[gentoo-commits] proj/sci:master commit in: sci-biology/NGSEPcore/, sci-biology/NGSEPcore/files/

[Martin Mokrejs]

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