* [gentoo-commits] proj/sci:master commit in: sci-biology/pileup/
@ 2014-03-24 1:22 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2014-03-24 1:22 UTC (permalink / raw
To: gentoo-commits
commit: 27b9edadf33754b1305771c3b657ed21c05b1267
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 24 01:20:53 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 24 01:20:53 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=27b9edad
sci-biology/pileup: new package; a pileup pipeline used along SSAHA2
---
sci-biology/pileup/ChangeLog | 10 ++++++
sci-biology/pileup/metadata.xml | 9 +++++
sci-biology/pileup/pileup-0.6.ebuild | 66 ++++++++++++++++++++++++++++++++++++
3 files changed, 85 insertions(+)
diff --git a/sci-biology/pileup/ChangeLog b/sci-biology/pileup/ChangeLog
new file mode 100644
index 0000000..ea30368
--- /dev/null
+++ b/sci-biology/pileup/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/pileup
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*pileup-0.6 (24 Mar 2014)
+
+ 24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +pileup-0.6.ebuild,
+ +metadata.xml:
+ new package; a pileup pipeline used along SSAHA2
+
diff --git a/sci-biology/pileup/metadata.xml b/sci-biology/pileup/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/pileup/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/pileup/pileup-0.6.ebuild b/sci-biology/pileup/pileup-0.6.ebuild
new file mode 100644
index 0000000..e78d5de
--- /dev/null
+++ b/sci-biology/pileup/pileup-0.6.ebuild
@@ -0,0 +1,66 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+DESCRIPTION="Pipeline to align reads into the format also understood by samtools, maq, pipeline maybe using ssaha2?"
+HOMEPAGE="http://www.sanger.ac.uk/resources/software/ssaha2/"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/pileup.tgz"
+
+# http://samtools.sourceforge.net/pileup.shtml
+#
+LICENSE=""
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/pileup_v"${PV}"
+
+src_prepare(){
+ sed -i "s/^CC= gcc/#CC= gcc/" ssaha_pileup/ssaha_pileup/makefile || die "sed failed to fix makefile"
+ sed -i "s/^CFLAGS= -O2/#CFLAGS= -O2/" ssaha_pileup/ssaha_pileup/makefile || die "sed failed to fix makefile"
+
+ for d in get_seqreads ssaha_split; do
+ sed -i "s/^CC = cc/#CC = cc/" ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
+ sed -i "s/^CFLAGS = -O4/#CFLAGS = -O4/" ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
+ done
+
+ for d in search_read ssaha_parseSNP; do
+ sed -i "s/^CC = gcc/#CC = gcc/" ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
+ sed -i "s/^CFLAGS = -Wall -O4/#CFLAGS = -Wall -O4/" ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
+ done
+}
+
+src_compile(){
+ cd ssaha_pileup/ssaha_pileup || die "Cannot cd to "${S}"ssaha_pileup/ssaha_pileup"
+ emake || die "emake failed"
+
+ for d in get_seqreads ssaha_split ssaha_parseSNP search_read; do
+ cd "${S}"/ssaha_pileup/other_codes/$d || die "Cannot cd to "${S}"ssaha_pileup/other_codes/"$d
+ make clean
+ emake || die "emake failed"
+ done
+}
+
+src_install(){
+ cd ssaha_pileup/ssaha_pileup || die "Cannot cd to "${S}"ssaha_pileup/ssaha_pileup"
+ dobin ssaha_pileup ssaha_solexa ssaha_pairs ssaha_clean ssaha_mates ssaha_cigar ssaha_indel view_pileup ssaha_reads ssaha_merge ssaha_check-cigar || die "dobin failed"
+
+ cd "${S}" || die
+ for f in ssaha_pileup/other_codes/get_seqreads/get_seqreads \
+ ssaha_pileup/other_codes/ssaha_split/ssaha_split \
+ ssaha_pileup/other_codes/ssaha_parseSNP/ssaha_parseSNP \
+ ssaha_pileup/other_codes/search_read/search_read; do
+ dobin $f || die "dobin failed"
+ done
+
+ # TODO:
+ # pileup_v0.6/ssaha_pileup/tag.pl
+
+ # Finally, a tcsh shell script has to be created with full paths to ssaha2 binaries
+ # convert the awk line from install.csh to a proper shellscript based on pileup.csh_src
+}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pileup/
@ 2014-03-24 1:35 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2014-03-24 1:35 UTC (permalink / raw
To: gentoo-commits
commit: 79e7216e5ab7821f6dd9a500624403074b36a074
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 24 01:34:09 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 24 01:34:09 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=79e7216e
sci-biology/pileup: dropped KEYWORDS due to misisng LICENSE
---
sci-biology/pileup/ChangeLog | 4 ++++
sci-biology/pileup/pileup-0.6.ebuild | 4 ++--
2 files changed, 6 insertions(+), 2 deletions(-)
diff --git a/sci-biology/pileup/ChangeLog b/sci-biology/pileup/ChangeLog
index ea30368..5589ac4 100644
--- a/sci-biology/pileup/ChangeLog
+++ b/sci-biology/pileup/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> pileup-0.6.ebuild,
+ metadata.xml:
+ dropped KEYWORDS due to misisng LICENSE
+
*pileup-0.6 (24 Mar 2014)
24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +pileup-0.6.ebuild,
diff --git a/sci-biology/pileup/pileup-0.6.ebuild b/sci-biology/pileup/pileup-0.6.ebuild
index e78d5de..c4d6f00 100644
--- a/sci-biology/pileup/pileup-0.6.ebuild
+++ b/sci-biology/pileup/pileup-0.6.ebuild
@@ -4,7 +4,7 @@
EAPI=3
-DESCRIPTION="Pipeline to align reads into the format also understood by samtools, maq, pipeline maybe using ssaha2?"
