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

5 files changed, 249 insertions, 10 deletions

diff --git a/sci-biology/salmon/Manifest b/sci-biology/salmon/Manifest
index 919ffdbd1..8a357c311 100644
--- a/sci-biology/salmon/Manifest
+++ b/sci-biology/salmon/Manifest
@@ -1,2 +1,7 @@
+DIST bwa-0.7.12.5.tar.gz 224584 BLAKE2B af273aa6751d73e82ce1891acdd42c7cbb0f332312157e1bcaf3f6175417f7358f1d73fd900ede7bddc4071b62f68ea8c79d1e0eb04f02ee618130bd0c33579f SHA512 c56a08c115fd15ca017f5ca5a2e053aef4df9fdf7b3a8f575646b2443cb38853dcd17e72588750dc0c8acdd7accca173d84894220d6cd06959ba0d994851f6c9
+DIST cereal-1.2.2.tar.gz 335759 BLAKE2B 6804b9aabb235a546758c70554502208f1b7b6bcab9b602fa075123335331f0522191a83027fdbac4ee947881c6866f24f48223a00b9490fca5ca961f3e4b260 SHA512 9567b2e19add9446b24f8afd122eea09ba6ecd1a090335cf0ab31fdc8f64c6c97daa3d9eaf0801c36a770737488e0eebf81d96d7b7a65deed30da6130f2d47eb
+DIST libgff-1.1.tgz 79006 BLAKE2B 626a62614c4c52d823104eae78e4f04e0976eb43cd2ea7b820ac6549535771fb2ecccbcf4476a22f53a66b5d8bea4fd260c6d3cee864a2c1b264c6f223744dac SHA512 af797fdc753c21a61a817f0b57da55c523220a9c831a71b73328a49ec66b667a503f1fcbddab714826f802a4e2becf310265535276973e2978d5ad73525fa0bb
 DIST salmon-0.10.2.tar.gz 10766806 BLAKE2B f9ba6f208a72a11f37c44a056e9b464f4bf018db88c13e67ce84fcdecee98d878046b2018b144dd48a152300f1ba0a178cf03c5c541b16358e210a5013fdfdce SHA512 828c3d5f3f8f42181bf4b563a49f789bdb82843cbdc9aec4555e7623642e2c663a2552ea7bfd1967cc4f8033e6f0678f8f6f82ce776bc2312bc0b4b8ab7ed19f
 DIST salmon-0.10.2_RapMap.zip 1141708 BLAKE2B 397341693e0388093af8ffe620fa91941c584de0887a648d219a3f5662ffd6f9af22179f205bfb83927bc8913756b4d68cbc9179cbfb11f9b329c6aed32220a1 SHA512 8aa593feb61a45d25cc757f39b907e6e0cc108831bad69857268f3ac19614d76cf88de6d8679e52d3eea43bcf5b603bfd55135ececf39acb1700a23408fca573
+DIST spdlog-0.16.1.tar.gz 162408 BLAKE2B c90b94bac128f8b143d85522d224223b1361f7d552d9caa8b253e494dd72de56a2149cbd8d568eb4305224d7caf80d8067fbce606a1071bd94f74c43b3245782 SHA512 0ef741f2abcae7c925808b44bba7d2e55aa8bd3b07a77ab6e785068beb505cdbcd7835d7d103e8e96094235e262954969a176d9f4977e9d373f1bee8e2716ff2
+DIST staden-io_lib-1.14.8.tar.gz 2506985 BLAKE2B 0d64847d0958e0efc763e87bf0600e3af90d30b67c77908b2effa20b18ce43a0d5ad1b213747c46f9e9000a75c4f1260759b3c90cd632be821e039870a26eb4b SHA512 535c6701e61a1786ceb7b22905afe702d277e0383816fba82f69af553dd22ca497bf00766f9768fd9173621632483a02ea9919437e1786008b2236c1c2c8c69f
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
 }