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* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/files/, sci-biology/salmon/
@ 2015-05-24  8:14 Justin Lecher
  0 siblings, 0 replies; 5+ messages in thread
From: Justin Lecher @ 2015-05-24  8:14 UTC (permalink / raw
  To: gentoo-commits

commit:     01e354c4ff4b1404ab3fc884363af8b73a799c3c
Author:     layman <layman <AT> localhost>
AuthorDate: Thu May 21 17:48:15 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu May 21 17:48:15 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=01e354c4

sci-biology/salmon: add salmon

Package-Manager: portage-2.2.14-prefix

 sci-biology/salmon/ChangeLog                       | 11 ++++++++++
 .../files/salmon-0.3.2-no-boost-static.patch       | 16 +++++++++++++++
 sci-biology/salmon/metadata.xml                    |  9 ++++++++
 sci-biology/salmon/salmon-0.3.2.ebuild             | 23 +++++++++++++++++++++
 sci-biology/salmon/salmon-9999.ebuild              | 24 ++++++++++++++++++++++
 5 files changed, 83 insertions(+)

diff --git a/sci-biology/salmon/ChangeLog b/sci-biology/salmon/ChangeLog
new file mode 100644
index 0000000..83c1c81
--- /dev/null
+++ b/sci-biology/salmon/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/salmon
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*salmon-0.3.2 (21 May 2015)
+*salmon-9999 (21 May 2015)
+
+  21 May 2015; Michael Schubert <mschu.dev@gmail.com>
+  +files/salmon-0.3.2-no-boost-static.patch, +metadata.xml,
+  +salmon-0.3.2.ebuild, +salmon-9999.ebuild:
+  sci-biology/salmon: add salmon

diff --git a/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch b/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch
new file mode 100644
index 0000000..6a00ebe
--- /dev/null
+++ b/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch
@@ -0,0 +1,16 @@
+--- CMakeLists.txt.orig	2015-05-19 23:39:27.969165466 +0100
++++ CMakeLists.txt	2015-05-19 23:39:40.154150194 +0100
+@@ -162,13 +162,6 @@ if ( DEFINED CUSTOM_BOOST_PATH )
+     set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH})
+ endif ( DEFINED CUSTOM_BOOST_PATH )
+ 
+-##
+-# We want static, multithreaded boost libraries
+-##
+-set (Boost_USE_STATIC_LIBS ON)
+-set (Boost_USE_MULTITHREADED ON)
+-#set (Boost_USE_STATIC_RUNTIME OFF)
+-
+ find_package (ZLIB)
+ if (NOT ZLIB_FOUND)
+ 	message (FATAL_ERROR "zlib must be installed before configuration & building can proceed")

diff --git a/sci-biology/salmon/metadata.xml b/sci-biology/salmon/metadata.xml
new file mode 100644
index 0000000..b7551a6
--- /dev/null
+++ b/sci-biology/salmon/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>mschu.dev@gmail.com</email>
+    <name>Michael Schubert</name>
+  </maintainer>
+</pkgmetadata>

diff --git a/sci-biology/salmon/salmon-0.3.2.ebuild b/sci-biology/salmon/salmon-0.3.2.ebuild
new file mode 100644
index 0000000..59ab07e
--- /dev/null
+++ b/sci-biology/salmon/salmon-0.3.2.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit cmake-utils
+
+DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
+HOMEPAGE="https://github.com/COMBINE-lab/salmon"
+SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	epatch "${FILESDIR}/${P}-no-boost-static.patch"
+}

diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
new file mode 100644
index 0000000..e631316
--- /dev/null
+++ b/sci-biology/salmon/salmon-9999.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit git-r3 cmake-utils
+
+DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
+HOMEPAGE="https://github.com/COMBINE-lab/salmon"
+SRC_URI=""
+EGIT_REPO_URI="https://github.com/COMBINE-lab/salmon.git"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	epatch "${FILESDIR}/${PN}-0.3.2-no-boost-static.patch"
+}


^ permalink raw reply related	[flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/files/, sci-biology/salmon/
@ 2015-05-24  8:14 Justin Lecher
  0 siblings, 0 replies; 5+ messages in thread
From: Justin Lecher @ 2015-05-24  8:14 UTC (permalink / raw
  To: gentoo-commits

commit:     dcb74cb59f386ac2a66e9daa3cca68b363296241
Author:     layman <layman <AT> localhost>
AuthorDate: Sat May 23 17:00:12 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat May 23 17:00:12 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=dcb74cb5

