commit: d011d086f475015f3e6c6583e4cdc853f26862bb
Author: Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Tue Sep 22 11:11:36 2020 +0000
Commit: Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Tue Sep 22 11:11:36 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d011d086
sci-biology/wgs-assembler: drop package
present in ::gentoo
Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>
.../wgs-assembler-8.3_rc2-rename-jellyfish.patch | 69 --------------------
sci-biology/wgs-assembler/metadata.xml | 11 ----
.../wgs-assembler/wgs-assembler-8.3_rc2.ebuild | 74 ----------------------
3 files changed, 154 deletions(-)
diff --git
a/sci-biology/wgs-assembler/files/wgs-assembler-8.3_rc2-rename-jellyfish.patch
b/sci-biology/wgs-assembler/files/wgs-assembler-8.3_rc2-rename-jellyfish.patch
deleted file mode 100644
index d98ba7b52..000000000
---
a/sci-biology/wgs-assembler/files/wgs-assembler-8.3_rc2-rename-jellyfish.patch
+++ /dev/null
@@ -1,69 +0,0 @@
---- src/AS_PBR/PBcR.pl.ori 2015-05-20 23:28:27.000000000 +0200
-+++ src/AS_PBR/PBcR.pl 2018-04-21 16:24:14.189313208 +0200
-@@ -1259,12 +1259,12 @@
- setGlobal("mhap", undef);
- }
-
--if (! -e "$JELLYFISH/jellyfish") {
-- if (-e "$CA/jellyfish") {
-+if (! -e "$JELLYFISH/jellyfish2") {
-+ if (-e "$CA/jellyfish2") {
- $JELLYFISH = $CA;
- } else {
- # try to use path
-- my $amosPath = `which jellyfish`;
-+ my $amosPath = `which jellyfish2`;
- chomp $amosPath;
- my @t = split '/', "$amosPath";
- pop @t; # blasr
-@@ -1698,7 +1698,7 @@
- }
-
- my $ignore = "";
--if (!defined(getGlobal("bowtie")) && $cutoffSpecified == 0 &&
!(defined(getGlobal("mhap")) && -e "$JELLYFISH/jellyfish")) {
-+if (!defined(getGlobal("bowtie")) && $cutoffSpecified == 0 &&
!(defined(getGlobal("mhap")) && -e "$JELLYFISH/jellyfish2")) {
- # run correction up thorough meryl
- if (! -e "$wrk/temp$libraryname/0-mercounts/$asm.nmers.ovl.fasta") {
- $cmd = "$CA/runCA ";
-@@ -1740,20 +1740,20 @@
- $inFile = `ls $wrk/*.$inMer.ignore |wc -l |awk '{print \$1}'`;
- }
- chomp $inFile;
--if ($inFile == 0 && !-e "$wrk/temp$libraryname/$asm.ignore" && -e
"$JELLYFISH/jellyfish" && defined(getGlobal("mhap"))) {
-+if ($inFile == 0 && !-e "$wrk/temp$libraryname/$asm.ignore" && -e
"$JELLYFISH/jellyfish2" && defined(getGlobal("mhap"))) {
- my $f = makeAbsolute($fastqFile);
- if ($f =~ /\.bz2$/i || $f =~ /\.zip$/i || $f =~ /\.gz$/i) {
- die "Input fastq file $f is compressed. This is currently not
supported, please uncompress the file and try again.";
- }
-- $cmd = "$JELLYFISH/jellyfish count ";
-+ $cmd = "$JELLYFISH/jellyfish2 count ";
- $cmd .= " -m " . getGlobal("merSize") . " -s 120000000 -t " .
getGlobal("merylThreads") . " -o $wrk/temp$libraryname/$asm.mers " .
