sci-biology/blue: remove pack, upstream gone

Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>

5 files changed, 0 insertions, 93 deletions

diff --git a/profiles/package.mask b/profiles/package.mask
index bfd691718..6f2346e7b 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -43,4 +43,3 @@ sci-biology/argo-bin
 sci-biology/bambino
 sci-biology/BBmap
 sci-biology/beagle
-sci-biology/blue
diff --git a/sci-biology/blue/Manifest b/sci-biology/blue/Manifest
deleted file mode 100644
index 9130b6b5b..000000000
--- a/sci-biology/blue/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-DIST blue-1.1.2-Changes_for_Blue_1.1.2.pdf 310372 BLAKE2B 4c3da1739a89d6b8b8b3b15d3244c65795269c6696d87c9c3e9ff32aa7e96de8cc44e1b929a3b03669d70dc78a476dfc067f903814b013c8dbf7d58e0cef549c SHA512 1f6d595018e880a9d10197816881fa88bbc1da9613fb83d0c3b77fe3ea22e614a9fc9783abfa7f649c242a4966a6929c53fcd1b845f98280d50c491b4cff8f73
-DIST blue-1.1.2-Correcting_reads_with_Blue.pdf 560129 BLAKE2B 19b58a7276ed0d2ae47caade89e4de94e9c085a7e3f5aa824d643e507e447393d5f56e89deeccf5e920d39f604adab059b6b7a74f9a9c792673b2b2b31289210 SHA512 1341a7f3d4c77b3a3f8d66f57b4cc976930bf7d28219d77a3a91efde0bc76f08bf0159c98df3227a2484dc0fe7d40904dbbde74dc03b6c110649285314a07585
-DIST blue-1.1.2.tar.gz 658544 SHA256 c038fa9fd76330cb70059cd47979327708368e2d6b6d7edae00825ba39dc23bd SHA512 933b2a8bb1e1f3fed241cff2eac9566d49d77c3f97b2f22f4a8194f3cdf25c09ae474b4d681ff65914d695598579fded6433f6a47ad06b78879c36d58402ea4b WHIRLPOOL 32c89ae39cfadab9beae038afd530cf85d8c8775a84bd5e2c29a2e67246d9b09d5c872492c1836dfab6fe20e9f59a1b0aaddc5dc051393030ccff39bb08fec8e
-DIST blue-1.1.3-Changes_for_Blue_1.1.3.pdf 310372 BLAKE2B 4c3da1739a89d6b8b8b3b15d3244c65795269c6696d87c9c3e9ff32aa7e96de8cc44e1b929a3b03669d70dc78a476dfc067f903814b013c8dbf7d58e0cef549c SHA512 1f6d595018e880a9d10197816881fa88bbc1da9613fb83d0c3b77fe3ea22e614a9fc9783abfa7f649c242a4966a6929c53fcd1b845f98280d50c491b4cff8f73
-DIST blue-1.1.3-Correcting_reads_with_Blue.pdf 560129 BLAKE2B 19b58a7276ed0d2ae47caade89e4de94e9c085a7e3f5aa824d643e507e447393d5f56e89deeccf5e920d39f604adab059b6b7a74f9a9c792673b2b2b31289210 SHA512 1341a7f3d4c77b3a3f8d66f57b4cc976930bf7d28219d77a3a91efde0bc76f08bf0159c98df3227a2484dc0fe7d40904dbbde74dc03b6c110649285314a07585
-DIST blue-1.1.3.tar.gz 717341 BLAKE2B 0be8bb8b8e30b7185cc01c8b9affe39521216cd3d487ad2952af28271d955eadd14f74cdaeb3ce47324845defadc1091fc230923ba30138a990003dff8f82105 SHA512 fc51965a063ced80304b3e59eb538742f6f4a2970d02cecc346aa8b15e961a242b6ce6cc3a847c8e4f478bee997ed5794f304d201554398130c1a16bceb84c30
diff --git a/sci-biology/blue/blue-1.1.2.ebuild b/sci-biology/blue/blue-1.1.2.ebuild
deleted file mode 100644
index 13c88494e..000000000
--- a/sci-biology/blue/blue-1.1.2.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Error corrector for Illummina and Roche/454, inculding insertions and deletions"
-HOMEPAGE="http://www.bioinformatics.csiro.au/blue"
-SRC_URI="
-	http://www.bioinformatics.csiro.au/public/files/Linux-${PV}.tar.gz -> ${P}.tar.gz
-	http://www.bioinformatics.csiro.au/public/files/Correcting_reads_with_Blue.pdf -> ${P}-Correcting_reads_with_Blue.pdf
-	http://www.bioinformatics.csiro.au/public/files/Changes_for_Blue_1.1.3.pdf -> ${P}-Changes_for_Blue_${PV}.pdf"
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="dev-lang/mono"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/Linux
-
-src_compile(){
-	Blue/compile.sh || die
-	Tessel/compile.sh || die
-	GenerateMerPairs/compile.sh || die
-}
-
-src_install(){
-	dobin Tessel.exe GenerateMerPairs.exe Blue.exe
-	# one could install also the *.exe.so files for speedup into /usr/bin/
-