sci-biology/salmon: clean patch

Package-Manager: portage-2.2.14-prefix

 sci-biology/salmon/ChangeLog                                | 4 ++++
 sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch | 8 ++++++--
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/sci-biology/salmon/ChangeLog b/sci-biology/salmon/ChangeLog
index e3d76fd..b897449 100644
--- a/sci-biology/salmon/ChangeLog
+++ b/sci-biology/salmon/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  23 May 2015; Michael Schubert <mschu.dev@gmail.com>
+  files/salmon-0.3.2-no-boost-static.patch:
+  sci-biology/salmon: clean patch
+
   21 May 2015; Michael Schubert <mschu.dev@gmail.com> salmon-0.3.2.ebuild,
   salmon-9999.ebuild:
   sci-biology/salmon: streamline ebuild

diff --git a/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch b/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch
index 6a00ebe..edc09e7 100644
--- a/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch
+++ b/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch
@@ -1,5 +1,9 @@
---- CMakeLists.txt.orig	2015-05-19 23:39:27.969165466 +0100
-+++ CMakeLists.txt	2015-05-19 23:39:40.154150194 +0100
+Do not force static and multithreaded boost libs, use what is available
+
+Patch by Michael Schubert
+
+--- CMakeLists.txt
++++ CMakeLists.txt
 @@ -162,13 +162,6 @@ if ( DEFINED CUSTOM_BOOST_PATH )
      set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH})
  endif ( DEFINED CUSTOM_BOOST_PATH )


^ permalink raw reply related	[flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/files/, sci-biology/salmon/
@ 2018-06-25 12:14 Martin Mokrejs
  0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2018-06-25 12:14 UTC (permalink / raw
  To: gentoo-commits

commit:     0f24b4873a8cc38eaf05aa590d26f40a640e4b4b
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jun 25 12:14:06 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jun 25 12:14:06 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0f24b487

sci-biology/salmon: drop calls to curl, fix libdir

This zaps all calls to curl downloads during compile time
except those for Google tbb. It should not get executed anyway
as the dev-cpp/tbb dependency is enforced.

Package-Manager: Portage-2.3.40, Repoman-2.3.9

 .../salmon/files/salmon-0.10.2_fix_lib_dir.patch   |  22 +++
 .../files/salmon-0.10.2_remove_curl_calls.patch    | 200 +++++++++++++++++++++
 sci-biology/salmon/salmon-0.10.2.ebuild            |  23 ++-
 sci-biology/salmon/salmon-9999.ebuild              |   9 +-
 4 files changed, 244 insertions(+), 10 deletions(-)

diff --git a/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch b/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch
new file mode 100644
index 000000000..eb606c00c
--- /dev/null
+++ b/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch
@@ -0,0 +1,22 @@
+--- salmon-0.10.2/src/CMakeLists.txt	2018-06-25 13:35:45.723519730 +0200
++++ salmon-0.10.2/src/CMakeLists.txt	2018-06-25 13:44:01.326139539 +0200
+@@ -296,6 +296,8 @@
+     )
+ ENDIF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+ 
++include(GNUInstallDirs)
++
+ set(INSTALL_LIB_DIR lib )
+ set(INSTALL_BIN_DIR bin )
+ set(INSTALL_INCLUDE_DIR include )
+@@ -311,8 +313,8 @@
+ 
+ install(TARGETS salmon salmon_core
+                 RUNTIME DESTINATION bin
+-                LIBRARY DESTINATION lib
+-                ARCHIVE DESTINATION lib
++                LIBRARY DESTINATION "${CMAKE_INSTALL_FULL_LIBDIR}"
++                ARCHIVE DESTINATION "${CMAKE_INSTALL_FULL_LIBDIR}"
+         )
+ 
+ add_custom_command(TARGET unitTests POST_BUILD

