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author | Andrew Ammerlaan <andrewammerlaan@gentoo.org> | 2021-08-31 11:20:38 +0200 |
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committer | Andrew Ammerlaan <andrewammerlaan@gentoo.org> | 2021-08-31 11:20:38 +0200 |
commit | 8f7b92289adb3326f0e6cb43697fdbcc4a8a950a (patch) | |
tree | b09ba8173337d282b8085b2dc1c3c1d891406684 | |
parent | sci-biology/prot4EST: remove last-rited pack (diff) | |
download | sci-8f7b9228.tar.gz sci-8f7b9228.tar.bz2 sci-8f7b9228.zip |
sci-biology/seqclean: remove last-rited pack
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
-rw-r--r-- | profiles/package.mask | 1 | ||||
-rw-r--r-- | sci-biology/seqclean/Manifest | 3 | ||||
-rw-r--r-- | sci-biology/seqclean/files/seqclean-110625-build.patch | 135 | ||||
-rw-r--r-- | sci-biology/seqclean/metadata.xml | 12 | ||||
-rw-r--r-- | sci-biology/seqclean/seqclean-110625.ebuild | 54 |
5 files changed, 0 insertions, 205 deletions
diff --git a/profiles/package.mask b/profiles/package.mask index f8e1e4d32..6b58c272e 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -37,7 +37,6 @@ # Bug #798015, removal in 30 days. # Perhaps these packages work with the newer ncbi-tools++? If anyone is actively # using these packages please open a bug report -sci-biology/seqclean sci-chemistry/talosn # revdep of seqclean sci-biology/rum diff --git a/sci-biology/seqclean/Manifest b/sci-biology/seqclean/Manifest deleted file mode 100644 index 5a742c218..000000000 --- a/sci-biology/seqclean/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST mdust-110625.tar.gz 7526 BLAKE2B 9d2f91025d6cfccb8c75b8f2d6c9f3df9b76469ef7b77a74c3bbd3e37c2d2ba0ce737eaca518200246e1c302d7862af4929bad4bffb6c53692fbfaa586dbf4d7 SHA512 349446115d3b778d28a184eb118ada112476b2c51a058dd7467ff539678f7550dab675a731c452f9aa002fda9a54f13576db02302df935946d034eb9e0d4566e -DIST seqcl_scripts-110625.tar.gz 14840 BLAKE2B 107ac1d966870f976c5b8f2bd74beb95f49cc1d57975c686e730ad4f519378c3435a626c086244f04e3e075d9f63d1f6541a9bf8dbae1c141ccc3bbd8c613fb5 SHA512 84cca02165856f51614b05e3fb416765695ca3442a8f9d47ee341946a375b6fc9ec6b77e5f18b58d21d5a6e93e21010a866efd2940dc60771f9e6e97722d5a96 -DIST trimpoly-110625.tar.gz 12747 BLAKE2B e395c19549e376b373028c9ca22197021dcf7a7465f2528e1b9051d5e9bbd27c8180103a0a849c3aa8de98eef0edeb71db18b457a62bd3a07e6fe68e083d4062 SHA512 74e7ed6169cbe5f9e9bdcaaffed8ceb74c4ea1ccce912fc656dc29f5ddf8bbeee2975814c97691a8b5eb419c202e332ba79634feb11ffac9a3ab3341db61076f diff --git a/sci-biology/seqclean/files/seqclean-110625-build.patch b/sci-biology/seqclean/files/seqclean-110625-build.patch deleted file mode 100644 index b5797618f..000000000 --- a/sci-biology/seqclean/files/seqclean-110625-build.patch +++ /dev/null @@ -1,135 +0,0 @@ - mdust/Makefile | 18 +++++++++--------- - mdust/fastafile.c | 3 ++- - mdust/mdust.c | 1 + - trimpoly/Makefile | 16 ++++++++-------- - 4 files changed, 20 insertions(+), 18 deletions(-) - -diff --git a/mdust/Makefile b/mdust/Makefile -index 81bf4e9..0c75e69 100644 ---- a/mdust/Makefile -+++ b/mdust/Makefile -@@ -1,40 +1,40 @@ - # Useful directories - - # Directories to search for header files --SEARCHDIRS := -I. -I- -+SEARCHDIRS := -I. -iquote - - - #SYSTYPE := $(shell uname) - --CC := gcc --CFLAGS = -O2 -Wall ${SEARCHDIRS} -D_REENTRANT -+CC ?