salmon: Transcript-level quantification of RNA-seq from lightweight alignments

2018-09-13 15:44:28 -05:00 · 2018-09-13 15:44:28 -05:00 · 32656ad631
parent 394417ddbc
commit 32656ad631
12 changed files with 398 additions and 0 deletions
--- a/1
+++ b/1
@ -4082,6 +4082,7 @@ SUBDIR+=	safekeep
 SUBDIR+=	sailor
 SUBDIR+=	sais
 SUBDIR+=	sais-demo-data
+SUBDIR+=	salmon
 SUBDIR+=	samhain
 SUBDIR+=	samtools0119
 SUBDIR+=	sara
--- a/salmon/DESCR
+++ b/salmon/DESCR
@ -0,0 +1,6 @@
+Salmon is a wicked-fast program to produce a highly-accurate, transcript-level
+quantification estimates from RNA-seq data. Salmon achieves is accuracy and
+speed via a number of different innovations, including the use of quasi-mapping
+(accurate but fast-to-compute proxies for traditional read alignments), and
+massively-parallel stochastic collapsed variational inference. The result is a
+versatile tool that fits nicely into many differnt pipelines.
--- a/salmon/Makefile
+++ b/salmon/Makefile
@ -0,0 +1,84 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Thu Sep 13 14:20:25 CDT 2018               #
+###########################################################
+
+###########################################################
+# Unconverted and partially converted FreeBSD port syntax:
+
+#LIBS+=		-L${PREFIX}/lib -lthr
+
+DISTNAME=	salmon-${PV}
+DIST_SUBDIR=	salmon
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=COMBINE-lab/} \
+		https://github.com/COMBINE-lab/RapMap/archive/ \
+		https://github.com/COMBINE-lab/libgff/archive/ \
+		https://github.com/COMBINE-lab/staden-io_lib/archive/
+DISTFILES=	salmon-0.11.3.tar.gz salmon-v0.11.3.zip v1.1.tar.gz v1.14.8.1.tar.gz
+EXTRACT_ONLY=	salmon-0.11.3.tar.gz v1.14.8.1.tar.gz
+#GITHUB_PROJECT=	salmon
+#GITHUB_TAG=	v${PV}
+
+MAINTAINER=	bacon@NetBSD.org
+HOMEPAGE=	https://github.com/COMBINE-lab/salmon
+COMMENT=	Transcript-level quantification of RNA-seq from lightweight alignments
+LICENSE=	gnu-gpl-v3
+
+SUBST_CLASSES+=		tbb
+SUBST_STAGE.tbb=	post-patch
+SUBST_SED.tbb+=		-e 's|tbbmalloc_proxy||g'
+SUBST_FILES.tbb+=	${WRKSRC}/CMakeLists.txt
+
+SUBST_CLASSES+=		staden
+SUBST_STAGE.staden=	post-patch
+SUBST_SED.staden+=	-e 's|&& make|&& gmake|g'
+SUBST_FILES.staden+=	${WRKSRC}/CMakeFiles/libstadenio.dir/build.make
+
+# Test and change if necessary.
+# MAKE_JOBS_SAFE=	no
+
+DEPENDS=	bash>=0:../../shells/bash \
+		autoconf>=0:../../devel/autoconf
+
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	cmake gmake
+# FreeBSD's SHEBANG_FILES may include bash, perl, python, etc.
+# I don't know which is which, so you'll have to finish.
+# Add bash, etc. to USE_TOOLS if used below.
+# 
+REPLACE_BASH=	scripts/*.sh
+REPLACE_PYTHON=	scripts/*.py
+USE_CMAKE=	yes
+CMAKE_ARGS+=	-DDISTDIR:PATH=${DISTDIR} \
+		https://github.com/COMBINE-lab/libgff/archive/ \
+		https://github.com/COMBINE-lab/staden-io_lib/archive/
+
+CONFIGURE_ENV+=	DISTDIR=${DISTDIR} DIST_SUBDIR=salmon
+#MAKE_ENV+=	WRKDIR=${WRKDIR} DISTDIR=${DISTDIR} DIST_SUBDIR=salmon
+LDFLAGS+=	-lz
+
+PV=		0.11.3
+DATADIR=	${PREFIX}/share/salmon
+DOCSDIR=	${PREFIX}/share/doc/salmon
+EXAMPLESDIR=	${PREFIX}/share/examples/salmon
+
+# Sets OPSYS, OS_VERSION, MACHINE_ARCH, etc..