diff --git a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch
new file mode 100644
index 000000000..438763960
--- /dev/null
+++ b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch
@@ -0,0 +1,200 @@
+--- salmon-0.10.2/CMakeLists.txt	2018-06-25 13:12:49.275828719 +0200
++++ salmon-0.10.2/CMakeLists.txt	2018-06-25 13:12:38.945565690 +0200
+@@ -235,31 +235,7 @@
+ 
+ find_package (LibLZMA)
+ if (NOT LIBLZMA_FOUND)
+-    message ("Will attempt to fetch and build liblzma")
+-    message ("=======================================")
+-ExternalProject_Add(liblzma
+-    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+-    ##
+-    DOWNLOAD_COMMAND curl -k -L http://tukaani.org/xz/xz-5.2.2.tar.gz -o xz-5.2.2.tar.gz &&
+-                     ${SHASUM} 73df4d5d34f0468bd57d09f2d8af363e95ed6cc3a4a86129d2f2c366259902a2 xz-5.2.2.tar.gz &&
+-                     tar -xzvf xz-5.2.2.tar.gz
+-    #URL http://tukaani.org/xz/xz-5.2.2.tar.gz
+-    #URL_HASH SHA1=14663612422ab61386673be78fbb2556f50a1f08
+-    ##
+-    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2
+-    INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+-    BUILD_IN_SOURCE TRUE
+-    CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} CPPFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} LDFLAGS=${EXTRA_CMAKE_LIBRARY_FLAGS}
+-    BUILD_COMMAND make ${QUIET_MAKE}
+-    INSTALL_COMMAND make ${QUIET_MAKE} install
+-)
+-
+-# Tell cmake that the external project generated a library so we can
+-# add dependencies here instead of later
+-set (LIBLZMA_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/liblzma.a)
+-set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib")
+-set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
+-set (FETCHED_LIBLZMA TRUE)
++    message (FATAL_ERROR "liblzma must be installed before configuration & building can proceed")
+ else()
+     message("Found liblzma library: ${LIBLZMA_LIBRARIES}")
+     message("===========================================")
+@@ -267,28 +243,7 @@
+ 
+ find_package (BZip2)
+ if (NOT BZIP2_FOUND)
+-    message ("Will attempt to fetch and build libbz2")
+-    message ("=======================================")
+-ExternalProject_Add(libbz2
+-    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+-    DOWNLOAD_COMMAND curl -k -L http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz -o bzip2-1.0.6.tar.gz &&
+-                     ${SHASUM} a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd bzip2-1.0.6.tar.gz &&
+-                     tar -xzvf  bzip2-1.0.6.tar.gz
+-    #URL http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
+-    #URL_HASH SHA1=3f89f861209ce81a6bab1fd1998c0ef311712002
+-    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bzip2-1.0.6
+-    INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+-    BUILD_IN_SOURCE TRUE
+-    CONFIGURE_COMMAND ""
+-    BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
+-    INSTALL_COMMAND make ${QUIET_MAKE} install PREFIX=<INSTALL_DIR>
+-)
+-# Tell cmake that the external project generated a library so we can
+-# add dependencies here instead of later
+-set (BZIP2_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/libbz2.a)
+-set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib -I${GAT_SOURCE_DIR}/external/install/include")
+-set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
+-set (FETCHED_LIBBZ2 TRUE)
++    message (FATAL_ERROR "libbz2 must be installed before configuration & building can proceed")
+ else()
+     message("Found libbz2 library: ${BZIP2_LIBRARIES}")
+     message("===========================================")
+@@ -333,61 +288,15 @@
+ # Either inform the user of how to obtain Boost, or, if they passed in the FETCH_BOOST
+ # option, go and grab it for them.
+ ##
+-if ((NOT Boost_FOUND) AND (NOT FETCH_BOOST))
++if (NOT Boost_FOUND)
+ 	message(FATAL_ERROR
+         "Salmon cannot be compiled without Boost.\n"
+         "It is recommended to visit http://www.boost.org/ and install Boost according to those instructions.\n"
+         "This build system can also download and install a local version of boost for you (this takes a lot of time).\n"
+         "To fetch and build boost locally, call cmake with -DFETCH_BOOST=TRUE"
+     )
+-elseif(FETCH_BOOST)
+-    ## Let the rest of the build process know we're going to be fetching boost
+-    set (BOOST_LIB_SUBSET --with-iostreams --with-atomic --with-chrono --with-container --with-date_time --with-exception
+-                          --with-filesystem --with-graph --with-graph_parallel --with-math
+-                          --with-program_options --with-system --with-thread
+-                          --with-timer)
+-    set (BOOST_WILL_RECONFIGURE TRUE)
+-    set (FETCH_BOOST FALSE)
+-    message("Build system will fetch and build Boost")
+-    message("==================================================================")
+-    ExternalProject_Add(libboost
+-        DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+-        DOWNLOAD_COMMAND curl -k -L  http://downloads.sourceforge.net/project/boost/boost/1.66.0/boost_1_66_0.tar.gz -o boost_1_66_0.tar.gz &&
+-                         ${SHASUM} bd0df411efd9a585e5a2212275f8762079fed8842264954675a4fddc46cfcf60 boost_1_66_0.tar.gz &&
+-                         tar xzf boost_1_66_0.tar.gz
+-        SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0
+-        INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+-        #PATCH_COMMAND patch -p2 < ${CMAKE_CURRENT_SOURCE_DIR}/external/boost156.patch
+-	CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/bootstrap.sh ${BOOST_CONFIGURE_TOOLSET} ${BOOST_BUILD_LIBS} --prefix=<INSTALL_DIR>
