual.pdf - https://sourceforge.net/projects/ngsep/files/training/Tutorial.txt -> ${P}_Tutorial.txt - https://sourceforge.net/projects/ngsep/files/training/QuickStart.txt -> ${P}_QuickStart.txt" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="" -IUSE="" - -DEPEND=" - dev-java/htsjdk - dev-java/jsci-bin" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${PN}_${PV}" - -PATCHES=( "${FILESDIR}"/NGSEPcore_drop_utf8_chars.patch ) - -src_prepare(){ - rm lib/htsjdk-1.129.jar || die - rm lib/jsci-core.jar || die - default -} - -src_compile(){ - emake -j1 -} - -src_install(){ - java-pkg_dojar *.jar lib/*.jar - dodoc "${DISTDIR}"/${P}_UserManual.pdf \ - "${DISTDIR}"/${P}_Tutorial.txt \ - "${DISTDIR}"/${P}_QuickStart.txt \ - README.txt -} diff --git a/sci-biology/NGSEPcore/files/NGSEPcore_drop_utf8_chars.patch b/sci-biology/NGSEPcore/files/NGSEPcore_drop_utf8_chars.patch deleted file mode 100644 index eb61747be..000000000 --- a/sci-biology/NGSEPcore/files/NGSEPcore_drop_utf8_chars.patch +++ /dev/null @@ -1,81 +0,0 @@ -From 5161e22e7730e2637376402718ed7048f838054a Mon Sep 17 00:00:00 2001 -From: jorge <jorge@jorge-0420006391> -Date: Thu, 28 Mar 2019 16:24:24 -0500 -Subject: [PATCH] Fixed encoding and manual compilation issues - ---- - makefile | 2 +- - src/ngsep/discovery/TillingPoolsIndividualGenotyper.java | 5 ++--- - src/ngsep/simulation/TillingPopulationSimulator.java | 2 +- - src/ngsep/variants/CalledSNV.java | 2 +- - 4 files changed, 5 insertions(+), 6 deletions(-) - -diff --git a/makefile b/makefile -index 517895d..0532725 100755 ---- a/makefile -+++ b/makefile -@@ -11,7 +11,7 @@ compile: - copy: - cp -f src/ngsep/transcriptome/ProteinTranslatorDefaultBundle.properties bin/ngsep/transcriptome/ - cp -f src/ngsep/main/CommandsDescriptor.xml bin/ngsep/main/ -- cp -f src/ngsep/assembly/GenomesAlignerLinearVisualizer.js bin/ngsep/assembly/ -+ cp -f src/ngsep/genome/GenomesAlignerLinearVisualizer.js bin/ngsep/genome/ - - jar: - mkdir dist -diff --git a/src/ngsep/discovery/TillingPoolsIndividualGenotyper.java b/src/ngsep/discovery/TillingPoolsIndividualGenotyper.java -index c8c3d42..2e7a7bf 100644 ---- a/src/ngsep/discovery/TillingPoolsIndividualGenotyper.java -+++ b/src/ngsep/discovery/TillingPoolsIndividualGenotyper.java -@@ -19,7 +19,6 @@ - import ngsep.main.CommandsDescriptor; - import ngsep.main.ProgressNotifier; - import ngsep.sequences.QualifiedSequenceList; --import ngsep.simulation.TillingPopulationSimulator; - import ngsep.variants.CalledGenomicVariant; - import ngsep.variants.CalledGenomicVariantImpl; - import ngsep.variants.GenomicVariant; -@@ -31,7 +30,7 @@ - - public class TillingPoolsIndividualGenotyper { - -- private Logger log = Logger.getLogger(TillingPopulationSimulator.class.getName()); -+ private Logger log = Logger.getLogger(TillingPoolsIndividualGenotyper.class.getName()); - private ProgressNotifier progressNotifier=null; - - private static HashMap<String,ArrayList<Integer>> poolConfiguration; -@@ -111,7 +110,7 @@ public void loadPools(String poolsDescriptor, int num_columnPools, int num_rowPo - while (line != null) { - - String[] indInfo = line.split(";"); -- ArrayList<Integer> pools = new ArrayList(); -+ ArrayList<Integer> pools = new ArrayList<>(); - pools.add(Integer.parseInt(indInfo[1])); - pools.add(Integer.parseInt(indInfo[2])); - pools.add(Integer.parseInt(indInfo[3])); -diff --git a/src/ngsep/simulation/TillingPopulationSimulator.java b/src/ngsep/simulation/TillingPopulationSimulator.java -index ea44db2..37f9d3b 100644 ---- a/src/ngsep/simulation/TillingPopulationSimulator.java -+++ b/src/ngsep/simulation/TillingPopulationSimulator.java -@@ -56,7 +56,7 @@ - /** - * - * @author Juanita -- * @author Juan Sebastián Andrade -+ * @author Juan Sebastian Andrade - * - */ - public class TillingPopulationSimulator { -diff --git a/src/ngsep/variants/CalledSNV.java b/src/ngsep/variants/CalledSNV.java -index a40c8ac..773abe7 100755 ---- a/src/ngsep/variants/CalledSNV.java -+++ b/src/ngsep/variants/CalledSNV.java -@@ -241,7 +241,7 @@ public void setGenotypeQuality(short genotypeQuality) { - /** - * Changes the number of As, Cs, Gs and Ts observed in the sample - * @param allCounts Array of length 4 with the number of times that each allele appears. -- * The order must be the cu¡ount for A, the count for C, the count for G, and the count for T -+ * The order must be the count for A, the count for C, the count for G, and the count for T - */ - public void setAllBaseCounts(int [] allCounts) { - this.countA = allCounts[0];
