* [gentoo-commits] repo/gentoo:master commit in: sci-biology/consed/
@ 2016-10-03 20:21 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2016-10-03 20:21 UTC (permalink / raw
To: gentoo-commits
commit: 405438b9ea1ae2f88e025718f2dc0e55740c1e7e
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 3 19:21:02 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Oct 3 20:21:16 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=405438b9
sci-biology/consed: Remove old ebuilds
Package-Manager: portage-2.3.1
sci-biology/consed/Manifest | 4 --
sci-biology/consed/consed-19-r2.ebuild | 71 ---------------------------
sci-biology/consed/consed-27.ebuild | 90 ----------------------------------
3 files changed, 165 deletions(-)
diff --git a/sci-biology/consed/Manifest b/sci-biology/consed/Manifest
index 6761fed..f1a492d 100644
--- a/sci-biology/consed/Manifest
+++ b/sci-biology/consed/Manifest
@@ -1,6 +1,2 @@
-DIST consed-19-linux.tar.gz 29835559 SHA256 27501d714e4cd7ea04def6a7f985b674bc454ed8bd7d1e86b41b0283e2b9e089
-DIST consed-19-sources.tar.gz 6867357 SHA256 1db37b17608e49470926dae261c76d400cf3f9eb5feea52cd732e0bfa4cadee3
-DIST consed-27-linux.tar.gz 1604 SHA256 d7baafcbcdbf1b25262578511da8a51758f48d97d9109b334978acd150461855 SHA512 dbafb8c8f40dbed82a0000314549452c372e447467ccd8ec1004f44946dd09fcffa065c36bcca4f3c0fd55a137e570c135f4f79820e3e6d98626f92413b2731b WHIRLPOOL ae319734572558dd0047dad085c9f907386be6f7f0041bac0df9e1ce5b7558c750d92ea747cc3e74c594c83bed4cd73f4b37b4d6b9e39fd7caa2a733d67d6e21
-DIST consed-27-sources.tar.gz 1604 SHA256 d7baafcbcdbf1b25262578511da8a51758f48d97d9109b334978acd150461855 SHA512 dbafb8c8f40dbed82a0000314549452c372e447467ccd8ec1004f44946dd09fcffa065c36bcca4f3c0fd55a137e570c135f4f79820e3e6d98626f92413b2731b WHIRLPOOL ae319734572558dd0047dad085c9f907386be6f7f0041bac0df9e1ce5b7558c750d92ea747cc3e74c594c83bed4cd73f4b37b4d6b9e39fd7caa2a733d67d6e21
DIST consed-29-linux.tar.gz 36172715 SHA256 98354e2507ef9026b82c89db199ff1de7e4ec3686fccd691d215acdcde34ce39 SHA512 63a95d84cb58009045a9d898c8b1a94f98516bed9189f624a5930338cc8f51562504257f309d945fafcc07e0811ffeea122b640789f75fbd6c94535178dab4dd WHIRLPOOL 26ebc1ee7114b0c609fd36c2c46b71c399bacb61f7db285ab36f296902964c14518c058e814a166b20a36c2d320280aeed0ca18b7104c6b503324bf27d4b57af
DIST consed-29-sources.tar.gz 3258845 SHA256 e7d3c2bf60e0bb22025e0416d16cf9864fec8091811ec285a39db4cb46bc3fc6 SHA512 fd711a65a02ef1238cca12b90fe7fa9b67da6c37d43cd105f38c7b6475fbc073c1f4d7f99703dec9d3a0a7a2a9317cb14999a114bb6f52589cb9b6e34700eb93 WHIRLPOOL 5ac363f049b6b40554112f830e812e7ab7d334a0f6707ea4da981ed1e468109f3bd7669382aa77e93cf12c78cc95fb1085711dcc972c7ff22ffe6b73056bb2c2
diff --git a/sci-biology/consed/consed-19-r2.ebuild b/sci-biology/consed/consed-19-r2.ebuild
deleted file mode 100644
index 3ce704e..00000000
--- a/sci-biology/consed/consed-19-r2.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=3
-
-inherit toolchain-funcs
-
-DESCRIPTION="A genome sequence finishing program"
-HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
-SRC_URI="${P}-sources.tar.gz
- ${P}-linux.tar.gz"
-
-LICENSE="phrap"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=x11-libs/motif-2.3:0"
-RDEPEND="${DEPEND}
- >=sci-biology/phred-000925
- >=sci-biology/phrap-1.080721"
-
-S="${WORKDIR}"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
- einfo "Please visit ${HOMEPAGE} and obtain the file"
- einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\""
- einfo "and place it in ${DISTDIR},"
- einfo "obtain the file"
- einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\""
- einfo "and place it in ${DISTDIR}"
-}
-
-src_prepare() {
- sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die
- sed -i \
- -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm/' \
- -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
- -e 's/CFLGS=/CFLGS= ${CFLAGS} /' "${S}/makefile" || die
- sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
- sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die
-}
-
-src_compile() {
- emake || die
- emake -C misc/mktrace || die
- emake -C misc/phd2fasta || die
- (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
-}
-
-src_install() {
- dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die
- dobin scripts/* contributions/* || die
- insinto /usr/lib/screenLibs
- doins misc/*.{fa*,seq} || die
- insinto /usr/share/${PN}/examples
- doins -r standard polyphred autofinish assembly_view 454_newbler \
- align454reads align454reads_answer solexa_example \
- solexa_example_answer selectRegions selectRegionsAnswer || die
- echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
- doenvd "${S}/99consed" || die
- dodoc README.txt *_announcement.txt || die
-}
-
-pkg_postinst() {
- einfo "Package documentation is available at"
- einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
-}
diff --git a/sci-biology/consed/consed-27.ebuild b/sci-biology/consed/consed-27.ebuild
deleted file mode 100644
index 0bf33a7..00000000
--- a/sci-biology/consed/consed-27.ebuild
+++ /dev/null
@@ -1,90 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="A genome sequence finishing program"
-HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
-SRC_URI="
- ${P}-sources.tar.gz
- ${P}-linux.tar.gz"
-
-LICENSE="phrap"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=x11-libs/motif-2.3:0"
-RDEPEND="${DEPEND}
- sci-biology/samtools
- >=sci-biology/phred-000925
- >=sci-biology/phrap-1.080721
- dev-lang/perl"
-
-S="${WORKDIR}"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
- einfo "Please visit ${HOMEPAGE} and obtain the file"
- einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\""
- einfo "and place it in ${DISTDIR},"
- einfo "obtain the file"
- einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\""
- einfo "and place it in ${DISTDIR}"
-}
-
-src_prepare() {
- sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die
- sed -i \
- -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \
- -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
- -e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
- -e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die
- sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
- sed \
- -e 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' \
- -i "${S}"/scripts/* || die
-}
-
-src_compile() {
- emake
- emake -C misc/mktrace
- emake -C misc/phd2fasta
- (cd misc/454; $(tc-getCC) ${CFLAGS} ${LDFLAGS} sff2scf.c -o sff2scf) || die
-}
-
-src_install() {
- dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf}
- dobin scripts/* contributions/*
- insinto /usr/lib/screenLibs
- doins misc/*.{fa*,seq}
- insinto /usr/share/${PN}/examples
- doins -r \
- standard polyphred autofinish assembly_view 454_newbler \
- align454reads align454reads_answer solexa_example \
- solexa_example_answer selectRegions selectRegionsAnswer
- echo 'CONSED_HOME="${EPREFIX}/usr"' > "${S}"/99consed || die
- echo 'CONSED_PARAMETERS="${EPREFIX}/etc/consedrc"' >> "${S}"/99consed || die
- mkdir -p "${ED}"/etc/consedrc || die
- touch "${ED}"/etc/consedrc || die
- doenvd "${S}/99consed" || die
- sed \
- -e "s#/usr/local/genome#${EPREFIX}/usr#" \
- -i "${ED}"/usr/bin/{*.perl,phredPhrap,phredPhrapWithPhdBalls} || die
- sed \
- -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' \
- -i "${ED}"/usr/bin/phredPhrap || die
- sed \
- -e 's#/wt1/gordon/genome#/usr/bin#' \
- -i "${ED}"/usr/bin/fastq2Phrap.perl || die
- dodoc README.txt *_announcement.txt || die
-}
-
-pkg_postinst() {
- einfo "Package documentation is available at"
- einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
-}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/consed/
@ 2018-01-13 23:04 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2018-01-13 23:04 UTC (permalink / raw