+-	BUILD_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/b2 -d0 -j2 ${BOOST_LIB_SUBSET} toolset=${BOOST_TOOLSET} ${BOOST_EXTRA_FLAGS} cxxflags=${BOOST_CXX_FLAGS} link=static install
+-        BUILD_IN_SOURCE 1
+-        INSTALL_COMMAND ""
+-    )
+-
+-    ##
+-    # After we've installed boost,
+-    ##
+-    SET( RECONFIG_FLAGS ${RECONFIG_FLAGS} -DBOOST_WILL_RECONFIGURE=FALSE -DBOOST_RECONFIGURE=TRUE -DFETCH_BOOST=FALSE)
+-    ExternalProject_Add_Step(libboost reconfigure
+-        COMMAND ${CMAKE_COMMAND} ${CMAKE_CURRENT_SOURCE_DIR} ${RECONFIG_FLAGS}
+-        DEPENDEES install
+-    )
+-    set (FETCHED_BOOST TRUE)
+ endif()
+ 
+-##
+-# If we're fetching boost and we need to have dummy paths for these variables
+-# so that CMake won't complain
+-##
+-if (BOOST_WILL_RECONFIGURE)
+-    message("Setting Temporary Boost paths")
+-    set(Boost_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
+-    set(Boost_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
+-    set(Boost_LIBRARY_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib)
+-    set(Boost_FOUND TRUE)
+-endif()
+-
+-
+ message("BOOST INCLUDE DIR = ${Boost_INCLUDE_DIR}")
+ message("BOOST INCLUDE DIRS = ${Boost_INCLUDE_DIRS}")
+ message("BOOST LIB DIR = ${Boost_LIBRARY_DIRS}")
+@@ -422,9 +331,9 @@
+ include(ExternalProject)
+ ExternalProject_Add(libcereal
+     DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+-    DOWNLOAD_COMMAND curl -k -L https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -o cereal-v1.2.2.tar.gz &&		 
+-                     ${SHASUM} 1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4  cereal-v1.2.2.tar.gz &&
+-                     tar -xzvf cereal-v1.2.2.tar.gz
++    DOWNLOAD_COMMAND cp ../../../distdir/cereal-1.2.2.tar.gz . &&		 
++                     ${SHASUM} 1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4  cereal-1.2.2.tar.gz &&
++                     tar -xzvf cereal-1.2.2.tar.gz
+ 
+     ##
+     #URL https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz
+@@ -455,12 +364,12 @@
+ ExternalProject_Add(libbwa
+     DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+     #URL https://github.com/COMBINE-lab/bwa/archive/0.7.12.3.tar.gz
+-    #DOWNLOAD_NAME bwa-master.tar.gz
+-    DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -o bwa-master.tar.gz &&
+-                    ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 bwa-master.tar.gz &&
+-                    mkdir -p bwa-master &&
+-                    tar -xzvf bwa-master.tar.gz --strip-components=1 -C bwa-master
+-    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-master
++    #DOWNLOAD_NAME bwa-0.7.12.5.tar.gz
++    DOWNLOAD_COMMAND cp ../../../distdir/bwa-0.7.12.5.tar.gz . &&
++                    ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 bwa-0.7.12.5.tar.gz &&
++                    mkdir -p bwa-0.7.12.5 &&
++                    tar -xzvf bwa-0.7.12.5.tar.gz --strip-components=1 -C bwa-0.7.12.5
++    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-0.7.12.5
+     INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+     CONFIGURE_COMMAND ""
+     BUILD_COMMAND sh -c "make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}"
+@@ -562,9 +471,9 @@
+ message("==================================================================")
+ ExternalProject_Add(libgff
+     DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+-    DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -o libgff.tgz &&
+-                     ${SHASUM} 34597ecd3718e6d6e7a1dd4350220664be2c1cd992070d1218564a20d7aa5697  libgff.tgz &&
+-                     tar -xzvf libgff.tgz 
++    DOWNLOAD_COMMAND cp ../../../distdir/libgff-1.1.tgz . &&
++                     ${SHASUM} 34597ecd3718e6d6e7a1dd4350220664be2c1cd992070d1218564a20d7aa5697 libgff-1.1.tgz &&
++                     tar -xzvf libgff-1.1.tgz
+     ##
+     #URL https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
+     #DOWNLOAD_NAME libff.tgz
+@@ -600,10 +509,10 @@
+ message("==================================================================")
+ ExternalProject_Add(libstadenio
+     DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+-    DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -o staden-io_lib-v1.14.8.tar.gz &&
+-                     ${SHASUM} f6f30eefa478cfb708f3109a35fb6ffa0e24951d9d971985df2cef5919dd0bc3 staden-io_lib-v1.14.8.tar.gz &&
++    DOWNLOAD_COMMAND cp ../../../distdir/staden-io_lib-1.14.8.tar.gz . &&
++                     ${SHASUM} f6f30eefa478cfb708f3109a35fb6ffa0e24951d9d971985df2cef5919dd0bc3 staden-io_lib-1.14.8.tar.gz &&
+                      mkdir -p staden-io_lib-1.14.8 &&
+-                     tar -xzf staden-io_lib-v1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 &&
++                     tar -xzf staden-io_lib-1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 &&
+                      rm -fr staden-io_lib &&
+                      mv -f staden-io_lib-1.14.8 staden-io_lib
+     SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/staden-io_lib
+@@ -620,9 +529,9 @@
+ message("==================================================================")
+ ExternalProject_Add(libspdlog
+     DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+-    DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -o spdlog-v0.16.1.tar.gz &&
+-                     ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-v0.16.1.tar.gz &&
+-                     tar -xzf spdlog-v0.16.1.tar.gz 
++    DOWNLOAD_COMMAND cp ../../../distdir/spdlog-0.16.1.tar.gz . &&
++                     ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-0.16.1.tar.gz &&
++                     tar -xzf spdlog-0.16.1.tar.gz 
+     ##
+     #URL https://github.com/COMBINE-lab/spdlog/archive/v0.12.0.tar.gz
+     #DOWNLOAD_NAME spdlog-v0.12.0.tar.gz

diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild
index 540225019..b3bdc6d53 100644
--- a/sci-biology/salmon/salmon-0.10.2.ebuild
+++ b/sci-biology/salmon/salmon-0.10.2.ebuild
@@ -8,7 +8,12 @@ inherit cmake-utils
 DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
 HOMEPAGE="https://github.com/COMBINE-lab/salmon"
 SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.10.2.zip -> ${P}_RapMap.zip"
+	https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.10.2.zip -> ${P}_RapMap.zip
+	https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -> cereal-1.2.2.tar.gz
+	https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -> bwa-0.7.12.5.tar.gz
+	https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -> libgff-1.1.tgz
+	https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -> staden-io_lib-1.14.8.tar.gz
+	https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -> spdlog-0.16.1.tar.gz"
 
 LICENSE="GPL-3"
 SLOT="0"
@@ -16,7 +21,9 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE=""
 
 PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch
-		"${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch )
+		"${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch
+		"${FILESDIR}"/salmon-0.10.2_remove_curl_calls.patch
+		"${FILESDIR}"/salmon-0.10.2_fix_lib_dir.patch )
 
 RDEPEND="${DEPEND}"
 # budled copies of:
@@ -31,15 +38,15 @@ RDEPEND="${DEPEND}"
 #
 # dev-libs/spdlog-0.16.1
 # cereal-1.2.2
-DEPEND="sys-libs/zlib
+
+# see the many curl executions:
+# salmon-0.10.2$ find . -type f | xargs grep curl 2>/dev/null
+#
+DEPEND="net-misc/curl
+		sys-libs/zlib
 		app-arch/bzip2
 		app-arch/xz-utils
 		dev-libs/boost:0[threads]
 		>=dev-libs/jemalloc-5.0.1
 		>=dev-cpp/tbb-2018.20180312"
 RDEPEND="${DEPEND}"
-
-src_install() {
-	cmake-utils_src_install
-	rm -r "${ED}"/usr/tests || die
-}

diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
index 0083648fb..b5e748fd2 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-9999.ebuild
@@ -29,7 +29,8 @@ PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch
 #
 # dev-libs/spdlog-0.16.1
 # cereal-1.2.2
-DEPEND="sys-libs/zlib
+DEPEND="net-misc/curl
+		sys-libs/zlib
 		app-arch/bzip2
 		app-arch/xz-utils
 		dev-libs/boost:0[threads]
@@ -53,6 +54,10 @@ RDEPEND="${DEPEND}"
 # and maybe more
 
 # See https://github.com/COMBINE-lab/salmon/issues/236 for Cmake tweaks needed by Debian
+
+# see the many curl executions:
+# salmon-0.10.2$ find . -type f | xargs grep curl 2>/dev/null
+#
 src_configure(){
 	local mycmakeargs=(
 		"-DBOOST_INCLUDEDIR=${EPREFIX}/usr/include/boost/"
@@ -67,5 +72,5 @@ src_configure(){
 
 src_install() {
 	cmake-utils_src_install
-	rm -r "${ED}"/usr/tests || die
+	rm -rf "${ED}"/usr/tests || die
 }


^ permalink raw reply related	[flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/files/, sci-biology/salmon/
@ 2018-06-26  8:51 Martin Mokrejs
  0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2018-06-26  8:51 UTC (permalink / raw
  To: gentoo-commits

commit:     be33780bc70d6cc463c236d5e2ceb2273170c191
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jun 26 08:51:34 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jun 26 08:51:34 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=be33780b

sci-biology/salmon: fix variablenames

Thanks to @kiwifb for spotting two improperly used variablenames

https://github.com/gentoo/sci/commit/a1d0487c37ba900c1f239f5d73f7d429f018359d#commitcomment-29493393
https://github.com/gentoo/sci/commit/a1d0487c37ba900c1f239f5d73f7d429f018359d#commitcomment-29493465