-	# The -hp option sets a flag that is checked when Blue is scanning along a read trying to find errors that could be corrected. There are a number of tests done at every base position, all based on depth of coverage. These tests will pick up random indel errors, but indels are so common at the end of homopolymer runs in 454 and IonTorrent data that multiple hp run lengths all look to be OK. For example, if our genome had AAAAAA then with Illumina data this is what we'd see almost all the time, with very rare indels at the end of the hp run resulting in runs of 5 or 7 As. With 454-like data, we'd probably get 5 As as frequently as 6 As so depth of coverage would say that neither of them are errors. The -hp flag looks out for the end of hp runs and forces an attempt at correction at that point. If the read wasn't in error, then no correction will be made.
-
-	# In general Blue will correct Ns - if a correct replacement can be found. The only time it doesn't do this is if there are too many consecutive Ns - as the process of finding likely replacements is combinatoric and the cost goes up exponentially with the number of consecutive Ns. In these cases, the read is abandoned and passed through uncorrected. Can you give an example of a read that you would like to see corrected differently?
-}
-
-# it's author uses 'mono-sgen /usr/bin/Blue.exe' to use the alternative garbage collector
diff --git a/sci-biology/blue/blue-1.1.3.ebuild b/sci-biology/blue/blue-1.1.3.ebuild
deleted file mode 100644
index cee0e8065..000000000
--- a/sci-biology/blue/blue-1.1.3.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Error corrector for Illummina and Roche/454, including insertions and deletions"
-HOMEPAGE="http://www.bioinformatics.csiro.au/blue"
-SRC_URI="
-	http://www.bioinformatics.csiro.au/public/files/Linux-${PV}.tar.gz -> ${P}.tar.gz
-	http://www.bioinformatics.csiro.au/public/files/Correcting_reads_with_Blue.pdf -> ${P}-Correcting_reads_with_Blue.pdf
-	http://www.bioinformatics.csiro.au/public/files/Changes_for_Blue_1.1.3.pdf -> ${P}-Changes_for_Blue_${PV}.pdf"
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="dev-lang/mono"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/Linux
-
-src_compile(){
-	Blue/compile.sh || die
-	Tessel/compile.sh || die
-	GenerateMerPairs/compile.sh || die
-}
-
-src_install(){
-	dobin Tessel.exe GenerateMerPairs.exe Blue.exe
-	# one could install also the *.exe.so files for speedup into /usr/bin/
-
-	# The -hp option sets a flag that is checked when Blue is scanning along a read trying to find errors that could be corrected. There are a number of tests done at every base position, all based on depth of coverage. These tests will pick up random indel errors, but indels are so common at the end of homopolymer runs in 454 and IonTorrent data that multiple hp run lengths all look to be OK. For example, if our genome had AAAAAA then with Illumina data this is what we'd see almost all the time, with very rare indels at the end of the hp run resulting in runs of 5 or 7 As. With 454-like data, we'd probably get 5 As as frequently as 6 As so depth of coverage would say that neither of them are errors. The -hp flag looks out for the end of hp runs and forces an attempt at correction at that point. If the read wasn't in error, then no correction will be made.
-
-	# In general Blue will correct Ns - if a correct replacement can be found. The only time it doesn't do this is if there are too many consecutive Ns - as the process of finding likely replacements is combinatoric and the cost goes up exponentially with the number of consecutive Ns. In these cases, the read is abandoned and passed through uncorrected. Can you give an example of a read that you would like to see corrected differently?
-}
-
-# it's author uses 'mono-sgen /usr/bin/Blue.exe' to use the alternative garbage collector
diff --git a/sci-biology/blue/metadata.xml b/sci-biology/blue/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/blue/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>