[gentoo-commits] proj/sci:master commit in: sci-biology/AlignGraph/

[gentoo-commits] proj/sci:master commit in: sci-biology/AlignGraph/

[Martin Mokrejs]

commit:     ab1f6781e9c576702f48058e7d9c86676973b693
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 25 19:04:23 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 25 19:04:23 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ab1f6781

sci-biology/AlignGraph: new package

Package-Manager: portage-2.2.18

 sci-biology/AlignGraph/AlignGraph-9999.ebuild | 53 +++++++++++++++++++++++++++
 sci-biology/AlignGraph/ChangeLog              |  9 +++++
 sci-biology/AlignGraph/metadata.xml           |  9 +++++
 3 files changed, 71 insertions(+)

diff --git a/sci-biology/AlignGraph/AlignGraph-9999.ebuild b/sci-biology/AlignGraph/AlignGraph-9999.ebuild
new file mode 100644
index 0000000..b7e2866
--- /dev/null
+++ b/sci-biology/AlignGraph/AlignGraph-9999.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit toolchain-funcs
+
+if [ "$PV" == "9999" ]; then
+	inherit git-r3
+fi
+
+DESCRIPTION="Asssemble contigs/scaffolds using related reference sequence"
+HOMEPAGE="https://github.com/baoe/AlignGraph
+	http://bioinformatics.oxfordjournals.org/content/30/12/i319.long"
+if [ "$PV" == "9999" ]; then
+	EGIT_REPO_URI="https://github.com/baoe/AlignGraph.git"
+	KEYWORDS=""
+else
+	SRC_URI=""
+	KEYWORDS=""
+fi
+
+LICENSE="Artistic-2"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	sci-biology/blat
+	sci-biology/bowtie"
+
+# AlignGraph runs the alignment steps with BLAT and Bowtie2 automatically, but both 
+# need to be installed on the system. AlignGraph’s run time is currently 23–57 min
+# per million aligned reads. In the performance tests of this study, the memory usage
+# was 36–50 GB, and it stays <100 GB even for entire mammalian genomes. These requirements
+# are more moderate than those of most de novo assemblers (Luo et al., 2012).
+
+# 8 threads are hardcoded. Currently users cannot make changes to this, since this is
+# a moderate choice for either single CPU machines (overhead for parallelization would
+# not be too large) or multiple CPU machines. Another reason is, the bottleneck for the
+# runtime is usually from BLAT, no matter how many threads there are for Bowtie2.
+src_compile(){
+	cd AlignGraph || die
+	$(tc-getCXX) ${CXXFLAGS} -o AlignGraph AlignGraph.cpp -lpthread
+	cd ../Eval-AlignGraph || die
+	$(tc-getCXX) ${CXXFLAGS} -o Eval-AlignGraph Eval-AlignGraph.cpp -lpthread
+}
+
+src_install(){
+	dobin AlignGraph/AlignGraph Eval-AlignGraph/Eval-AlignGraph
+	dodoc README.md
+}

diff --git a/sci-biology/AlignGraph/ChangeLog b/sci-biology/AlignGraph/ChangeLog
new file mode 100644
index 0000000..d6c0196
--- /dev/null
+++ b/sci-biology/AlignGraph/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/AlignGraph
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*AlignGraph-9999 (25 May 2015)
+
+  25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +AlignGraph-9999.ebuild, +metadata.xml:
+  sci-biology/AlignGraph: new package

diff --git a/sci-biology/AlignGraph/metadata.xml b/sci-biology/AlignGraph/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/AlignGraph/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>

[gentoo-commits] proj/sci:master commit in: sci-biology/AlignGraph/

[Martin Mokrejs]

commit:     add8084e363c64f4730fbee8ac16324401972495
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 10 23:22:10 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 10 23:22:10 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=add8084e

sci-biology/AlignGraph: improve package DESCR

Package-Manager: portage-2.2.28

 sci-biology/AlignGraph/AlignGraph-9999.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/AlignGraph/AlignGraph-9999.ebuild b/sci-biology/AlignGraph/AlignGraph-9999.ebuild
index 4a52cfd..9754ee5 100644
--- a/sci-biology/AlignGraph/AlignGraph-9999.ebuild
+++ b/sci-biology/AlignGraph/AlignGraph-9999.ebuild
@@ -10,7 +10,7 @@ if [ "$PV" == "9999" ]; then
 	inherit git-r3
 fi
 
-DESCRIPTION="Asssemble contigs/scaffolds using related reference sequence"
+DESCRIPTION="Reference-assisted asssembly of contigs/scaffolds"
 HOMEPAGE="https://github.com/baoe/AlignGraph
 	http://bioinformatics.oxfordjournals.org/content/30/12/i319.long"
 if [ "$PV" == "9999" ]; then

