reinit the tree, so we can have metadata

6 files changed, 274 insertions, 0 deletions

diff --git a/sci-biology/last/Manifest b/sci-biology/last/Manifest
new file mode 100644
index 000000000000..ab42266146cf
--- /dev/null
+++ b/sci-biology/last/Manifest
@@ -0,0 +1,9 @@
+AUX last-299-fix-build-system.patch 2021 SHA256 d963e2478ae16605d41fb152ad5680bbf7940ae114e583696790d512c4587a4e SHA512 42df26ce39dd8d263581f20aee0a3fbea0c849fcb5b1627554f9d0b3d3cea55a13b7f42fca9048611a50fdd9e784fa2b537a876b6ded411601c78b2e13e2e19c WHIRLPOOL 688375499b15d031fd55f68a8337e45418ced59bd374026950fd21e0bd6b6af1aa0d026306c591ef6d350de8219091434e13b1fd70aea054fa69c946b5f9711d
+AUX last-299-portable-shebangs.patch 2762 SHA256 79c7de9eb995bd645ca0ef1273ea9ae75b2d4753e9c2ac0de520181e2e3d58f4 SHA512 343483b421e79996aee5480608cdf8b085e8c9c48f5b1f6a6e6e6bbddca9f8d9e1e3561924bc29bc9c60f30cc4c5e7e81d79e60847e35b3a9f7a53f7e3b8c3f6 WHIRLPOOL db49e2271a961a7ea7a3e9c6349a82f81f9bd21b692d9b3fb1148ef979c16e6e83d5eb9850075319a9d923c003877733620a3f70244935c610f1b6a68a00b63d
+DIST last-230.zip 418077 SHA256 8d55ee95e05a08afa72690df9086886e97142adcfbf750cf5cf6015b91215484 SHA512 46c858c2bd4a9aa00ac3b448ce78bdee6c1edd4f6569cff3c81ec8a7c661d89a9b5e7a888cbc6da190b243f0ec83c485b4574dadc6a58669d9b955eb70c329d1 WHIRLPOOL aaa0483a58821cca0fdd7875cb4e7c62493fd724729d957df1d51c7612e92e3acefae2727789f63a248f02c976a45c3209d6bac2c39f54d84f02d1106c2d0f85
+DIST last-299.zip 453159 SHA256 cc68e9c0b5220da67fd0239c9663dc0d1a05e63b337a6c98cfef6d5c38d0c54c SHA512 74e89129cc17482ec1a99e2d940ca62374c130fea2fa53ea7d2c3703b6ca5751f348110909d61562c4839d8fb1793619c2f41c25c8968b3ab53f0c7191f4a00b WHIRLPOOL 12e826c22c2d91845e89aa0c6e99af785973e8a276dec4f97ed292e144327c7c58024622d3f7285c6107bca7af1bf3c29a23ec9d22dc88ff5dc041a0df96f3ce
+EBUILD last-230.ebuild 710 SHA256 eb99af8d511ed321989eedab99360bdb0d40508497995339050193d168bc7269 SHA512 dc8a8ed6a4fd31daeb188cd79da40593e71ebbcc9567815ea4d445b033fe82ce6730af4e82cd9c2a5e17e07b97193b91ca2f034c636cfa7aae815208c1f3c591 WHIRLPOOL 312056810c29b56feb5ad3c266571edfcc76d7de82cb4ceb4fb26a1cd0abf3639479ff6b7b30e164fd7a09fb81115dfa88752014fb4f6e2c13aebb5479ecbc3f
+EBUILD last-299-r1.ebuild 843 SHA256 9c07fdc5055a051b2fa6c5fa7b2be074ae422d3a72e03d45d3a17ad320d62a78 SHA512 7892c3a4ab3f6a23af11a5b548f4f7d992497c25bb4eed8e0a9dcac3da9b9a41d7b8f2b97f88599c7831fee5c064b421b0876fe0b3c444395015a4a0918f57e2 WHIRLPOOL c3ef323bb099c34a700b46467c66eb2af4b274dde3e1da8acf20533724000a888c0ff27ccb753d423d21a810bb5db3c0458db1e6e5b5d511a3ea122f255664c9
+MISC ChangeLog 2847 SHA256 9544554cb68e63816bb0e828fbb40615102db57f2d93ce99d7a11436c19824b5 SHA512 fbd3a490a48f89d8a3f5e7ad56f8e4448cd6f477635956e3adf1a2ed5e92800b155f01ff5031452bfd0c3afe3674f68b9ddee19ba371be799c960c954ad947f4 WHIRLPOOL 4632684e3964e3b9ff89e2eeca8ec6948ab9577e577c33741dd8f929972393e3eb0d68b972f1f8973467fdbf385d4f458b2ff470e0f0ede317971d56b61bcc14
+MISC ChangeLog-2015 3254 SHA256 4908f33d57ebe1598f3e134db57e86213fb9c11dee4535e51a7049bdffa19145 SHA512 c7cbea0b018c9b171a0948ac272a4e4d43065ade440a206922a356bf6351de2bd60fed4d9d4e99df51bfc9a6b6ebaad3766cf260f49885dcf1aeb3e7000d7fad WHIRLPOOL 311707a2b58ff4a9c6f08b5e7fa18066b5c594d2e725242c47d2d393cef27a8df36cdb6cf4f883714cbe07a8c9ba4c83724cea71c6037b9c9f7de718c9b6cd34
