From 1a264b0465fa3f8d9bcdf54f8df01d34c4d331e8 Mon Sep 17 00:00:00 2001 From: Andrew Ammerlaan Date: Sun, 10 Jan 2021 13:20:39 +0100 Subject: sci-biology/NGSEPcore: cleanup old Package-Manager: Portage-3.0.12, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan --- sci-biology/NGSEPcore/Manifest | 4 -- sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild | 46 ------------ .../files/NGSEPcore_drop_utf8_chars.patch | 81 ---------------------- 3 files changed, 131 deletions(-) delete mode 100644 sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild delete mode 100644 sci-biology/NGSEPcore/files/NGSEPcore_drop_utf8_chars.patch diff --git a/sci-biology/NGSEPcore/Manifest b/sci-biology/NGSEPcore/Manifest index 382f0b245..ef9c10376 100644 --- a/sci-biology/NGSEPcore/Manifest +++ b/sci-biology/NGSEPcore/Manifest @@ -1,8 +1,4 @@ -DIST NGSEPcore-3.3.1_QuickStart.txt 23701 BLAKE2B 0b3433a771e0121d4f38362f331e87c2597b7cbca4b63f26504807b2a84de2a3636e711c6bdee86c575810d6aff44996cb75663739ff5e184542f7f598f546be SHA512 d1eff40ca54a1e9bbdbda59511eb9e63ace2b001024df4119f0751b2e00dcf9219eb2eaa6407b2ccd1df71cf93d9b8e39088a59b7a6200fd966502c1b680eedd -DIST NGSEPcore-3.3.1_Tutorial.txt 17070 BLAKE2B 9af46173da8cb1b1746118d186da0794c0b9ad11d22109bdf96ed9df6d21df2495e8be3e5e75ef013a11922aa697ceb85ee280199eebbb2afadc180d3d86c0a6 SHA512 844138e0be2038d3f4656a55a8129819f08361cb6447a7fdb261b48c1f50e7aad1234079cbb01746bc7084d59c79589538883ecc0b0bb4bd8e07f61861ef80c1 -DIST NGSEPcore-3.3.1_UserManual.pdf 29071950 BLAKE2B fd16b44e3668f61013772965378bf4fa604b2467839810392d26a27e1a6e52f961cecc5097728bb67d10b68556bd406ec044b439c5ad1b3e614bfc7866afed43 SHA512 6d697f6945bdecb4f30712d3ae94615c85180a53750ba92357f81bf060b3f5bec3f6d1a03115c1a3791f5bf050b115cd09fd8729d885d4ec34b10024082ebb3c DIST NGSEPcore-4.0.3_QuickStart.txt 21313 BLAKE2B b897e25945d337f85f0c525ce93221440f6f1577ad1bde6fa3884a74e4366c2e17d7ef1d8603acba02ab21bdaa63fdfcc4d4251273f5e77b938e2318b13bdc19 SHA512 f5d528555c6115cdbddddbfc1c24939d1ca4776b16a5b848b4b9321cb882903d70eeef00c08e032dce4b6fe5551cea881570fc6f5975837e4f9eaf646de0c363 DIST NGSEPcore-4.0.3_Tutorial.txt 16946 BLAKE2B 0f397c6cd6d0f57f219d3f7963df32263347345a2e6231c7ccbc1a433d8de6350c6653e1a260182aa3ea5fa6a0bf88f47b659df236c78c8289914823b92f5778 SHA512 b110a0058962e1dc899183d3ca73cdfdd5f9b729561d35fe8d25e2fbeaa9b4647cbb768b047fa6df80b7926b1a34e4dc87c13979b66e6e6fe83f6f0c991fe6a8 DIST NGSEPcore-4.0.3_UserManual.pdf 10516580 BLAKE2B abe69a790413851181cbd210c8389fd302d917a1f6b4d425fbda2389808234290d38f31532933c0fc8505ca8b530f1b778bb58ce041783d184a85c2d5a716cd9 SHA512 cff9176f0a791b5b3e24fdba681bd71a3c39cb4593c01631e722e60e238140c80f292286454b7337a741a2f54fa6d5db30146c5bfdb02d5d5dd8d65322e3dc6e -DIST NGSEPcore_3.3.1.tar.gz 19818149 BLAKE2B 4233730649263cbca5a870b4eb9e041359b7b368b52465203d7b713ff924d3fbdfbe0fbbce0a11dd2d0fc5e190edeb3e89e176fd3f3ed2ecef7adf3853799f85 SHA512 f81b2e626d7b5c6367b58613e1cbf72dbdc782396bca8284501f5fbab2173290a91e4a89a2cbda1b316638254aea26a281e3a586773709577b14a889a07eca20 DIST NGSEPcore_4.0.3.tar.gz 11668258 BLAKE2B de8bdeee18c8647e93dcf8adf0751660618bb54208160a15de184680459122ef6fb62ea6c1ae8d3e81b6ada11ab4a1b2f18ee575b4fdc4543f3c30b9077ffc1d SHA512 12c73243cc026fc37424fc8b5112179288bf569c3e06208bfc768420874dc676a23f10a8fd067eb0120fa8f188556e2a91e22fc4e54a8cd3e7851a0b2e32e036 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 -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> poolConfiguration; -@@ -111,7 +110,7 @@ public void loadPools(String poolsDescriptor, int num_columnPools, int num_rowPo - while (line != null) { - - String[] indInfo = line.split(";"); -- ArrayList pools = new ArrayList(); -+ ArrayList 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]; -- cgit v1.2.3-65-gdbad