To: gentoo-commits
commit: 7edf74c6a660e65e6932de2d5b73b262696bc16d
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 13 23:01:44 2018 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Jan 13 23:01:44 2018 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7edf74c6
sci-biology/consed: Rehash
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/consed/Manifest | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/consed/Manifest b/sci-biology/consed/Manifest
index f1a492de74c..eb7d7f06c3e 100644
--- a/sci-biology/consed/Manifest
+++ b/sci-biology/consed/Manifest
@@ -1,2 +1,2 @@
-DIST consed-29-linux.tar.gz 36172715 SHA256 98354e2507ef9026b82c89db199ff1de7e4ec3686fccd691d215acdcde34ce39 SHA512 63a95d84cb58009045a9d898c8b1a94f98516bed9189f624a5930338cc8f51562504257f309d945fafcc07e0811ffeea122b640789f75fbd6c94535178dab4dd WHIRLPOOL 26ebc1ee7114b0c609fd36c2c46b71c399bacb61f7db285ab36f296902964c14518c058e814a166b20a36c2d320280aeed0ca18b7104c6b503324bf27d4b57af
-DIST consed-29-sources.tar.gz 3258845 SHA256 e7d3c2bf60e0bb22025e0416d16cf9864fec8091811ec285a39db4cb46bc3fc6 SHA512 fd711a65a02ef1238cca12b90fe7fa9b67da6c37d43cd105f38c7b6475fbc073c1f4d7f99703dec9d3a0a7a2a9317cb14999a114bb6f52589cb9b6e34700eb93 WHIRLPOOL 5ac363f049b6b40554112f830e812e7ab7d334a0f6707ea4da981ed1e468109f3bd7669382aa77e93cf12c78cc95fb1085711dcc972c7ff22ffe6b73056bb2c2
+DIST consed-29-linux.tar.gz 36172715 BLAKE2B 6706576b404c0bccb7ed28ab6fe2dec86fdac6f7651406d3f30e35caac3e49a66b4762edace2133d2dfb776bbeb730b74797c7323deb950f2648a46c4594fe98 SHA512 63a95d84cb58009045a9d898c8b1a94f98516bed9189f624a5930338cc8f51562504257f309d945fafcc07e0811ffeea122b640789f75fbd6c94535178dab4dd
+DIST consed-29-sources.tar.gz 3258845 BLAKE2B 508763ff2a240047cff0a43ba4b9b9a7f9302c0a023478c6b08f86bb77fb2c12a62a9b16165fe6257fe6c86af853dabe279bd9e05632c3e112e3fb7fad2c6bd3 SHA512 fd711a65a02ef1238cca12b90fe7fa9b67da6c37d43cd105f38c7b6475fbc073c1f4d7f99703dec9d3a0a7a2a9317cb14999a114bb6f52589cb9b6e34700eb93
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/consed/
@ 2019-02-05 18:08 Ben Kohler
0 siblings, 0 replies; 3+ messages in thread
From: Ben Kohler @ 2019-02-05 18:08 UTC (permalink / raw
To: gentoo-commits
commit: 207f91c6d7009bccefafea108d00553ef21a5cdf
Author: Ben Kohler <bkohler <AT> gentoo <DOT> org>
AuthorDate: Tue Feb 5 18:06:09 2019 +0000
Commit: Ben Kohler <bkohler <AT> gentoo <DOT> org>
CommitDate: Tue Feb 5 18:07:39 2019 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=207f91c6
sci-biology/consed: don't reference ${DISTDIR} in pkg_nofetch
Package-Manager: Portage-2.3.59, Repoman-2.3.12
Signed-off-by: Ben Kohler <bkohler <AT> gentoo.org>
sci-biology/consed/consed-29.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild
index d5417e31028..32eba4cb16d 100644
--- a/sci-biology/consed/consed-29.ebuild
+++ b/sci-biology/consed/consed-29.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -45,10 +45,10 @@ PATCHES=(
pkg_nofetch() {
einfo "Please visit ${HOMEPAGE} and obtain the file"
einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\""
- einfo "and place it in ${DISTDIR},"
+ einfo "and place it into your DISTDIR directory,"
einfo "obtain the file"
einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\""
- einfo "and place it in ${DISTDIR}"
+ einfo "and place it into your DISTDIR directory."
}
src_prepare() {
^ permalink raw reply related [flat|nested] 3+ messages in thread
end of thread, other threads:[~2019-02-05 18:08 UTC | newest]
Thread overview: 3+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2019-02-05 18:08 [gentoo-commits] repo/gentoo:master commit in: sci-biology/consed/ Ben Kohler
-- strict thread matches above, loose matches on Subject: below --
2018-01-13 23:04 David Seifert
2016-10-03 20:21 David Seifert
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox