commit: 0495ef801513cebc129bbcd392d955e86dea2fc9 Author: Martin Mokrejs <mmokrejs <AT> gmail <DOT> com> AuthorDate: Fri Jan 10 15:55:18 2020 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Fri Jan 10 15:57:51 2020 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0495ef80
sci-biology/NGSEPcore: cleanup the ebuild Package-Manager: Portage-2.3.84, Repoman-2.3.20 Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com> sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild | 23 ++++-- .../files/NGSEPcore_drop_utf8_chars.patch | 81 ++++++++++++++++++++++ .../files/NGSEPcore_fix_compilation.patch | 0 3 files changed, 97 insertions(+), 7 deletions(-) diff --git a/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild b/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild index 3f844bf16..24445eb0d 100644 --- a/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild +++ b/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -6,7 +6,8 @@ EAPI=7 inherit java-pkg-2 java-ant-2 DESCRIPTION="NGSEP (CNV and indel discovery)" -HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home"; +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 -> ${P}_Tutorial.txt @@ -17,21 +18,29 @@ SLOT="0" KEYWORDS="" IUSE="" -DEPEND="dev-java/htsjdk" +DEPEND=" + dev-java/htsjdk + dev-java/jsci-bin" RDEPEND="${DEPEND}" S="${WORKDIR}/${PN}_${PV}" +PATCHES=( "${FILESDIR}"/NGSEPcore_drop_utf8_chars.patch "${FILESDIR}"/NGSEPcore_fix_compilation.patch ) + src_prepare(){ - rm -f *.jar lib/htsjdk-1.129.jar || die + rm lib/htsjdk-1.129.jar || die + rm lib/jsci-core.jar || die default } src_compile(){ - make -j1 + emake -j1 } src_install(){ - java-pkg_dojar *.jar - dodoc "$DISTDIR}"/${P}_user_manual.pdf + java-pkg_dojar *.jar lib/*.jar + dodoc "${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 new file mode 100644 index 000000000..eb61747be --- /dev/null +++ b/sci-biology/NGSEPcore/files/NGSEPcore_drop_utf8_chars.patch @@ -0,0 +1,81 @@ +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]; diff --git a/sci-biology/NGSEPcore/files/NGSEPcore_fix_compilation.patch b/sci-biology/NGSEPcore/files/NGSEPcore_fix_compilation.patch new file mode 100644 index 000000000..e69de29bb