+# .include "../../mk/bsd.prefs.mk"
+
+# Keep this if there are user-selectable options.
+# .include "options.mk"
+
+# Specify which directories to create before install.
+# You should only need this if using your own install target.
+INSTALLATION_DIRS=	bin include lib ${PKGMANDIR}/man1 share/doc share/examples
+
+# Convert any _DEPENDS above that have a buildlink3.mk
+.include "../../devel/libgetopt/buildlink3.mk"
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../devel/boost-libs/buildlink3.mk"
+.include "../../wip/cereal/buildlink3.mk"
+.include "../../wip/tbb/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
--- a/salmon/PLIST
+++ b/salmon/PLIST
@ -0,0 +1 @@
+@comment $NetBSD$
--- a/salmon/distinfo
+++ b/salmon/distinfo
@ -0,0 +1,25 @@
+$NetBSD$
+
+SHA1 (salmon/salmon-0.11.3.tar.gz) = 3f385630c608c12ddd16523dda022119ad2616ef
+RMD160 (salmon/salmon-0.11.3.tar.gz) = eb763cfe9dedfd50253202c68978da3182eca6b1
+SHA512 (salmon/salmon-0.11.3.tar.gz) = adc7ee27e8096142f48f57d2d88d18bef81abfc509683737a22ecc0a5bfe8323faf4a63256972b2e6a03774399c13f3b7d9dfd50d4362c9bf195e231537a5100
+Size (salmon/salmon-0.11.3.tar.gz) = 10945588 bytes
+SHA1 (salmon/salmon-v0.11.3.zip) = 5a473884afd4382d70a1467b67401b2b9f351ab7
+RMD160 (salmon/salmon-v0.11.3.zip) = 91dba61d070a18a78eed6c60fd455f1240889a9c
+SHA512 (salmon/salmon-v0.11.3.zip) = e5bca29c25cb5f02804a64850d87e4956e87be7dd42544878494d12db1e8a78de46975c8e091b88fd702208595f96b4ebccd547365f4a43b00291d8199212025
+Size (salmon/salmon-v0.11.3.zip) = 1163389 bytes
+SHA1 (salmon/v1.1.tar.gz) = 37b3147d78391d1fabbe6a0df313fbf516abbc6f
+RMD160 (salmon/v1.1.tar.gz) = f7f3b410799d16d95af3cf14d3550c8b14477b1c
+SHA512 (salmon/v1.1.tar.gz) = af797fdc753c21a61a817f0b57da55c523220a9c831a71b73328a49ec66b667a503f1fcbddab714826f802a4e2becf310265535276973e2978d5ad73525fa0bb
+Size (salmon/v1.1.tar.gz) = 79006 bytes
+SHA1 (salmon/v1.14.8.1.tar.gz) = c79897aa508b0cda2d96e8d1760c74b9c4e7e94e
+RMD160 (salmon/v1.14.8.1.tar.gz) = f8cfaf1198d9ae738321dffd89752a4732898399
+SHA512 (salmon/v1.14.8.1.tar.gz) = 535c6701e61a1786ceb7b22905afe702d277e0383816fba82f69af553dd22ca497bf00766f9768fd9173621632483a02ea9919437e1786008b2236c1c2c8c69f
+Size (salmon/v1.14.8.1.tar.gz) = 2506985 bytes
+SHA1 (patch-.._staden-io__lib-1.14.8.1_progs_scram__flagstat.c) = 2ac5b7bea94d4738102da0c729c4ee75c8214300
+SHA1 (patch-.._staden-io__lib-1.14.8.1_progs_scram__merge.c) = 09ee761a3630a0c9ff8ff8d1ffa7ac0faeacd91b
+SHA1 (patch-.._staden-io__lib-1.14.8.1_progs_scram__test.c) = d707e1d76817ca92862193dea5d66ca5b8a2de89
+SHA1 (patch-CMakeLists.txt) = db36ef16c1b889091fd6231e61f5a0fe926de596
+SHA1 (patch-scripts_fetchRapMap.sh) = 616f79e16a67575f9d684ce351f7e31d002912f3
+SHA1 (patch-src_CMakeLists.txt) = 824564cd7592f02902e607206c8bbb0bd4049f04
+SHA1 (patch-work_staden-io__lib-1.14.8.1_progs_scram__merge.c) = adc83b19e793491b1c6ea0fd8b46cd9f32e592fc
--- a/salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__flagstat.c
+++ b/salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__flagstat.c
@ -0,0 +1,14 @@
+$NetBSD$
+
+--- ../staden-io_lib-1.14.8.1/progs/scram_flagstat.c.orig	2018-09-13 20:14:26.052077584 +0000
+++ ../staden-io_lib-1.14.8.1/progs/scram_flagstat.c
+@@ -45,9 +45,7 @@
+ #include <ctype.h>
+ #include <errno.h>
+ 
+-#if defined(__MINGW32__) || defined(__FreeBSD__) || defined(__APPLE__)
+ #   include <getopt.h>
+-#endif
+ 
+ #include <io_lib/scram.h>
+ #include <io_lib/os.h>
--- a/salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__merge.c
+++ b/salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__merge.c
@ -0,0 +1,14 @@
+$NetBSD$
+
+--- ../staden-io_lib-1.14.8.1/progs/scram_merge.c.orig	2018-09-13 20:12:38.101447761 +0000
+++ ../staden-io_lib-1.14.8.1/progs/scram_merge.c
+@@ -45,9 +45,7 @@
+ #include <ctype.h>
+ #include <errno.h>
+ 
+-#if defined(__MINGW32__) || defined(__FreeBSD__) || defined(__APPLE__)
+ #   include <getopt.h>
+-#endif
+ 
+ #include <io_lib/scram.h>
+ #include <io_lib/os.h>
--- a/salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__test.c
+++ b/salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__test.c
@ -0,0 +1,14 @@
+$NetBSD$
+
+--- ../staden-io_lib-1.14.8.1/progs/scram_test.c.orig	2018-09-13 20:14:39.851669404 +0000
+++ ../staden-io_lib-1.14.8.1/progs/scram_test.c
+@@ -45,9 +45,7 @@
+ #include <ctype.h>
+ #include <errno.h>
+ 
+-#if defined(__MINGW32__) || defined(__FreeBSD__) || defined(__APPLE__)
+ #   include <getopt.h>
+-#endif
+ 
+ #include <io_lib/scram.h>
+ #include <io_lib/os.h>
--- a/salmon/patches/patch-CMakeLists.txt
+++ b/salmon/patches/patch-CMakeLists.txt
@ -0,0 +1,200 @@
+$NetBSD$
+
+--- CMakeLists.txt.orig	2018-08-29 22:38:43.000000000 +0000
+++ CMakeLists.txt
+@@ -47,7 +47,7 @@ set(CPACK_PACKAGE_NAME
+ set(CPACK_SOURCE_PACKAGE_FILE_NAME
+   "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}-Source")
+ 
+-set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
+set (CMAKE_MODULE_PATH "/usr/pkgsrc/wip/salmon/work/.buildlink/cmake-Modules" ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
+ 
+ # Set a default build type if none was specified
+ set(default_build_type "Release")
+@@ -499,14 +499,14 @@ ExternalProject_Add_Step(libdivsufsort m
+  
+ set(SUFFARRAY_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
+ 
+-message("Build system will fetch and build the Cereal serialization library")
+-message("==================================================================")
+-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
+#message("Build system will fetch and build the Cereal serialization library")
+#message("==================================================================")
+#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
+ 
+     ##
+     #URL https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz
+@@ -514,22 +514,23 @@ ExternalProject_Add(libcereal
+     #TLS_VERIFY FALSE
+     #URL_HASH SHA1=ffddf5fc5313cfbb893e07823ca8c473084eebca
+     ##
+-    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/cereal-1.2.2
+-    INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+    #SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/cereal-1.2.2
+    #INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+    #INSTALL_DIR ${LOCALBASE}
+     #UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
+-    BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/cereal-1.2.2/build
+-    CONFIGURE_COMMAND ""
+-    BUILD_COMMAND ""
+-    INSTALL_COMMAND sh -c "mkdir -p <INSTALL_DIR>/include && cp -r <SOURCE_DIR>/include/cereal <INSTALL_DIR>/include"
+-)
+-ExternalProject_Add_Step(libcereal makedir
+-  COMMAND mkdir -p <SOURCE_DIR>/build 
+-  COMMENT "Make build directory"
+-  DEPENDEES download 
+-  DEPENDERS configure)
+    #BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/cereal-1.2.2/build
+    #CONFIGURE_COMMAND ""
+    #BUILD_COMMAND ""
+    #INSTALL_COMMAND sh -c "mkdir -p <INSTALL_DIR>/include && cp -r <SOURCE_DIR>/include/cereal <INSTALL_DIR>/include"
+#)