+DESCRIPTION="SSAHA2-based pipeline to align reads into format also understood by samtools, maq"
HOMEPAGE="http://www.sanger.ac.uk/resources/software/ssaha2/"
SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/pileup.tgz"
@@ -12,7 +12,7 @@ SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/pileup.tgz"
#
LICENSE=""
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
IUSE=""
DEPEND=""
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pileup/
@ 2014-09-16 4:07 Christoph Junghans
0 siblings, 0 replies; 5+ messages in thread
From: Christoph Junghans @ 2014-09-16 4:07 UTC (permalink / raw
To: gentoo-commits
commit: fcdfc1c08e92743a81214d3e10ccd4d335f883f1
Author: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 16 03:03:33 2014 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Sep 16 03:03:33 2014 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=fcdfc1c0
added license
Package-Manager: portage-2.2.8-r1
---
sci-biology/pileup/ChangeLog | 4 +++-
sci-biology/pileup/pileup-0.6.ebuild | 4 ++--
2 files changed, 5 insertions(+), 3 deletions(-)
diff --git a/sci-biology/pileup/ChangeLog b/sci-biology/pileup/ChangeLog
index 5589ac4..d93a5cf 100644
--- a/sci-biology/pileup/ChangeLog
+++ b/sci-biology/pileup/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> pileup-0.6.ebuild:
+ added license
+
24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> pileup-0.6.ebuild,
metadata.xml:
dropped KEYWORDS due to misisng LICENSE
@@ -11,4 +14,3 @@
24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +pileup-0.6.ebuild,
+metadata.xml:
new package; a pileup pipeline used along SSAHA2
-
diff --git a/sci-biology/pileup/pileup-0.6.ebuild b/sci-biology/pileup/pileup-0.6.ebuild
index c4d6f00..cb010b3 100644
--- a/sci-biology/pileup/pileup-0.6.ebuild
+++ b/sci-biology/pileup/pileup-0.6.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=3
+EAPI=5
DESCRIPTION="SSAHA2-based pipeline to align reads into format also understood by samtools, maq"
HOMEPAGE="http://www.sanger.ac.uk/resources/software/ssaha2/"
@@ -10,7 +10,7 @@ SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/pileup.tgz"
# http://samtools.sourceforge.net/pileup.shtml
#
-LICENSE=""
+LICENSE="GRL"
SLOT="0"
KEYWORDS=""
IUSE=""
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pileup/
@ 2021-01-19 16:26 Andrew Ammerlaan
0 siblings, 0 replies; 5+ messages in thread
From: Andrew Ammerlaan @ 2021-01-19 16:26 UTC (permalink / raw
To: gentoo-commits
commit: 5262c63cac26f9a2ff857d3f00750ed769957080
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 16:26:40 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 16:26:40 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5262c63c
sci-biology/pileup: properly name tarball
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/pileup/pileup-0.6.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/pileup/pileup-0.6.ebuild b/sci-biology/pileup/pileup-0.6.ebuild
index ac9359081..54c16576b 100644
--- a/sci-biology/pileup/pileup-0.6.ebuild
+++ b/sci-biology/pileup/pileup-0.6.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=5
DESCRIPTION="SSAHA2-based pipeline to align reads"
HOMEPAGE="http://www.sanger.ac.uk/resources/software/ssaha2/"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/pileup.tgz"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/pileup.tgz -> ${P}.tgz"
# http://samtools.sourceforge.net/pileup.shtml
#
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pileup/
@ 2021-02-03 4:49 Andrew Ammerlaan
0 siblings, 0 replies; 5+ messages in thread
From: Andrew Ammerlaan @ 2021-02-03 4:49 UTC (permalink / raw