Package-Manager: Portage-2.3.40, Repoman-2.3.9

 .../salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch    | 11 +++++++++++
 sci-biology/salmon/salmon-0.10.2.ebuild                       |  3 ++-
 sci-biology/salmon/salmon-9999.ebuild                         |  3 ++-
 3 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch b/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch
new file mode 100644
index 000000000..81edf96f5
--- /dev/null
+++ b/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch
@@ -0,0 +1,11 @@
+--- salmon-0.10.2/cmake/TestSalmonQuasi.cmake	2018-06-26 10:39:51.061971241 +0200
++++ salmon-0.10.2/cmake/TestSalmonQuasi.cmake	2018-06-26 10:40:22.372822258 +0200
+@@ -5,7 +5,7 @@
+                 )
+ 
+ if (SALMON_QUASI_INDEX_RESULT)
+-    message(FATAL_ERROR "Error running ${SALMON_QUASI_INDEX_COMMAND}")
++    message(FATAL_ERROR "Error running ${SALMON_QUASI_INDEX_CMD}")
+ endif()
+ 
+ set(SALMON_QUANT_COMMAND ${CMAKE_BINARY_DIR}/salmon quant -i sample_salmon_quasi_index -l IU -1 reads_1.fastq -2 reads_2.fastq -o sample_salmon_quasi_quant)

diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild
index 84d73ea9e..088fea331 100644
--- a/sci-biology/salmon/salmon-0.10.2.ebuild
+++ b/sci-biology/salmon/salmon-0.10.2.ebuild
@@ -24,7 +24,8 @@ PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch
 		"${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch
 		"${FILESDIR}"/salmon-0.10.2_remove_curl_calls.patch
 		"${FILESDIR}"/salmon-0.10.2_fix_lib_dir.patch
-		"${FILESDIR}"/salmon-0.10.2_fix_tests.patch )
+		"${FILESDIR}"/salmon-0.10.2_fix_tests.patch
+		"${FILESDIR}"/salmon-0.10.2_TestSalmonQuasi.cmake.patch )
 
 RDEPEND="${DEPEND}"
 # budled copies of:

diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
index 0b19da725..8862ff790 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-9999.ebuild
@@ -23,7 +23,8 @@ PATCHES=( "${FILESDIR}"/salmon-0.10.2-no-boost-static.patch
 	"${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch
 	"${FILESDIR}"/salmon-0.10.2_remove_curl_calls.patch
 	"${FILESDIR}"/salmon-0.10.2_fix_lib_dir.patch
-	"${FILESDIR}"/salmon-0.10.2_fix_tests.patch )
+	"${FILESDIR}"/salmon-0.10.2_fix_tests.patch
+	"${FILESDIR}"/salmon-0.10.2_TestSalmonQuasi.cmake.patch )
 
 # budled copies of:
 # sci-biology/bwa-0.7.12.5


^ permalink raw reply related	[flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/files/, sci-biology/salmon/
@ 2022-01-25 13:06 Andrew Ammerlaan
  0 siblings, 0 replies; 5+ messages in thread
From: Andrew Ammerlaan @ 2022-01-25 13:06 UTC (permalink / raw
  To: gentoo-commits

commit:     5514f84d164bf7fb697b19eb7f7661e14ad0b718
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 13:05:59 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 13:05:59 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5514f84d

sci-biology/salmon: bump to 1.6.0

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 .../salmon/files/salmon-1.6.0-find-boost.patch     | 116 +++++++++++++++++++++
 sci-biology/salmon/salmon-1.4.0.ebuild             |  38 -------
 sci-biology/salmon/salmon-1.6.0.ebuild             |  70 +++++++++++++
 3 files changed, 186 insertions(+), 38 deletions(-)