makeAbsolute($fastqFile);
- runCommand("$wrk/temp$libraryname", $cmd);
- if ( -e "$wrk/temp$libraryname/$asm.mers_0") {
-- $cmd = "$JELLYFISH/jellyfish merge -s 120000000 -o
$wrk/temp$libraryname/$asm.mers $wrk/temp$libraryname/$asm.mers_*";
-+ $cmd = "$JELLYFISH/jellyfish2 merge -s 120000000 -o
$wrk/temp$libraryname/$asm.mers $wrk/temp$libraryname/$asm.mers_*";
- runCommand("$wrk/temp$libraryname", $cmd);
- }
-
-- $cmd = "$JELLYFISH/jellyfish histo -t " . getGlobal("merylThreads") . "
-f $wrk/temp$libraryname/$asm.mers > $wrk/temp$libraryname/$asm.hist";
-+ $cmd = "$JELLYFISH/jellyfish2 histo -t " . getGlobal("merylThreads") . "
-f $wrk/temp$libraryname/$asm.mers > $wrk/temp$libraryname/$asm.hist";
- runCommand("$wrk/temp$libraryname", $cmd);
- my $total = 0;
- my $runningSum = 0;
-@@ -1763,7 +1763,7 @@
- chomp $cut;
- $cut++;
-
-- $cmd = "$JELLYFISH/jellyfish dump -c -t -L $cut
$wrk/temp$libraryname/$asm.mers |awk -v TOTAL=$sum
'{printf(\"\%s\\t\%0.10f\\t\%d\\t\%d\\n\", \$1, \$2/TOTAL, \$2, TOTAL)}' |sort
-T . -rnk2> $wrk/temp$libraryname/$asm.ignore";
-+ $cmd = "$JELLYFISH/jellyfish2 dump -c -t -L $cut
$wrk/temp$libraryname/$asm.mers |awk -v TOTAL=$sum
'{printf(\"\%s\\t\%0.10f\\t\%d\\t\%d\\n\", \$1, \$2/TOTAL, \$2, TOTAL)}' |sort
-T . -rnk2> $wrk/temp$libraryname/$asm.ignore";
- runCommand("$wrk/temp$libraryname", $cmd);
- runCommand("$wrk/temp$libraryname", "rm $wrk/temp$libraryname/$asm.mers*");
- } elsif (!-e "$wrk/temp$libraryname/$asm.ignore" &&
defined(getGlobal("mhap"))) {
---- src/AS_PBR/Makefile.ori 2015-02-20 23:54:49.000000000 +0100
-+++ src/AS_PBR/Makefile 2018-04-21 16:24:50.730272421 +0200
-@@ -222,4 +222,4 @@
- @echo "!!!!!!! WARNING pbutgcns not supplied for $(LOCAL_NAME).
Please add to your PATH if installed."
-
- jellyfish_missing:
-- @echo "!!!!!!! WARNING jellyfish not supplied for $(LOCAL_NAME).
Please add to your PATH if installed."
-+ @echo "!!!!!!! WARNING jellyfish2 not supplied for $(LOCAL_NAME).
Please add to your PATH if installed."
diff --git a/sci-biology/wgs-assembler/metadata.xml
b/sci-biology/wgs-assembler/metadata.xml
deleted file mode 100644
index 530c31d3e..000000000
--- a/sci-biology/wgs-assembler/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biol...@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">wgs-assembler</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild
b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild
deleted file mode 100644
index ce6d289c4..000000000
--- a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils python-single-r1 toolchain-funcs
-
-MY_PV="${PV/_}" # convert from _rc2 to rc2
-
-DESCRIPTION="De novo whole-genome shotgun DNA sequence OLC assembler"
-HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/";
-SRC_URI="http://sourceforge.net/projects/${PN}/files/${PN}/wgs-8.3/wgs-${MY_PV}.tar.bz2";
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="static-libs"
-
-DEPEND="
- x11-libs/libXt
- !x11-terms/terminator"
-RDEPEND="${DEPEND}
- app-shells/tcsh
- dev-perl/Log-Log4perl
- sci-biology/jellyfish:2"
-
-S="${WORKDIR}/wgs-${MY_PV}"
-
-src_prepare() {
- epatch "${FILESDIR}"/${P}-rename-jellyfish.patch
- tc-export CC CXX
-}
-
-src_configure() {
- cd "${S}/kmer" || die
- ./configure.sh || die
-}
-
-src_compile() {
- # not really an install target
- emake -C kmer -j1 install
- emake -C src -j1 SITE_NAME=LOCAL
-}
-
-src_install() {
- OSTYPE=$(uname)
- MACHTYPE=$(uname -m)
- MACHTYPE=${MACHTYPE/x86_64/amd64}
- MY_S="${OSTYPE}-${MACHTYPE}"
- sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) ||
die
-
- sed -i '/sub getBinDirectory ()/ a return "/usr/bin";'
${MY_S}/bin/runCA* || die
- sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";'
${MY_S}/bin/runCA* || die
- sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name
'*.p*') || die
-
- dobin kmer/"${MY_S}"/bin/*
- insinto /usr/$(get_libdir)/"${PN}"
- use static-libs && doins kmer/"${MY_S}"/lib/*
-
- insinto /usr/include/"${PN}"
- doins kmer/"${MY_S}"/include/*
-
- insinto /usr/share/${PN}/lib
- doins -r "${MY_S}"/bin/TIGR
- rm -rf "${MY_S}"/bin/TIGR || die
- dobin "${MY_S}"/bin/*
- use static-libs && dolib.a ${MY_S}/lib/*
- dodoc README
-
- # drop bundled jellyfish-2.0.0
- rm "${ED}"/usr/bin/jellyfish || die
-}