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
diff --git a/sci-biology/last/files/last-299-fix-build-system.patch b/sci-biology/last/files/last-299-fix-build-system.patch
new file mode 100644
index 000000000000..0a89cea60278
--- /dev/null
+++ b/sci-biology/last/files/last-299-fix-build-system.patch
@@ -0,0 +1,74 @@
+Make build system respect user flags
+
+--- a/makefile
++++ b/makefile
+@@ -1,6 +1,5 @@
+-CXXFLAGS = -O3
+ all:
+-	@cd src && $(MAKE) CXXFLAGS="$(CXXFLAGS)"
++	$(MAKE) -C src
+ 
+ prefix = /usr/local
+ exec_prefix = $(prefix)
+@@ -10,15 +9,15 @@
+ 	cp src/last?? scripts/*.?? $(bindir)
+ 
+ clean:
+-	@cd src && $(MAKE) clean
++	$(MAKE) -C src clean
+ 
+ html:
+-	@cd doc && $(MAKE)
++	$(MAKE) -C doc
+ 
+ distdir = last-`hg id -n`
+ 
+ dist: log html
+-	@cd src && $(MAKE) version.hh
++	$(MAKE) -C src version.hh
+ 	rsync -rC --exclude 'last??' doc examples makefile s* *.txt $(distdir)
+ 	zip -qrm $(distdir) $(distdir)
+ 
+--- a/src/makefile
++++ b/src/makefile
+@@ -1,12 +1,9 @@
+-CXX = g++
+-CC  = gcc
+-
+-CXXFLAGS = -O3 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef	\
+--Wcast-align -Wno-long-long -ansi -pedantic
++last_CXXFLAGS = -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef	\
++-Wcast-align -Wno-long-long -pedantic
+ # -Wconversion
+ # -fomit-frame-pointer ?
+ 
+-CFLAGS = -Wall
++last_CFLAGS = -Wall
+ 
+ DBSRC = Alphabet.cc MultiSequence.cc CyclicSubsetSeed.cc	\
+ SubsetSuffixArray.cc LastdbArguments.cc io.cc fileMap.cc	\
+@@ -49,17 +46,20 @@
+ 
+ all: lastdb lastal lastex
+ 
++.cpp.o:
++	$(CXX) $(CPPFLAGS) $(last_CXXFLAGS) $(CXXFLAGS) -c -o $@ $<
++
+ lastdb: $(DBSRC) $(DBINC) makefile
+-	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(DBSRC)
++	$(CXX) $(CPPFLAGS) $(last_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(DBSRC)
+ 
+ lastal: $(ALSRC) $(ALINC) makefile $(OBJ)
+-	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(ALSRC) $(OBJ)
++	$(CXX) $(CPPFLAGS) $(last_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(ALSRC) $(OBJ)
+ 
+ lastex: $(EXSRC) $(EXINC) makefile
+-	$(CXX) -Igumbel_params $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(EXSRC)
++	$(CXX) $(CPPFLAGS) -Igumbel_params $(last_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(EXSRC)
+ 
+ $(OBJ): CA_code/*.c CA_code/*.h makefile
+-	$(CC) $(CPPFLAGS) $(CFLAGS) -c CA_code/lambda_calculator.c
++	$(CC) $(CPPFLAGS) $(last_CFLAGS) $(CFLAGS) -c -o $@ CA_code/lambda_calculator.c
+ 
+ clean:
+ 	rm -f lastdb lastal lastex $(OBJ)
diff --git a/sci-biology/last/files/last-299-portable-shebangs.patch b/sci-biology/last/files/last-299-portable-shebangs.patch
new file mode 100644
index 000000000000..03ecbdcbde20
--- /dev/null
+++ b/sci-biology/last/files/last-299-portable-shebangs.patch
@@ -0,0 +1,99 @@
+Make shebangs portable and prefix friendly
+See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/
+
+--- a/scripts/last-dotplot.py
++++ b/scripts/last-dotplot.py
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#!/usr/bin/env python2
+ 
+ # Read pair-wise alignments in MAF or LAST tabular format: write an
+ # "Oxford grid", a.k.a. dotplot.
