* [gentoo-commits] proj/sci:master commit in: sci-biology/nanopolish/
@ 2017-07-28 20:05 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2017-07-28 20:05 UTC (permalink / raw
To: gentoo-commits
commit: cef6f206bd05567e80c11b9f9b1e850f74e06731
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 28 19:23:07 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 28 20:05:19 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=cef6f206
sci-biology/nanopolish: new package
Package-Manager: Portage-2.3.6, Repoman-2.3.3
sci-biology/nanopolish/metadata.xml | 12 +++++++
sci-biology/nanopolish/nanopolish-9999.ebuild | 48 +++++++++++++++++++++++++++
2 files changed, 60 insertions(+)
diff --git a/sci-biology/nanopolish/metadata.xml b/sci-biology/nanopolish/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/nanopolish/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/nanopolish/nanopolish-9999.ebuild b/sci-biology/nanopolish/nanopolish-9999.ebuild
new file mode 100644
index 000000000..92c5f41d3
--- /dev/null
+++ b/sci-biology/nanopolish/nanopolish-9999.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit git-r3
+
+DESCRIPTION="Signal-level analysis of Oxford Nanopore sequencing data"
+HOMEPAGE="https://github.com/jts/nanopolish"
+EGIT_REPO_URI="https://github.com/jts/nanopolish.git"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# HDF5 is not thread safe by default and nanopolish currently requires a threadsafe HDF5.
+# This is one reason we download the compile it ourself (the main reason is to make it
+# easier for most users). The other options cxx, fortran, mpi are not needed by nanopolish
+# (we use the C bindings in nanopolish only).
+# The bundled version of htslib in is 1.2.1 as of now although 1.5.1 already exists
+DEPEND=">=sci-libs/hdf5-1.8.14[threads]
+ >=dev-cpp/eigen-3.2.5
+ sci-libs/htslib:0
+ sci-libs/fast5"
+RDEPEND="${DEPEND}
+ sci-biology/biopython"
+
+src_prepare(){
+ default
+ rm -rf hdf5* eigen htslib || die # TODO; zap also fast5
+}
+
+src_compile(){
+ # >=gcc-4.8 but <gcc-7 is needed
+ # https://github.com/jts/nanopolish/issues/145
+ emake HDF5="noinstall" EIGEN="nofetch" HTS_LIB=-lhts HTS_INCLUDE=-I/usr/include/htslib EIGEN_INCLUDE=-I/usr/include/eigen3 # TODO: FAST5_INCLUDE=-I/usr/include/fast5
+}
+
+src_install(){
+ rm -rf lib || die # zap libs eventually compiled from the bundled copies
+ dobin nanopolish
+ # add scripts/ subdirectory to PATH
+}
+
+src_test(){
+ nanopolish_test || die
+}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/nanopolish/
@ 2018-01-24 20:58 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2018-01-24 20:58 UTC (permalink / raw
To: gentoo-commits
commit: 3f6ffb94adc1d3f7209d7ac33edb1fe0165bd487
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 24 20:58:04 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 24 20:58:04 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3f6ffb94
sci-biology/nanopolish: update compile procedure and deps
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/nanopolish/nanopolish-9999.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/nanopolish/nanopolish-9999.ebuild b/sci-biology/nanopolish/nanopolish-9999.ebuild
index 92c5f41d3..cea5cce27 100644
--- a/sci-biology/nanopolish/nanopolish-9999.ebuild
+++ b/sci-biology/nanopolish/nanopolish-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -21,7 +21,7 @@ IUSE=""
# The bundled version of htslib in is 1.2.1 as of now although 1.5.1 already exists
DEPEND=">=sci-libs/hdf5-1.8.14[threads]
>=dev-cpp/eigen-3.2.5
- sci-libs/htslib:0
+ >=sci-libs/htslib-1.4:0
sci-libs/fast5"
RDEPEND="${DEPEND}
sci-biology/biopython"
@@ -34,7 +34,7 @@ src_prepare(){
src_compile(){
# >=gcc-4.8 but <gcc-7 is needed
# https://github.com/jts/nanopolish/issues/145
- emake HDF5="noinstall" EIGEN="nofetch" HTS_LIB=-lhts HTS_INCLUDE=-I/usr/include/htslib EIGEN_INCLUDE=-I/usr/include/eigen3 # TODO: FAST5_INCLUDE=-I/usr/include/fast5
+ emake HDF5="noinstall" EIGEN="noinstall" HTS="noinstall" HTS_LIB=-lhts HTS_INCLUDE=-I/usr/include/htslib EIGEN_INCLUDE=-I/usr/include/eigen3 # TODO: FAST5_INCLUDE=-I/usr/include/fast5
}
src_install(){
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/nanopolish/
@ 2021-03-06 12:49 Andrew Ammerlaan
0 siblings, 0 replies; 3+ messages in thread
From: Andrew Ammerlaan @ 2021-03-06 12:49 UTC (permalink / raw
To: gentoo-commits
commit: c371e248d4b8d2717acc82ed4f902d5c37d7787d
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar 6 12:49:19 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar 6 12:49:19 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c371e248
sci-biology/nanopolish: EAPI bump
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/nanopolish/nanopolish-9999.ebuild | 11 ++---------
1 file changed, 2 insertions(+), 9 deletions(-)
diff --git a/sci-biology/nanopolish/nanopolish-9999.ebuild b/sci-biology/nanopolish/nanopolish-9999.ebuild
index cea5cce27..5ca92904f 100644
--- a/sci-biology/nanopolish/nanopolish-9999.ebuild
+++ b/sci-biology/nanopolish/nanopolish-9999.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
inherit git-r3
@@ -12,7 +12,6 @@ EGIT_REPO_URI="https://github.com/jts/nanopolish.git"
LICENSE="MIT"
SLOT="0"
KEYWORDS=""
-IUSE=""
# HDF5 is not thread safe by default and nanopolish currently requires a threadsafe HDF5.
# This is one reason we download the compile it ourself (the main reason is to make it
@@ -32,8 +31,6 @@ src_prepare(){
}
src_compile(){
- # >=gcc-4.8 but <gcc-7 is needed
- # https://github.com/jts/nanopolish/issues/145
emake HDF5="noinstall" EIGEN="noinstall" HTS="noinstall" HTS_LIB=-lhts HTS_INCLUDE=-I/usr/include/htslib EIGEN_INCLUDE=-I/usr/include/eigen3 # TODO: FAST5_INCLUDE=-I/usr/include/fast5
}
@@ -42,7 +39,3 @@ src_install(){
dobin nanopolish
# add scripts/ subdirectory to PATH
}
-
-src_test(){
- nanopolish_test || die
-}
^ permalink raw reply related [flat|nested] 3+ messages in thread
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