diff --git a/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch b/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch
new file mode 100644
index 000000000..76ef25547
--- /dev/null
+++ b/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch
@@ -0,0 +1,116 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 1be02ab..48ffda2 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -428,9 +428,9 @@ endif()
+ ##
+ # Set the latest version and look for what we need
+ ##
+-set(Boost_ADDITIONAL_VERSIONS "1.59.0" "1.60.0" "1.61.0" "1.62.0" "1.63.0" "1.64.0" "1.65.0" "1.66.0" "1.67.0" "1.68.0" "1.69.0" "1.70.0" "1.71.0")
++set(Boost_ADDITIONAL_VERSIONS "1.59.0" "1.60.0" "1.61.0" "1.62.0" "1.63.0" "1.64.0" "1.65.0" "1.66.0" "1.67.0" "1.68.0" "1.69.0" "1.70.0" "1.71.0" "1.77.0" "1.78.0")
+ if (NOT BOOST_RECONFIGURE)
+-find_package(Boost 1.59.0 COMPONENTS iostreams filesystem system timer chrono program_options)
++find_package(Boost 1.59.0 COMPONENTS ALL)
+ message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
+ message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
+ message("Boost_FOUND = ${Boost_FOUND}")
+@@ -610,7 +610,7 @@ if (NOT CEREAL_FOUND)
+ endif()
+ 
+ ## Try and find TBB first
+-find_package(TBB 2019.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy)
++find_package(TBB)
+ 
+ ## NOTE: we actually require at least 2019 U4 or greater
+ ## since we are using tbb::global_control.  However, they 
+@@ -618,12 +618,8 @@ find_package(TBB 2019.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy)
+ ## source.  Check before release if we can bump to the 2020
+ ## version (requires having tbb 2020 for OSX).
+ if (${TBB_FOUND})
+-  if (${TBB_VERSION} VERSION_GREATER_EQUAL 2019.0)
+   message("FOUND SUITABLE TBB VERSION : ${TBB_VERSION}")
+   set(TBB_TARGET_EXISTED TRUE)
+-  else()
+-    set(TBB_TARGET_EXISTED FALSE)
+-  endif()
+ else()
+   set(TBB_TARGET_EXISTED FALSE)
+ endif()
+@@ -750,10 +746,6 @@ if(NOT libgff_FOUND)
+   message("Build system will compile libgff")
+   message("==================================================================")
+   externalproject_add(libgff
+-    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+-    DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/libgff/archive/v2.0.0.tar.gz -o libgff.tgz &&
+-      ${SHASUM} 7656b19459a7ca7d2fd0fcec4f2e0fd0deec1b4f39c703a114e8f4c22d82a99c libgff.tgz &&
+-      tar -xzvf libgff.tgz
+     ##
+     #URL https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
+     #DOWNLOAD_NAME libff.tgz
+diff --git a/cmake/Modules/FindTBB.cmake b/cmake/Modules/FindTBB.cmake
+index c8b3eb5..b4c23da 100644
+--- a/cmake/Modules/FindTBB.cmake
++++ b/cmake/Modules/FindTBB.cmake
+@@ -184,7 +184,6 @@ if(NOT TBB_FOUND)
+   ##################################
+ 
+   if(TBB_INCLUDE_DIRS)
+-    file(READ "${TBB_INCLUDE_DIRS}/tbb/tbb_stddef.h" _tbb_version_file)
+     string(REGEX REPLACE ".*#define TBB_VERSION_MAJOR ([0-9]+).*" "\\1"
+         TBB_VERSION_MAJOR "${_tbb_version_file}")
+     string(REGEX REPLACE ".*#define TBB_VERSION_MINOR ([0-9]+).*" "\\1"
+diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh
+index d32e131..1b5cbf2 100755
+--- a/scripts/fetchPufferfish.sh
++++ b/scripts/fetchPufferfish.sh
+@@ -10,18 +10,6 @@ CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+ EXTERNAL_DIR=${CURR_DIR}/../external
+ INSTALL_DIR=${CURR_DIR}/../external/install
+ 
+-if [ -d ${EXTERNAL_DIR}/pufferfish ] ; then
+-    rm -fr ${EXTERNAL_DIR}/pufferfish
+-fi
+-
+-if [ -d ${INSTALL_DIR}/include/pufferfish ] ; then
+-    rm -fr ${INSTALL_DIR}/include/pufferfish
+-fi
+-
+-if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then
+-    rm -fr ${INSTALL_DIR}/src/pufferfish
+-fi
+-
+ SVER=salmon-v1.6.0
+ #SVER=develop
+ #SVER=sketch-mode
+@@ -29,31 +17,6 @@ SVER=salmon-v1.6.0
+ EXPECTED_SHA256=f71b3c08f254200fcdc2eb8fe3dcca8a8e9489e79ef5952a4958d8b9979831dc
+ 
+ mkdir -p ${EXTERNAL_DIR}
+-curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip
+-
+-hashcheck=""
+-if exists sha256sum; then
+-	hashcheck="sha256sum"
+-elif exists shasum; then
+-	hashcheck="shasum -a256"
+-else
+-	unset hashcheck
+-fi
+-
+-if [ -z "${hashcheck-}" ]; then
+-    echo "Couldn't find shasum command; can't verify contents of downloaded pufferfish";
+-else
+-    if [[ $SVER != develop ]]; then
+-        echo "${EXPECTED_SHA256}  ${EXTERNAL_DIR}/pufferfish.zip" | ${hashcheck} -c - || { echo "pufferfish.zip did not match expected SHA1! Exiting."; exit 1; }
+-    else
+-        echo "not testing sha since pulling from develop"
+-    fi
+-fi
+-
+-
+-rm -fr ${EXTERNAL_DIR}/pufferfish
+-unzip ${EXTERNAL_DIR}/pufferfish.zip -d ${EXTERNAL_DIR}
+-mv ${EXTERNAL_DIR}/pufferfish-${SVER} ${EXTERNAL_DIR}/pufferfish
+ 
+ mkdir -p ${INSTALL_DIR}/include/pufferfish
+ 