To: gentoo-commits
commit: 717a929b44dd20599cfb826e521397cebda099ce
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Feb 3 04:49:05 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Feb 3 04:49:05 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=717a929b
sci-biology/pileup: EAPI bump
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/pileup/pileup-0.6.ebuild | 41 ++++++++++++++++--------------------
1 file changed, 18 insertions(+), 23 deletions(-)
diff --git a/sci-biology/pileup/pileup-0.6.ebuild b/sci-biology/pileup/pileup-0.6.ebuild
index 54c16576b..ad978f70f 100644
--- a/sci-biology/pileup/pileup-0.6.ebuild
+++ b/sci-biology/pileup/pileup-0.6.ebuild
@@ -1,36 +1,36 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
DESCRIPTION="SSAHA2-based pipeline to align reads"
-HOMEPAGE="http://www.sanger.ac.uk/resources/software/ssaha2/"
+HOMEPAGE="https://www.sanger.ac.uk/resources/software/ssaha2/"
SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/pileup.tgz -> ${P}.tgz"
# http://samtools.sourceforge.net/pileup.shtml
#
LICENSE="GRL"
SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/pileup_v"${PV}"
+S="${WORKDIR}/pileup_v${PV}"
src_prepare(){
- sed -i "s/^CC= gcc/#CC= gcc/" ssaha_pileup/ssaha_pileup/makefile || die "sed failed to fix makefile"
- sed -i "s/^CFLAGS= -O2/#CFLAGS= -O2/" ssaha_pileup/ssaha_pileup/makefile || die "sed failed to fix makefile"
+ default
+ sed -i -e "s/^CC= gcc/#CC= gcc/" \
+ -e "s/^CFLAGS= -O2/#CFLAGS= -O2/" \
+ ssaha_pileup/ssaha_pileup/makefile || die "sed failed to fix makefile"
for d in get_seqreads ssaha_split; do
- sed -i "s/^CC = cc/#CC = cc/" ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
- sed -i "s/^CFLAGS = -O4/#CFLAGS = -O4/" ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
+ sed -i -e "s/^CC = cc/#CC = cc/" \
+ -e "s/^CFLAGS = -O4/#CFLAGS = -O4/" \
+ ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
done
for d in search_read ssaha_parseSNP; do
- sed -i "s/^CC = gcc/#CC = gcc/" ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
- sed -i "s/^CFLAGS = -Wall -O4/#CFLAGS = -Wall -O4/" ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
+ sed -i -e "s/^CC = gcc/#CC = gcc/" \
+ -e "s/^CFLAGS = -Wall -O4/#CFLAGS = -Wall -O4/" \
+ ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
done
}
@@ -40,22 +40,17 @@ src_compile(){
for d in get_seqreads ssaha_split ssaha_parseSNP search_read; do
cd "${S}"/ssaha_pileup/other_codes/$d || die "Cannot cd to "${S}"ssaha_pileup/other_codes/"$d
- make clean
+ emake clean
default
done
}
src_install(){
cd ssaha_pileup/ssaha_pileup || die "Cannot cd to "${S}"ssaha_pileup/ssaha_pileup"
- dobin ssaha_pileup ssaha_solexa ssaha_pairs ssaha_clean ssaha_mates ssaha_cigar ssaha_indel view_pileup ssaha_reads ssaha_merge ssaha_check-cigar "dobin failed"
+ dobin ssaha_pileup ssaha_solexa ssaha_pairs ssaha_clean ssaha_mates ssaha_cigar ssaha_indel view_pileup ssaha_reads ssaha_merge ssaha_check-cigar
- cd "${S}" || die
- for f in ssaha_pileup/other_codes/get_seqreads/get_seqreads \
- ssaha_pileup/other_codes/ssaha_split/ssaha_split \
- ssaha_pileup/other_codes/ssaha_parseSNP/ssaha_parseSNP \
- ssaha_pileup/other_codes/search_read/search_read; do
- dobin $f "dobin failed"
- done
+ cd "${S}/ssaha_pileup/other_codes" || die
+ dobin get_seqreads/get_seqreads ssaha_split/ssaha_split ssaha_parseSNP/ssaha_parseSNP search_read/search_read
# TODO:
# pileup_v0.6/ssaha_pileup/tag.pl
^ permalink raw reply related [flat|nested] 5+ messages in thread
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