diff options
author | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
---|---|---|
committer | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
commit | 4f2d7949f03e1c198bc888f2d05f421d35c57e21 (patch) | |
tree | ba5f07bf3f9d22d82e54a462313f5d244036c768 /sci-biology/last |
reinit the tree, so we can have metadata
Diffstat (limited to 'sci-biology/last')
-rw-r--r-- | sci-biology/last/Manifest | 9 | ||||
-rw-r--r-- | sci-biology/last/files/last-299-fix-build-system.patch | 74 | ||||
-rw-r--r-- | sci-biology/last/files/last-299-portable-shebangs.patch | 99 | ||||
-rw-r--r-- | sci-biology/last/last-230.ebuild | 39 | ||||
-rw-r--r-- | sci-biology/last/last-299-r1.ebuild | 45 | ||||
-rw-r--r-- | sci-biology/last/metadata.xml | 8 |
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> |