Merge branch 'develop'

.travis.yml

@@ -7,8 +7,11 @@ matrix:
       compiler : gcc-7
       addons:
         apt:
-          sources: ['ubuntu-toolchain-r-test']
-          packages: ['g++-7', 'gcc-7', 'cmake', 'cmake-data', 'zlib1g-dev', 'libbz2-dev']
+          update: true
+          sources:
+              - sourceline: 'ppa:mhier/libboost-latest'
+              - ubuntu-toolchain-r-test
+          packages: ['g++-7', 'gcc-7', 'zlib1g-dev', 'libbz2-dev']
 
 install:
     - export CXX="g++-7"
@@ -19,21 +22,32 @@ install:
     - export PATH=$PWD/latest-gcc-symlinks:$PATH
     - export AR=gcc-ar-7
     - export RANLIB=gcc-ranlib-7
-
+    - DEPS_DIR="${TRAVIS_BUILD_DIR}/deps"
+    - mkdir ${DEPS_DIR} && cd ${DEPS_DIR}
+    - travis_retry wget --no-check-certificate https://cmake.org/files/v3.12/cmake-3.12.0-Linux-x86_64.tar.gz
+    - tar -xzvf cmake-3.12.0-Linux-x86_64.tar.gz > /dev/null
+    - mv cmake-3.12.0-Linux-x86_64 cmake-install
+    - PATH=${DEPS_DIR}/cmake-install:${DEPS_DIR}/cmake-install/bin:$PATH
+    - cd ${TRAVIS_BUILD_DIR}
+
 script: 
     - mkdir build 
     - cd build 
     - cmake -DFETCH_BOOST=TRUE -DNO_RTM=TRUE .. 
     - travis_wait 45 make 
     - travis_wait make install
+    - LD_LIBRARY_PATH=${TRAVIS_BUILD_DIR}/lib:$LD_LIBRARY_PATH
+    - ./src/salmon -h
     - travis_wait make test VERBOSE=1
 
 after_success: 
     - cd $TRAVIS_BUILD_DIR
     - ./scripts/push-binary.sh
 
 after_failure:
-    - cat $TRAVIS_BUILD_DIR/build/Testing/Temporary/LastTest.log
+    - echo "Failure"
+    - ls -laR $TRAVIS_BUILD_DIR/build/Testing/
+    - cat $TRAVIS_BUILD_DIR/build/Testing/Temporary/*
 
 #whitelist
 #sudo: required

CMakeLists.txt

@@ -4,10 +4,26 @@ enable_testing()
 
 project (Salmon)
 
-set(CPACK_PACKAGE_VERSION "0.11.0")
-set(CPACK_PACKAGE_VERSION_MAJOR "0")
-set(CPACK_PACKAGE_VERSION_MINOR "11")
-set(CPACK_PACKAGE_VERSION_PATCH "0")
+# auto-populate version:
+# from https://stackoverflow.com/questions/47066115/cmake-get-version-from-multi-line-text-file
+file(READ "current_version.txt" ver)
+
+string(REGEX MATCH "VERSION_MAJOR ([0-9]*)" _ ${ver})
+set(ver_major ${CMAKE_MATCH_1})
+
+string(REGEX MATCH "VERSION_MINOR ([0-9]*)" _ ${ver})
+set(ver_minor ${CMAKE_MATCH_1})
+
+string(REGEX MATCH "VERSION_PATCH ([0-9]*)" _ ${ver})
+set(ver_patch ${CMAKE_MATCH_1})
+
+set(CPACK_PACKAGE_VERSION_MAJOR ${ver_major})
+set(CPACK_PACKAGE_VERSION_MINOR ${ver_minor})
+set(CPACK_PACKAGE_VERSION_PATCH ${ver_patch})
+
+set(CPACK_PACKAGE_VERSION "${ver_major}.${ver_minor}.${ver_patch}")
+message("version: ${CPACK_PACKAGE_VERSION}")
+
 set(PROJECT_VERSION ${CPACK_PACKAGE_VERSION})
 set(CPACK_GENERATOR "TGZ")
 set(CPACK_SOURCE_GENERATOR "TGZ")
@@ -20,10 +36,16 @@ set(CPACK_SOURCE_PACKAGE_FILE_NAME
 
