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salmon: Transcript-level quantification of RNA-seq from lightweight alignments
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Thu Sep 13 15:44:28 2018 -0500
Changeset: 32656ad631a5f1c0ec3f4711cfa58a530d1e7b2a
Modified Files:
Makefile
Added Files:
salmon/DESCR
salmon/Makefile
salmon/PLIST
salmon/distinfo
salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__flagstat.c
salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__merge.c
salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__test.c
salmon/patches/patch-CMakeLists.txt
salmon/patches/patch-scripts_fetchRapMap.sh
salmon/patches/patch-src_CMakeLists.txt
salmon/patches/patch-work_staden-io__lib-1.14.8.1_progs_scram__merge.c
Log Message:
salmon: Transcript-level quantification of RNA-seq from lightweight alignments
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=32656ad631a5f1c0ec3f4711cfa58a530d1e7b2a
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
Makefile | 1 +
salmon/DESCR | 6 +
salmon/Makefile | 84 +++++++++
salmon/PLIST | 1 +
salmon/distinfo | 25 +++
...staden-io__lib-1.14.8.1_progs_scram__flagstat.c | 14 ++
....._staden-io__lib-1.14.8.1_progs_scram__merge.c | 14 ++
...-.._staden-io__lib-1.14.8.1_progs_scram__test.c | 14 ++
salmon/patches/patch-CMakeLists.txt | 200 +++++++++++++++++++++
salmon/patches/patch-scripts_fetchRapMap.sh | 13 ++
salmon/patches/patch-src_CMakeLists.txt | 24 +++
...rk_staden-io__lib-1.14.8.1_progs_scram__merge.c | 2 +
12 files changed, 398 insertions(+)
diffs:
diff --git a/Makefile b/Makefile
index 3ded76bf98..52f28f705a 100644
--- a/Makefile
+++ b/Makefile
@@ -4082,6 +4082,7 @@ SUBDIR+= safekeep
SUBDIR+= sailor
SUBDIR+= sais
SUBDIR+= sais-demo-data
+SUBDIR+= salmon
SUBDIR+= samhain
SUBDIR+= samtools0119
SUBDIR+= sara
diff --git a/salmon/DESCR b/salmon/DESCR
new file mode 100644
index 0000000000..e3a823249c
--- /dev/null
+++ 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.
diff --git a/salmon/Makefile b/salmon/Makefile
new file mode 100644
index 0000000000..f1eb8434ff
--- /dev/null
+++ 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@localhost
+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"
diff --git a/salmon/PLIST b/salmon/PLIST
new file mode 100644
index 0000000000..48d96a5493
--- /dev/null
+++ b/salmon/PLIST
@@ -0,0 +1 @@
+@comment $NetBSD$
diff --git a/salmon/distinfo b/salmon/distinfo
new file mode 100644
index 0000000000..7538b15ee2
--- /dev/null
+++ 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
diff --git 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
new file mode 100644
index 0000000000..58611a7a40
--- /dev/null
+++ 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>
diff --git 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
new file mode 100644
index 0000000000..9815811a84
--- /dev/null
+++ 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>
diff --git 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
new file mode 100644
index 0000000000..3e5bc4db8b
--- /dev/null
+++ 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>
diff --git a/salmon/patches/patch-CMakeLists.txt b/salmon/patches/patch-CMakeLists.txt
new file mode 100644
index 0000000000..0adbd8b02f
--- /dev/null
+++ 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 ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib/libjemalloc.a)
++ # set (HAVE_FAST_MALLOC TRUE)
++ # set (FETCHED_JEMALLOC TRUE)
++ # if (FETCHED_LIBBZ2)
++ # add_dependencies(libjemalloc libbz2)
++ # endif()
++
++ # if (FETCHED_LIBLZMA)
++ # add_dependencies(libjemalloc liblzma)
++ # endif()
+
+- if (FETCHED_LIBLZMA)
+- add_dependencies(libjemalloc liblzma)
+- endif()
+-
+-endif ()
++# endif ()
+
+ ###
+ #
diff --git a/salmon/patches/patch-scripts_fetchRapMap.sh b/salmon/patches/patch-scripts_fetchRapMap.sh
new file mode 100644
index 0000000000..8f2ee529c2
--- /dev/null
+++ b/salmon/patches/patch-scripts_fetchRapMap.sh
@@ -0,0 +1,13 @@
+$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 ${EXTERNAL_DIR}/rapmap.zip
+
+ hashcheck=""
+ if exists sha256sum; then
diff --git a/salmon/patches/patch-src_CMakeLists.txt b/salmon/patches/patch-src_CMakeLists.txt
new file mode 100644
index 0000000000..9414aef0c9
--- /dev/null
+++ b/salmon/patches/patch-src_CMakeLists.txt
@@ -0,0 +1,24 @@
+$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)
diff --git 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
new file mode 100644
index 0000000000..afc76512f4
--- /dev/null
+++ b/salmon/patches/patch-work_staden-io__lib-1.14.8.1_progs_scram__merge.c
@@ -0,0 +1,2 @@
+$NetBSD$
+
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