= gcc -+CFLAGS += ${SEARCHDIRS} -D_REENTRANT -+CXXFLAGS += ${SEARCHDIRS} -D_REENTRANT - - %.o : %.c - ${CC} ${CFLAGS} -c $< -o $@ - - %.o : %.cc -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - %.o : %.C -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - %.o : %.cpp -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - %.o : %.cxx -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - # C/C++ linker - - LINKER := gcc --LDFLAGS = - LOADLIBES := - - .PHONY : all - all: mdust - - mdust: ./mdust.o ./dust.o ./fastafile.o -- ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} -+ ${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} - - # target for removing all object files - -diff --git a/mdust/fastafile.c b/mdust/fastafile.c -index 6c14b99..5f70f14 100644 ---- a/mdust/fastafile.c -+++ b/mdust/fastafile.c -@@ -1,7 +1,8 @@ - #include <stdio.h> - #include <ctype.h> - #include <malloc.h> -- -+#include <string.h> -+#include <stdlib.h> - #include "fastafile.h" - - -diff --git a/mdust/mdust.c b/mdust/mdust.c -index f2bae99..c3ee686 100644 ---- a/mdust/mdust.c -+++ b/mdust/mdust.c -@@ -1,6 +1,7 @@ - #include <stdlib.h> - #include <stdio.h> - #include <ctype.h> -+#include <string.h> - #include "dust.h" - #include "fastafile.h" - -diff --git a/trimpoly/Makefile b/trimpoly/Makefile -index 84db22d..71145c2 100644 ---- a/trimpoly/Makefile -+++ b/trimpoly/Makefile -@@ -3,28 +3,28 @@ - # Directories to search for header files - SEARCHDIRS := -I. - --CC := gcc --CFLAGS = -O2 -Wall ${SEARCHDIRS} -D_REENTRANT -+CC ?= gcc -+CFLAGS += ${SEARCHDIRS} -D_REENTRANT -+CXXFLAGS += ${SEARCHDIRS} -D_REENTRANT - - %.o : %.c - ${CC} ${CFLAGS} -c $< -o $@ - - %.o : %.cc -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - %.o : %.C -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - %.o : %.cpp -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - %.o : %.cxx -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - # C/C++ linker - - LINKER := gcc --LDFLAGS = - LOADLIBES = - SYSTYPE := $(shell uname) - #ifeq ($(SYSTYPE), Linux) -@@ -37,7 +37,7 @@ SYSTYPE := $(shell uname) - all: trimpoly - - trimpoly: ./trimpoly.o color_c.o -- ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} -+ ${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} - - # target for removing all object files - diff --git a/sci-biology/seqclean/metadata.xml b/sci-biology/seqclean/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/seqclean/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/seqclean/seqclean-110625.ebuild b/sci-biology/seqclean/seqclean-110625.ebuild deleted file mode 100644 index f98fdf3b8..000000000 --- a/sci-biology/seqclean/seqclean-110625.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -DESCRIPTION="Trimpoly and mdust for trimming and validation of ESTs/DNA sequences" -HOMEPAGE="https://web.archive.org/web/20140726030702/http://compbio.dfci.harvard.edu/tgi/software/" -for i in seqcl_scripts mdust trimpoly; do - SRC_URI="${SRC_URI} ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/seqclean/${i}.tar.gz -> ${i}-${PV}.tar.gz" -done - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -DEPEND=" - dev-lang/perl - sci-biology/ncbi-tools" -RDEPEND="${DEPEND}" - -S=${WORKDIR} - -PATCHES=( - "${FILESDIR}"/${P}-build.patch -) - -src_prepare() { - default - # disable the necessity to install Mailer.pm with this tool - einfo "Disabling mailer feature within seqclean" - sed -i 's/use Mailer;/#use Mailer;/' "${S}"/"${PN}"/"${PN}" || die - tc-export CC CXX -} - -src_compile() { - for i in mdust trimpoly; do - LDLFAGS="${LDFLAGS}" \ - emake -C "${S}"/${i} - done -} - -src_install() { - dobin seqclean/{seqclean,cln2qual,bin/seqclean.psx} - newdoc seqclean/README README.seqclean - for i in mdust trimpoly; do - dobin ${i}/${i} - done - - einfo "Optionally, you may want to download UniVec from NCBI if you do not have your own" - einfo "fasta file with vector sequences you want to remove from sequencing" - einfo "reads. See http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html" -} |