+#ExternalProject_Add_Step(libcereal makedir
+  #COMMAND mkdir -p <SOURCE_DIR>/build 
+  #COMMENT "Make build directory"
+  #DEPENDEES download 
+  #DEPENDERS configure)
+ 
+ ## Try and find TBB first
+-find_package(TBB 2018.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy )
+find_package(TBB 2018.0 COMPONENTS tbb tbbmalloc  )
+ 
+ ##
+ #
+@@ -627,9 +628,7 @@ message("Build system will compile libgf
+ 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 tar -xzf ${DISTDIR}/salmon/v1.1.tar.gz
+     ##
+     #URL https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
+     #DOWNLOAD_NAME libff.tgz
+@@ -665,12 +664,9 @@ message("Build system will compile Stade
+ 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 &&
+-                     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 &&
+    DOWNLOAD_COMMAND mkdir -p staden-io_lib-1.14.8 &&
+                      rm -fr staden-io_lib &&
+-                     mv -f staden-io_lib-1.14.8 staden-io_lib
+                     ln -s ../../staden-io_lib-1.14.8.1 staden-io_lib
+     SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/staden-io_lib
+     INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+     CONFIGURE_COMMAND ./configure --enable-shared=no --without-libcurl --prefix=<INSTALL_DIR> LDFLAGS=${LIBSTADEN_LDFLAGS} CFLAGS=${LIBSTADEN_CFLAGS} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
+@@ -681,58 +677,59 @@ ExternalProject_Add(libstadenio
+     INSTALL_COMMAND make install
+ )
+ 
+-set (FAST_MALLOC_LIB "")
+-set (HAVE_FAST_MALLOC FALSE)
+# jemalloc is FreeBSD's built-in allocator
+# set (FAST_MALLOC_LIB "")
+set (HAVE_FAST_MALLOC TRUE)
+ 
+ # See if we have Jemalloc
+-find_package(Jemalloc)
+-if (Jemalloc_FOUND)
+# find_package(Jemalloc)
+# if (Jemalloc_FOUND)
+   ##
+   # Don't be so stringent about the version yet
+   ##
+   #if (NOT (${JEMALLOC_VERSION} VERSION_LESS 5.1.0))
+-    message("Found Jemalloc library --- using this memory allocator")
+-    set (FAST_MALLOC_LIB ${JEMALLOC_LIBRARIES})
+-    set (HAVE_FAST_MALLOC TRUE)
+    # message("Found Jemalloc library --- using this memory allocator")
+    # set (FAST_MALLOC_LIB ${JEMALLOC_LIBRARIES})
+    # set (HAVE_FAST_MALLOC TRUE)
+   #else()
+   #  message("Fond Jemalloc version ${JEMALLOC_VERSION}, but require >= 5.1.0. Downloading newer version")
+   #endif()
+-endif()
+# endif()
+ 
+-if(CONDA_BUILD)
+-  set (JEMALLOC_FLAGS "CC=${CMAKE_C_COMPILER} CFLAGS=-fPIC CPPFLAGS=-fPIC")
+-else ()
+-  set (JEMALLOC_FLAGS "CC=${CMAKE_C_COMPILER}")
+-endif()
+-
+-if (NOT HAVE_FAST_MALLOC)
+-    message("Build system will fetch and use JEMalloc")
+-    message("==================================================================")
+-    ExternalProject_Add(libjemalloc
+-        DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+-        DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/jemalloc/archive/5.1.0.tar.gz -o jemalloc-5.1.0.tar.gz &&
+-                         ${SHASUM} ff28aef89df724bd7b6bd6fde8597695514e0e3404d1afad2f1eb8b55ef378d3  jemalloc-5.1.0.tar.gz &&
+-                         tar -xzf jemalloc-5.1.0.tar.gz
+-
+-        SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jemalloc-5.1.0
+-        BUILD_IN_SOURCE TRUE
+-        INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+-        CONFIGURE_COMMAND sh -c "${JEMALLOC_FLAGS} ./autogen.sh --disable-debug --prefix=<INSTALL_DIR>"
+-        INSTALL_COMMAND cp -r lib <INSTALL_DIR>/ && cp -r include <INSTALL_DIR>/
+-        )
