sci-biology/salmon: drop deps on static boost, some ebuild cleanup

Document zillions of cryptic dependencies of a lousy package

https://github.com/Kingsford-Group/libgff/issues/1
https://github.com/COMBINE-lab/salmon/issues/236
https://github.com/COMBINE-lab/salmon/issues/19

Incomplete install docs are deemed to be at:
http://salmon.readthedocs.io/en/latest/building.html#requirements-for-building-from-source

Try the command below to see yourself:
salmon-0.10.2 $ find . -type f | xargs grep curl 2>/dev/null

Thanks to @kiwifb for comments at
  https://github.com/gentoo/sci/commit/a1d0487c37ba900c1f239f5d73f7d429f018359d

Package-Manager: Portage-2.3.40, Repoman-2.3.9

11 files changed, 94 insertions, 135 deletions

diff --git a/sci-biology/salmon/Manifest b/sci-biology/salmon/Manifest
index 06187fd6c..919ffdbd1 100644
--- a/sci-biology/salmon/Manifest
+++ b/sci-biology/salmon/Manifest
@@ -1,5 +1,2 @@
 DIST salmon-0.10.2.tar.gz 10766806 BLAKE2B f9ba6f208a72a11f37c44a056e9b464f4bf018db88c13e67ce84fcdecee98d878046b2018b144dd48a152300f1ba0a178cf03c5c541b16358e210a5013fdfdce SHA512 828c3d5f3f8f42181bf4b563a49f789bdb82843cbdc9aec4555e7623642e2c663a2552ea7bfd1967cc4f8033e6f0678f8f6f82ce776bc2312bc0b4b8ab7ed19f
-DIST salmon-0.3.2.tar.gz 1674131 BLAKE2B 2b6d124a01900db3e9a4c6c97b3559f0240a8376b612455bedce9187e5e73cb241ffe22128ba0af48c9f93d8f7862cce2d0692db6c76692e8556aae94e05b5c1 SHA512 d9db133d8fb009a4b23251bce209a869644eb6139e0e4b9133f947999e0be4c30039f5cb8617dc4b73977cd690837abb407549a619ef82e6bb82577ff082becf
-DIST salmon-0.4.2.tar.gz 1711949 BLAKE2B 0f4be6b394a0c37a3d721e89cfc5e3b28872128074fd805f2680b9a2d14e7cffc9416b3cff5b04867f84778f23d7a26bff6a1d09e2200c18c036367b24938759 SHA512 28d823d3a97a46861972594d13737fe173583a0ac6dc2ebdc5f117e880493a057b34f8fea0d26fb2827d17ebcc38a06358dfea08db70f4a76c7fbe553f2b031d
-DIST salmon-0.5.0.tar.gz 1651002 BLAKE2B dbeaa2ea5c63cd5a82a487224c215d92ce701ba45e73e6b71e51f22f0638b7dc9744f7bf5d4574ed670e99b79944bc1026df71036f7626e383308ede631ab214 SHA512 c695cbbfbf6a8ecbb20a46bfcc428b3be458200b4296baa686b2ed4f664fa40a7db719620a8f2c1d1b482600d9d0f0cecfe5f00af6407e6fc6f8f263f227b4e0
-DIST salmon-0.9.1.tar.gz 1793728 BLAKE2B fe317aa6c5289474b75ca51cdbddcb6c27480f25596806d92127d25b2f868dac0c7f6452791b27a46bc623fc53a1c6629b527b1b37554d055958c5d90dca889c SHA512 836302b7e9117fc9378bc637a9e5fedce166fbddd4edf71ddd1f8c0f66932d379069cc250fa29f6860116531364786b266265a75bad442e2611b8ae153626b96
+DIST salmon-0.10.2_RapMap.zip 1141708 BLAKE2B 397341693e0388093af8ffe620fa91941c584de0887a648d219a3f5662ffd6f9af22179f205bfb83927bc8913756b4d68cbc9179cbfb11f9b329c6aed32220a1 SHA512 8aa593feb61a45d25cc757f39b907e6e0cc108831bad69857268f3ac19614d76cf88de6d8679e52d3eea43bcf5b603bfd55135ececf39acb1700a23408fca573
diff --git a/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch b/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch
new file mode 100644
index 000000000..ac561d793
--- /dev/null
+++ b/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch
@@ -0,0 +1,18 @@
+--- salmon-0.10.2/CMakeLists.txt	2018-06-25 10:51:47.179712781 +0200
++++ salmon-0.10.2/CMakeLists.txt	2018-06-25 10:52:47.951289159 +0200
+@@ -213,15 +213,6 @@
+     set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH})
+ endif ( DEFINED CUSTOM_BOOST_PATH )
+ 
+-##
+-# We want static, multithreaded boost libraries
+-##
+-if(CONDA_BUILD)
+-  set (Boost_USE_STATIC_LIBS OFF)
+-else ()
+-  set (Boost_USE_STATIC_LIBS ON)
+-endif(CONDA_BUILD)
+-
+ set (Boost_USE_MULTITHREADED ON)
+ #set (Boost_USE_STATIC_RUNTIME OFF)
+ 
diff --git a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch
new file mode 100644
index 000000000..8eddc6e3a
--- /dev/null
+++ b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch
@@ -0,0 +1,12 @@
+--- salmon-9999/scripts/fetchRapMap.sh	2018-06-25 11:11:07.019798309 +0200
++++ salmon-9999/scripts/fetchRapMap.sh	2018-06-25 11:12:25.131824486 +0200
+@@ -29,7 +29,8 @@
+ EXPECTED_SHA256=c4ca27de299bee395b404d117d9d98ad9f0d6ee256ea1deb2890ea402893e688
+ 
+ mkdir -p ${EXTERNAL_DIR}
+-curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${SVER}.zip -o ${EXTERNAL_DIR}/rapmap.zip
++# curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${SVER}.zip -o ${EXTERNAL_DIR}/rapmap.zip
++cp ../../distdir/salmon-0.10.2_RapMap.zip ${EXTERNAL_DIR}/rapmap.zip
+ 
+ hashcheck=""
+ if exists sha256sum; then
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
deleted file mode 100644
index 7ac3d0882..000000000
--- a/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-Do not force static and multithreaded boost libs, use what is available
-
-Patch by Michael Schubert
-
---- a/CMakeLists.txt
-+++ b/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 )
- 
--##
--# 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/files/salmon-9999-no-boost-static.patch b/sci-biology/salmon/files/salmon-9999-no-boost-static.patch
new file mode 100644
index 000000000..1a9665251
--- /dev/null
+++ b/sci-biology/salmon/files/salmon-9999-no-boost-static.patch
@@ -0,0 +1,18 @@
+--- salmon-9999/CMakeLists.txt	2018-06-25 10:51:47.179712781 +0200
++++ salmon-9999/CMakeLists.txt	2018-06-25 10:52:47.951289159 +0200
+@@ -213,15 +213,6 @@
+     set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH})
+ endif ( DEFINED CUSTOM_BOOST_PATH )
+ 
+-##
+-# We want static, multithreaded boost libraries
+-##
+-if(CONDA_BUILD)
+-  set (Boost_USE_STATIC_LIBS OFF)
+-else ()
+-  set (Boost_USE_STATIC_LIBS ON)
+-endif(CONDA_BUILD)
+-
+ set (Boost_USE_MULTITHREADED ON)
+ #set (Boost_USE_STATIC_RUNTIME OFF)
+ 
diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild
index f97a32f18..540225019 100644
--- a/sci-biology/salmon/salmon-0.10.2.ebuild
+++ b/sci-biology/salmon/salmon-0.10.2.ebuild
@@ -7,15 +7,35 @@ 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 -> ${P}.tar.gz"
+SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
+	https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.10.2.zip -> ${P}_RapMap.zip"
 
 LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE=""
 
