commit: e2ebfd402720453ee963b6a7ee1e648653405d00
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 15:27:39 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 15:27:39 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e2ebfd40
sci-biology/pufferfish: new dep of salmon
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
.../pufferfish/files/pufferfish-do-not-fetch.patch | 31 +++++++++++++++++++
sci-biology/pufferfish/metadata.xml | 11 +++++++
sci-biology/pufferfish/pufferfish-1.4.0.ebuild | 35 ++++++++++++++++++++++
3 files changed, 77 insertions(+)
diff --git a/sci-biology/pufferfish/files/pufferfish-do-not-fetch.patch
b/sci-biology/pufferfish/files/pufferfish-do-not-fetch.patch
new file mode 100644
index 000000000..c86fe847f
--- /dev/null
+++ b/sci-biology/pufferfish/files/pufferfish-do-not-fetch.patch
@@ -0,0 +1,31 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 7f1516a..90f7cdd 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -282,12 +282,9 @@ message("TBB_LIBRARIES = ${TBB_LIBRARIES}")
+
+
+ ExternalProject_Add(libseqlib
+-GIT_REPOSITORY https://github.com/COMBINE-lab/SeqLib.git
+-GIT_TAG master
+ UPDATE_COMMAND ""
+ UPDATE_DISCONNECTED 1
+ BUILD_IN_SOURCE TRUE
+-DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/seqlib
+ SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/seqlib
+ INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+ CONFIGURE_COMMAND ./configure
+@@ -300,13 +297,10 @@ INSTALL_COMMAND mkdir -p <INSTALL_DIR>/lib && mkdir -p
<INSTALL_DIR>/include &
+ )
+
+ ExternalProject_Add(libSetCover
+- GIT_REPOSITORY https://github.com/martin-steinegger/setcover.git
+- GIT_TAG master
+ UPDATE_COMMAND ""
+ CONFIGURE_COMMAND ""
+ UPDATE_DISCONNECTED 1
+ BUILD_IN_SOURCE TRUE
+- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/setcover
+ SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/setcover
+ INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+ BUILD_COMMAND make -j8
diff --git a/sci-biology/pufferfish/metadata.xml
b/sci-biology/pufferfish/metadata.xml
new file mode 100644
index 000000000..7b582e896
--- /dev/null
+++ b/sci-biology/pufferfish/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
+<pkgmetadata>
+ <maintainer type="project">
+ <email>[email protected]</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">COMBINE-lab/pufferfish</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/pufferfish/pufferfish-1.4.0.ebuild
b/sci-biology/pufferfish/pufferfish-1.4.0.ebuild
new file mode 100644
index 000000000..588970e06
--- /dev/null
+++ b/sci-biology/pufferfish/pufferfish-1.4.0.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+SC_COMMIT="b1de7919c0a4d0e65c5cd0b6d78963516e44be25"
+SL_COMMIT="340dad36dff67ca96815bd412fe65587d4d64479"
+HL_COMMIT="be22a2a1082f6e570718439b9ace2db17a609eae"
+
+DESCRIPTION="Index for the colored, compacted, de Bruijn graph"
+HOMEPAGE="https://github.com/COMBINE-lab/pufferfish";
+SRC_URI="https://github.com/COMBINE-lab/pufferfish/archive/salmon-v${PV}.tar.gz
-> ${P}.tar.gz
+
https://github.com/martin-steinegger/setcover/archive/${SC_COMMIT}.tar.gz ->
setcover-${P}.tar.gz
+ https://github.com/COMBINE-lab/SeqLib/archive/${SL_COMMIT}.tar.gz ->
seqlib-${P}.tar.gz
+ https://github.com/samtools/htslib/archive/${HL_COMMIT}.tar.gz ->
htslib-${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+
+DEPEND="dev-cpp/tbb"
+
+S="${WORKDIR}/${PN}-salmon-v${PV}"
+
+PATCHES=( "${FILESDIR}/${PN}-do-not-fetch.patch" )
+
+src_prepare() {
+ mkdir -p external/{setcover,seqlib}
+ mv "../setcover-${SC_COMMIT}"/* external/setcover || die
+ mv "../SeqLib-${SL_COMMIT}"/* external/seqlib || die
+ mv "../htslib-${HL_COMMIT}"/* external/seqlib/htslib || die
+ cmake_src_prepare
+}