+--- a/scripts/last-map-probs.py
++++ b/scripts/last-map-probs.py
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#!/usr/bin/env python2
+ 
+ # Copyright 2010, 2011, 2012 Martin C. Frith
+ 
+--- a/scripts/last-merge-batches.py
++++ b/scripts/last-merge-batches.py
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#!/usr/bin/env python2
+ 
+ # Copyright 2010, 2011 Martin C. Frith
+ 
+--- a/scripts/last-pair-probs.py
++++ b/scripts/last-pair-probs.py
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#!/usr/bin/env python2
+ 
+ # Copyright 2011, 2012, 2013 Martin C. Frith
+ 
+--- a/scripts/last-reduce-alignments.sh
++++ b/scripts/last-reduce-alignments.sh
+@@ -1,4 +1,4 @@
+-#! /bin/sh
++#!/usr/bin/env sh
+ 
+ # This script reads MAF-format alignments with lastal header
+ # information, removes "uninteresting" alignments, and writes the
+--- a/scripts/last-remove-dominated.py
++++ b/scripts/last-remove-dominated.py
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#!/usr/bin/env python2
+ 
+ # Read MAF-format alignments, and write those are not "dominated" by
+ # any other one.  X dominates Y if they overlap on the top sequence,
+--- a/scripts/last-split-probs.py
++++ b/scripts/last-split-probs.py
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#!/usr/bin/env python2
+ 
+ # Copyright 2012 Martin C. Frith
+ 
+--- a/scripts/maf-convert.py
++++ b/scripts/maf-convert.py
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#!/usr/bin/env python2
+ # Copyright 2010, 2011 Martin C. Frith
+ # Read MAF-format alignments: write them in other formats.
+ # Seems to work with Python 2.x, x>=4
+--- a/scripts/maf-cull.py
++++ b/scripts/maf-cull.py
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#!/usr/bin/env python2
+ 
+ # Read MAF-format alignments.  Write them, omitting alignments whose
+ # coordinates in the top-most sequence are contained in those of >=
+--- a/scripts/maf-join.py
++++ b/scripts/maf-join.py
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#!/usr/bin/env python2
+ 
+ # Copyright 2009, 2010, 2011 Martin C. Frith
+ 
+--- a/scripts/maf-sort.sh
++++ b/scripts/maf-sort.sh
+@@ -1,4 +1,4 @@
+-#! /bin/sh
++#!/usr/bin/env sh
+ 
+ # Sort MAF-format alignments by sequence name, then strand, then start
+ # position, then end position, of the top sequence.  Also, merge
+--- a/scripts/maf-swap.py
++++ b/scripts/maf-swap.py
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#!/usr/bin/env python2
+ 
+ # Read MAF-format alignments, and write them, after moving the Nth
+ # sequence to the top in each alignment.
diff --git a/sci-biology/last/last-230.ebuild b/sci-biology/last/last-230.ebuild
new file mode 100644
index 000000000000..29134bb908df
--- /dev/null
+++ b/sci-biology/last/last-230.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Genome-scale comparison of biological sequences"
+HOMEPAGE="http://last.cbrc.jp/"
+SRC_URI="http://last.cbrc.jp/archive/${P}.zip"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+src_prepare() {
+	sed \
+		-e 's:-o $@:$(LDFLAGS) -o $@:g' \
+		-i src/makefile || die
+}
+
+src_compile() {
+	emake \
+		-e -C src \
+		CXX="$(tc-getCXX)" \
+		CC="$(tc-getCC)" \
+		STRICT="" || die
+}
+
+src_install() {
+	dobin src/last{al,db,ex}
+	exeinto /usr/share/${PN}/scripts
+	doexe scripts/*
+	dodoc doc/*.txt ChangeLog.txt README.txt
+}
diff --git a/sci-biology/last/last-299-r1.ebuild b/sci-biology/last/last-299-r1.ebuild
new file mode 100644
index 000000000000..b6adee215970
--- /dev/null
+++ b/sci-biology/last/last-299-r1.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit toolchain-funcs python-single-r1
+
+DESCRIPTION="Genome-scale comparison of biological sequences"
+HOMEPAGE="http://last.cbrc.jp/"
+SRC_URI="http://last.cbrc.jp/${P}.zip"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}"
+DEPEND="app-arch/unzip"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-299-fix-build-system.patch
+	"${FILESDIR}"/${PN}-299-portable-shebangs.patch
+)
+
+src_configure() {
+	tc-export CC CXX
+}
+
+src_install() {
+	local DOCS=( doc/*.txt ChangeLog.txt README.txt )
+	local HTML_DOCS=( doc/*html )
+	einstalldocs
+
+	dobin src/last{al,db,ex}
+
+	cd scripts || die
+	local i
+	for i in *py; do
+		newbin ${i} ${i%.py}
+	done
+	dobin *sh
+}
diff --git a/sci-biology/last/metadata.xml b/sci-biology/last/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/last/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>