+-
+-    set (FAST_MALLOC_LIB ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib/libjemalloc.a)
+-    set (HAVE_FAST_MALLOC TRUE)
+-    set (FETCHED_JEMALLOC TRUE)
+-    if (FETCHED_LIBBZ2)
+-       add_dependencies(libjemalloc libbz2)
+-    endif()
+# if(CONDA_BUILD)
+  # set (JEMALLOC_FLAGS "CC=${CMAKE_C_COMPILER} CFLAGS=-fPIC CPPFLAGS=-fPIC")
+# else ()
+  # set (JEMALLOC_FLAGS "CC=${CMAKE_C_COMPILER}")
+# endif()
+
+# if (NOT HAVE_FAST_MALLOC)
+    # message("Build system will fetch and use JEMalloc")
+    # message("==================================================================")
+    # ExternalProject_Add(libjemalloc
+        # DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+        # DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/jemalloc/archive/5.1.0.tar.gz -o jemalloc-5.1.0.tar.gz &&
+                         # ${SHASUM} ff28aef89df724bd7b6bd6fde8597695514e0e3404d1afad2f1eb8b55ef378d3  jemalloc-5.1.0.tar.gz &&
+                         # tar -xzf jemalloc-5.1.0.tar.gz
+
+        # SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jemalloc-5.1.0
+        # BUILD_IN_SOURCE TRUE
+        # INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+        # CONFIGURE_COMMAND sh -c "${JEMALLOC_FLAGS} ./autogen.sh --disable-debug --prefix=<INSTALL_DIR>"
+        # INSTALL_COMMAND cp -r lib <INSTALL_DIR>/ && cp -r include <INSTALL_DIR>/
+        # )
+
+    # set (FAST_MALLOC_LIB ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib/libjemalloc.a)
+    # set (HAVE_FAST_MALLOC TRUE)
+    # set (FETCHED_JEMALLOC TRUE)
+    # if (FETCHED_LIBBZ2)
+       # add_dependencies(libjemalloc libbz2)
+    # endif()
+
+    # if (FETCHED_LIBLZMA)
+       # add_dependencies(libjemalloc liblzma)
+    # endif()
+ 
+-    if (FETCHED_LIBLZMA)
+-       add_dependencies(libjemalloc liblzma)
+-    endif()
+-
+-endif ()
+# endif ()
+ 
+ ###
+ #
--- a/salmon/patches/patch-scripts_fetchRapMap.sh
+++ b/salmon/patches/patch-scripts_fetchRapMap.sh
@ -0,0 +1,13 @@
+$NetBSD$
+
+--- scripts/fetchRapMap.sh.orig	2018-09-11 14:54:51 UTC
+++ scripts/fetchRapMap.sh
+@@ -30,7 +30,7 @@ EXPECTED_SHA256=b863548383448c21a862cc56
+ 
+ 
+ mkdir -p ${EXTERNAL_DIR}
+-curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${SVER}.zip -o ${EXTERNAL_DIR}/rapmap.zip
+cp ${DISTDIR}/${DIST_SUBDIR}/${SVER}.zip ${EXTERNAL_DIR}/rapmap.zip
+ 
+ hashcheck=""
+ if exists sha256sum; then
--- a/salmon/patches/patch-src_CMakeLists.txt
+++ b/salmon/patches/patch-src_CMakeLists.txt
@ -0,0 +1,24 @@
+$NetBSD$
+
+--- src/CMakeLists.txt.orig	2018-09-10 20:40:46 UTC
+++ src/CMakeLists.txt
+@@ -2,7 +2,7 @@ include_directories(
+ ${GAT_SOURCE_DIR}/include
+ ${GAT_SOURCE_DIR}/include/eigen3
+ ${GAT_SOURCE_DIR}/external
+-${GAT_SOURCE_DIR}/external/cereal/include
+#${GAT_SOURCE_DIR}/external/cereal/include
+ ${GAT_SOURCE_DIR}/external/install/include
+ #${GAT_SOURCE_DIR}/external/install/include/bwa
+ ${ZLIB_INCLUDE_DIR}
+@@ -272,8 +272,8 @@ if (${FETCHED_TBB})
+    add_dependencies(salmon libtbb)
+ endif()
+ 
+-add_dependencies(salmon_core libcereal)
+-add_dependencies(salmon libcereal)
+#add_dependencies(salmon_core libcereal)
+#add_dependencies(salmon libcereal)
+ add_dependencies(alevin_core libstadenio)
+ add_dependencies(salmon_core libstadenio)
+ add_dependencies(salmon libstadenio)
--- a/salmon/patches/patch-work_staden-io__lib-1.14.8.1_progs_scram__merge.c
+++ b/salmon/patches/patch-work_staden-io__lib-1.14.8.1_progs_scram__merge.c
@ -0,0 +1,2 @@
+$NetBSD$
+