-DEPEND="dev-libs/boost:0
-		dev-libs/jemalloc
+PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch
+		"${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch )
+
+RDEPEND="${DEPEND}"
+# budled copies of:
+# sci-biology/bwa-0.7.12.5
+# sci-biology/jellyfish
+# sci-biology/staden-1.14.8.1
+# sci-biology/gfftools
+#
+# libgff-1.1 from https://github.com/Kingsford-Group/libgff
+#    actually unreleased version from https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
+#    https://github.com/Kingsford-Group/libgff/issues/1
+#
+# dev-libs/spdlog-0.16.1
+# cereal-1.2.2
+DEPEND="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}"
 
diff --git a/sci-biology/salmon/salmon-0.3.2.ebuild b/sci-biology/salmon/salmon-0.3.2.ebuild
deleted file mode 100644
index b9a50ebd1..000000000
--- a/sci-biology/salmon/salmon-0.3.2.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-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 -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch )
-
-DEPEND="dev-libs/boost:0
-		dev-libs/jemalloc
-		dev-cpp/tbb"
-RDEPEND="${DEPEND}"
-
-src_install() {
-	cmake-utils_src_install
-	rm -r "${ED}"/usr/tests || die
-}
diff --git a/sci-biology/salmon/salmon-0.4.2.ebuild b/sci-biology/salmon/salmon-0.4.2.ebuild
deleted file mode 100644
index 42ccf1e6c..000000000
--- a/sci-biology/salmon/salmon-0.4.2.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils
-
-DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
-HOMEPAGE="https://github.com/COMBINE-lab/salmon"
-SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch )
-
-DEPEND="dev-libs/boost:0
-		dev-libs/jemalloc
-		dev-cpp/tbb"
-RDEPEND="${DEPEND}"
-
-src_install() {
-	cmake-utils_src_install
-	rm -r "${ED}"/usr/tests || die
-}
diff --git a/sci-biology/salmon/salmon-0.5.0.ebuild b/sci-biology/salmon/salmon-0.5.0.ebuild
deleted file mode 100644
index 42ccf1e6c..000000000
--- a/sci-biology/salmon/salmon-0.5.0.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils
-
-DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
-HOMEPAGE="https://github.com/COMBINE-lab/salmon"
-SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch )
-
-DEPEND="dev-libs/boost:0
-		dev-libs/jemalloc
-		dev-cpp/tbb"
-RDEPEND="${DEPEND}"
-
-src_install() {
-	cmake-utils_src_install
-	rm -r "${ED}"/usr/tests || die
-}
diff --git a/sci-biology/salmon/salmon-0.9.1.ebuild b/sci-biology/salmon/salmon-0.9.1.ebuild
deleted file mode 100644
index 34a425403..000000000
--- a/sci-biology/salmon/salmon-0.9.1.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils
-
-DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
-HOMEPAGE="https://github.com/COMBINE-lab/salmon"
-SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND="dev-libs/boost:0
-		dev-libs/jemalloc
-		dev-cpp/tbb"
-RDEPEND="${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 ab0f9c368..0083648fb 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-9999.ebuild
@@ -8,15 +8,35 @@ inherit multilib cmake-utils git-r3
 DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
 HOMEPAGE="https://github.com/COMBINE-lab/salmon"
 EGIT_REPO_URI="https://github.com/COMBINE-lab/salmon.git"
+# SRC_URI="https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.10.2.zip -> ${PN}-0.10.2_RapMap.zip"
 
 LICENSE="GPL-3"
 SLOT="0"
 IUSE=""
 
-DEPEND="dev-libs/boost:0
-		dev-libs/jemalloc
+PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch
+		"${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch )
+
+# budled copies of:
+# sci-biology/bwa-0.7.12.5
+# sci-biology/jellyfish
+# sci-biology/staden-1.14.8.1
+# sci-biology/gfftools
+#
+# libgff-1.1 from https://github.com/Kingsford-Group/libgff
+#    actually unreleased version from https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
+#    https://github.com/Kingsford-Group/libgff/issues/1
+#
+# dev-libs/spdlog-0.16.1
+# cereal-1.2.2
+DEPEND="sys-libs/zlib
+		app-arch/bzip2
+		app-arch/xz-utils
+		dev-libs/boost:0[threads]
+		>=dev-libs/jemalloc-5.0.1
 		>=dev-cpp/tbb-2018.20180312"
 RDEPEND="${DEPEND}"
+
 # https://github.com/COMBINE-lab/salmon/issues/19
 #
 # contains bundled copies of https://github.com/jemalloc/jemalloc