diff --git a/sci-biology/salmon/salmon-1.4.0.ebuild b/sci-biology/salmon/salmon-1.4.0.ebuild
deleted file mode 100644
index 420cb2ae2..000000000
--- a/sci-biology/salmon/salmon-1.4.0.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
-HOMEPAGE="https://github.com/COMBINE-lab/salmon"
-SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-
-RDEPEND="
-	dev-libs/boost:=[threads(-)]
-	sys-libs/zlib
-"
-
-DEPEND="${RDEPEND}
-	app-arch/bzip2
-	app-arch/xz-utils
-	>=dev-libs/jemalloc-5.0.1
-	>=dev-cpp/tbb-2018.20180312
-	sci-biology/pufferfish
-	dev-libs/cereal
-"
-
-BDEPEND="
-	app-arch/unzip
-	net-misc/curl
-"
-
-PATCHES=(
-	"${FILESDIR}/${P}-do-not-fetch-pufferfish.patch"
-	"${FILESDIR}/${P}-allow-newer-boost.patch"
-)

diff --git a/sci-biology/salmon/salmon-1.6.0.ebuild b/sci-biology/salmon/salmon-1.6.0.ebuild
new file mode 100644
index 000000000..6c19ff58f
--- /dev/null
+++ b/sci-biology/salmon/salmon-1.6.0.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake
+
+DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
+HOMEPAGE="https://github.com/COMBINE-lab/salmon"
+SRC_URI="
+	https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
+	https://github.com/COMBINE-lab/pufferfish/archive/salmon-v${PV}.tar.gz -> pufferfish-${P}.tar.gz
+	https://github.com/COMBINE-lab/libgff/archive/v2.0.0.tar.gz -> libgff-${P}.tar.gz
+"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	dev-libs/boost:=
+	sys-libs/zlib
+"
+
+DEPEND="${RDEPEND}
+	app-arch/bzip2
+	app-arch/xz-utils
+	>=dev-libs/jemalloc-5.0.1
+	>=dev-cpp/tbb-2018.20180312
+	dev-libs/cereal
+	sci-libs/io_lib[static-libs]
+"
+
+BDEPEND="
+	app-arch/unzip
+	net-misc/curl
+"
+
+PATCHES=(
+	"${FILESDIR}/${P}-find-boost.patch"
+)
+
+src_unpack() {
+	default
+	mkdir -p "${S}/external/install/lib" || die
+	mv "${WORKDIR}/pufferfish-${PN}-v${PV}" "${S}/external/pufferfish" || die
+	mv "${WORKDIR}/libgff-2.0.0" "${S}/external/libgff-2.0.0" || die
+	ln -s "${EPREFIX}/usr/lib64/libtbb.so" "${S}/external/install/lib/libtbb.so" || die
+	ln -s "${EPREFIX}/usr/lib64/libtbbmalloc.so" "${S}/external/install/lib/libtbbmalloc.so" || die
+	ln -s "${EPREFIX}/usr/lib64/libtbbmalloc_proxy.so" "${S}/external/install/lib/libtbbmalloc_proxy.so" || die
+}
+
+src_prepare() {
+	cmake_src_prepare
+	sed -e 's:tbb/mutex.h:oneapi/tbb/mutex.h:g' \
+		-i external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h \
+		-i external/pufferfish/external/twopaco/common/streamfastaparser.h || die
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DFETCH_BOOST=FALSE
+		-DBOOST_INCLUDEDIR="${EPREFIX}/usr/include/boost"
+		-DBOOST_LIBRARYDIR="${EPREFIX}/usr/lib64"
+		-DBoost_ALL_FOUND=TRUE
+		-Dboost_headers_FOUND=TRUE
+		-DBoost_FOUND=TRUE
+	)
+	cmake_src_configure
+}


^ permalink raw reply related	[flat|nested] 5+ messages in thread
end of thread, other threads:[~2022-01-25 13:06 UTC | newest]

Thread overview: 5+ messages (download: mbox.gz follow: Atom feed
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  -- strict thread matches above, loose matches on Subject: below --
2018-06-26  8:51 Martin Mokrejs
2018-06-25 12:14 Martin Mokrejs
2015-05-24  8:14 Justin Lecher
2015-05-24  8:14 Justin Lecher

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