[gentoo-commits] proj/sci:master commit in: sci-biology/SEECER/, sci-biology/SEECER/files/

[Martin Mokrejs]

commit:     d4e2d5a53d73f9a69ca36fbd54fff4ac161398bb
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 30 21:59:43 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 30 21:59:43 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d4e2d5a5

sci-biology/SEECER: added upstream 'patch'; do more proper install process

Package-Manager: portage-2.2.18

 sci-biology/SEECER/ChangeLog              |   7 +++++-
 sci-biology/SEECER/SEECER-0.1.3-r1.ebuild |  35 ++++++++++++++++++++++++++++++
 sci-biology/SEECER/SEECER-0.1.3.ebuild    |  34 -----------------------------
 sci-biology/SEECER/files/replace_ids.cc   | Bin 0 -> 1006 bytes
 4 files changed, 41 insertions(+), 35 deletions(-)

diff --git a/sci-biology/SEECER/ChangeLog b/sci-biology/SEECER/ChangeLog
index 1ac7a38..a57cf30 100644
--- a/sci-biology/SEECER/ChangeLog
+++ b/sci-biology/SEECER/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*SEECER-0.1.3-r1 (30 Apr 2015)
+
+  30 Apr 2015; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
+  +SEECER-0.1.3-r1.ebuild, +files/replace_ids.cc, -SEECER-0.1.3.ebuild:
+  sci-biology/SEECER: added upstream 'patch'; do more proper install process
+
   10 Jan 2015; Justin Lecher <jlec@g.o> SEECER-0.1.3.ebuild:
   Fix license
 
@@ -10,4 +16,3 @@
   07 Jan 2015; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
   +SEECER-0.1.3.ebuild, +metadata.xml:
   initial ebuild
-

diff --git a/sci-biology/SEECER/SEECER-0.1.3-r1.ebuild b/sci-biology/SEECER/SEECER-0.1.3-r1.ebuild
new file mode 100644
index 0000000..bfebed9
--- /dev/null
+++ b/sci-biology/SEECER/SEECER-0.1.3-r1.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="SEquencing Error Corrector for RNA-Seq reads"
+HOMEPAGE="http://sb.cs.cmu.edu/seecer/"
+SRC_URI="
+	http://sb.cs.cmu.edu/seecer/downloads/"${P}".tar.gz
+	http://sb.cs.cmu.edu/seecer/downloads/manual.pdf -> "${PN}"-manual.pdf"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+# although has bundled jellyfish-1.1.11 copy it just calls the executable during runtime
+DEPEND="
+	sci-libs/gsl
+	sci-biology/seqan"
+RDEPEND="${DEPEND}
+	sci-biology/jellyfish"
+
+S="${S}"/SEECER
+
+src_prepare(){
+	# http://seecer-rna-read-error-correction-mailing-list.21961.x6.nabble.com/Segmentation-fault-in-step-4-td41.html
+	cp -p "${FILESDIR}"/replace_ids.cc "${S}"/src/ || die
+}
+
+src_install(){
+	dobin bin/seecer bin/random_sub_N bin/replace_ids bin/run_jellyfish.sh
+	dodoc README "${DISTDIR}"/"${PN}"-manual.pdf
+}

diff --git a/sci-biology/SEECER/SEECER-0.1.3.ebuild b/sci-biology/SEECER/SEECER-0.1.3.ebuild
deleted file mode 100644
index d415a01..0000000
--- a/sci-biology/SEECER/SEECER-0.1.3.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-DESCRIPTION="Error corrector for RNA-Seq reads"
-HOMEPAGE="http://sb.cs.cmu.edu/seecer/"
-SRC_URI="
-	http://sb.cs.cmu.edu/seecer/downloads/SEECER-0.1.3.tar.gz
-	http://sb.cs.cmu.edu/seecer/downloads/manual.pdf"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	sci-libs/gsl
-	sci-biology/seqan
-	sci-biology/jellyfish"
-RDEPEND="${DEPEND}"
-
-S="${S}"/SEECER
-
-# doh, it install /usr/bin/seecer (note the lowercase letters)
-
-# checking for x86_64-pc-linux-gnu-gcc option to support OpenMP... -fopenmp
-# 
-# Uses:
-#         libgomp.so.1 => /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.3/libgomp.so.1 (0x00007f7853faf000)
-
-# dobin bin/run_seecer.sh
-# dodoc "${DISTDIR}"/manual.pdf

diff --git a/sci-biology/SEECER/files/replace_ids.cc b/sci-biology/SEECER/files/replace_ids.cc
new file mode 100644
index 0000000..0a77819
Binary files /dev/null and b/sci-biology/SEECER/files/replace_ids.cc differ