[gentoo-commits] proj/sci:master commit in: sci-biology/AlignGraph/

[Martin Mokrejs]

commit:     0da82a1a33fe2e91643dc2da891cfd5841417efe
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 23 15:06:01 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 23 15:06:01 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0da82a1a

sci-biology/AlignGraph: improve DESCR; add mummer DEPEND

Package-Manager: portage-2.2.28

 sci-biology/AlignGraph/AlignGraph-9999.ebuild | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sci-biology/AlignGraph/AlignGraph-9999.ebuild b/sci-biology/AlignGraph/AlignGraph-9999.ebuild
index 9754ee5..f6ea6bb 100644
--- a/sci-biology/AlignGraph/AlignGraph-9999.ebuild
+++ b/sci-biology/AlignGraph/AlignGraph-9999.ebuild
@@ -10,7 +10,7 @@ if [ "$PV" == "9999" ]; then
 	inherit git-r3
 fi
 
-DESCRIPTION="Reference-assisted asssembly of contigs/scaffolds"
+DESCRIPTION="Reference-genome-assisted asssembly of contigs/scaffolds using PE reads"
 HOMEPAGE="https://github.com/baoe/AlignGraph
 	http://bioinformatics.oxfordjournals.org/content/30/12/i319.long"
 if [ "$PV" == "9999" ]; then
@@ -27,6 +27,7 @@ IUSE=""
 
 DEPEND=""
 RDEPEND="${DEPEND}
+	sci-biology/mummer
 	sci-biology/blat
 	sci-biology/bowtie"
 

[gentoo-commits] proj/sci:master commit in: sci-biology/AlignGraph/

[Andrew Ammerlaan]

commit:     a0c50cfcca14d8f8884a99ce9d6e95e601471475
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Fri Mar  5 15:19:55 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Fri Mar  5 15:29:11 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a0c50cfc

sci-biology/AlignGraph: EAPI bump

Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/AlignGraph/AlignGraph-9999.ebuild | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/sci-biology/AlignGraph/AlignGraph-9999.ebuild b/sci-biology/AlignGraph/AlignGraph-9999.ebuild
index 46d1029fd..60ea9d6b6 100644
--- a/sci-biology/AlignGraph/AlignGraph-9999.ebuild
+++ b/sci-biology/AlignGraph/AlignGraph-9999.ebuild
@@ -1,18 +1,15 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 inherit toolchain-funcs
 
-if [ "$PV" == "9999" ]; then
-	inherit git-r3
-fi
-
 DESCRIPTION="Reference-genome-assisted asssembly of contigs/scaffolds using PE reads"
 HOMEPAGE="https://github.com/baoe/AlignGraph
 	http://bioinformatics.oxfordjournals.org/content/30/12/i319.long"
 if [ "$PV" == "9999" ]; then
+	inherit git-r3
 	EGIT_REPO_URI="https://github.com/baoe/AlignGraph.git"
 	KEYWORDS=""
 else
@@ -22,13 +19,13 @@ fi
 
 LICENSE="Artistic-2"
 SLOT="0"
-IUSE=""
 
 DEPEND=""
 RDEPEND="${DEPEND}
 	sci-biology/mummer
 	sci-biology/blat
-	sci-biology/bowtie"
+	sci-biology/bowtie
+"
 
 # AlignGraph runs the alignment steps with BLAT and Bowtie2 automatically, but both
 # need to be installed on the system. AlignGraph’s run time is currently 23–57 min

[gentoo-commits] proj/sci:master commit in: sci-biology/AlignGraph/

[Andrew Ammerlaan]

commit:     ca24f2e19942faa1d906b1716b7975458db3bd04
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar 20 11:19:35 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar 20 11:19:35 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ca24f2e1

sci-biology/AlignGraph: fix MultipleKeywordsLines

Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/AlignGraph/AlignGraph-9999.ebuild | 1 -
 1 file changed, 1 deletion(-)

diff --git a/sci-biology/AlignGraph/AlignGraph-9999.ebuild b/sci-biology/AlignGraph/AlignGraph-9999.ebuild
index 60ea9d6b6..f48b436ee 100644
--- a/sci-biology/AlignGraph/AlignGraph-9999.ebuild
+++ b/sci-biology/AlignGraph/AlignGraph-9999.ebuild
@@ -11,7 +11,6 @@ HOMEPAGE="https://github.com/baoe/AlignGraph
 if [ "$PV" == "9999" ]; then
 	inherit git-r3
 	EGIT_REPO_URI="https://github.com/baoe/AlignGraph.git"
-	KEYWORDS=""
 else
 	SRC_URI=""
 	KEYWORDS=""