commit: 8f7b92289adb3326f0e6cb43697fdbcc4a8a950a
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Aug 31 09:20:38 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Aug 31 09:20:38 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8f7b9228
sci-biology/seqclean: remove last-rited pack
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
profiles/package.mask | 1 -
.../seqclean/files/seqclean-110625-build.patch | 135 ---------------------
sci-biology/seqclean/metadata.xml | 12 --
sci-biology/seqclean/seqclean-110625.ebuild | 54 ---------
4 files changed, 202 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/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, $^} ${LOADLIBES}
-
- # target for removing all object files
-
diff --git a/sci-biology/seqclean/metadata.xml
b/sci-biology/seqclean/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/seqclean/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
-<pkgmetadata>
- <maintainer type="person">
- <email>[email protected]</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>[email protected]</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/seqclean/seqclean-110625.ebuild
b/sci-biology/seqclean/seqclean-110625.ebuild
deleted file mode 100644
index f98fdf3b8..000000000
--- a/sci-biology/seqclean/seqclean-110625.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="Trimpoly and mdust for trimming and validation of ESTs/DNA
sequences"
-HOMEPAGE="https://web.archive.org/web/20140726030702/http://compbio.dfci.harvard.edu/tgi/software/";
-for i in seqcl_scripts mdust trimpoly; do
- SRC_URI="${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";
-}