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
 
-if( NOT CMAKE_BUILD_TYPE )
-  set( CMAKE_BUILD_TYPE Release CACHE STRING
-       "Choose the type of build, options are: Debug Release."
-       FORCE )
+# Set a default build type if none was specified
+set(default_build_type "Release")
+
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  message(STATUS "Setting build type to '${default_build_type}' as none was specified.")
+  set(CMAKE_BUILD_TYPE "${default_build_type}" CACHE
+      STRING "Choose the type of build." FORCE)
+  # Set the possible values of build type for cmake-gui
+  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS
+    "Debug" "Release")
 endif()
 
 ## Set the standard required compile flags
@@ -45,7 +67,7 @@ if(CONDA_BUILD)
   set(CMAKE_CXX_STANDARD_REQUIRED ON)
   set(CMAKE_CXX_EXTENSIONS OFF)
   set(CXXSTDFLAG "-std=c++11")
-  set(GCCVERSION "4.8.5")
+  set(GCCVERSION "4.8.2")
 else ()
   set(CMAKE_CXX_STANDARD 11)
   set(CMAKE_CXX_STANDARD_REQUIRED ON)
@@ -339,7 +361,7 @@ if (BOOST_RECONFIGURE)
     set(CMAKE_PREFIX_PATH ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
     set(Boost_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
     set(Boost_LIBRARY_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib)
-    find_package(Boost 1.59.0 COMPONENTS iostreams filesystem system timer chrono program_options REQUIRED)
+    find_package(Boost 1.59.0 COMPONENTS iostreams filesystem system timer chrono program_options locale REQUIRED)
     set(FETCH_BOOST FALSE)
 endif()
 
@@ -360,7 +382,7 @@ 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-program_options --with-system  --with-locale
                           --with-timer)
     set (BOOST_WILL_RECONFIGURE TRUE)
     set (FETCH_BOOST FALSE)
@@ -380,6 +402,12 @@ elseif(FETCH_BOOST)
         INSTALL_COMMAND ""
     )
 
+    ExternalProject_Add_Step(libboost makedir
+  	COMMAND mkdir -p <SOURCE_DIR>/build 
+	COMMENT "Make build directory"
+  	DEPENDEES download 
+  	DEPENDERS configure)
+
     ##
     # After we've installed boost,
     ##
@@ -403,7 +431,7 @@ if (BOOST_WILL_RECONFIGURE)
     set(Boost_FOUND TRUE)
 endif()
 
-
+message("BOOST ROOT = ${BOOST_ROOT}")
 message("BOOST INCLUDE DIR = ${Boost_INCLUDE_DIR}")
 message("BOOST INCLUDE DIRS = ${Boost_INCLUDE_DIRS}")
 message("BOOST LIB DIR = ${Boost_LIBRARY_DIRS}")
@@ -462,28 +490,6 @@ ExternalProject_Add_Step(libcereal makedir
   DEPENDEES download 
   DEPENDERS configure)
 
-message("Build system will fetch and build BWA (for Salmon)")
-message("==================================================================")
-##
-# This mode will likely go away soon, but until then, consider bundling directly with Salmon
-##
-include(ExternalProject)
-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
-    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}"
-    INSTALL_COMMAND sh -c "mkdir -p <INSTALL_DIR>/lib && mkdir -p <INSTALL_DIR>/include/bwa && cp libbwa.a <INSTALL_DIR>/lib && cp *.h <INSTALL_DIR>/include/bwa && cp is.c bwtindex.c bwt_gen.c QSufSort.c ${CMAKE_CURRENT_SOURCE_DIR}/src/"
-    BUILD_IN_SOURCE TRUE
-)
-
 ## Try and find TBB first
 find_package(TBB 2018.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy )
 
@@ -532,7 +538,7 @@ ExternalProject_Add(libtbb
     PATCH_COMMAND "${TBB_PATCH_STEP}"
     CONFIGURE_COMMAND ""
     BUILD_COMMAND make ${QUIET_MAKE} CXXFLAGS=${TBB_CXXFLAGS} lambdas=1 compiler=${TBB_COMPILER} cfg=release tbb_build_prefix=LIBS
-    INSTALL_COMMAND sh -c "cp ${TBB_SOURCE_DIR}/build/LIBS_release/*.${SHARED_LIB_EXTENSION}* ${TBB_INSTALL_DIR}/lib && cp -r ${TBB_SOURCE_DIR}/include/* ${TBB_INSTALL_DIR}/include"
+    INSTALL_COMMAND sh -c "mkdir -p ${TBB_INSTALL_DIR}/include && mkdir -p ${TBB_INSTALL_DIR}/lib && cp ${TBB_SOURCE_DIR}/build/LIBS_release/*.${SHARED_LIB_EXTENSION}* ${TBB_INSTALL_DIR}/lib && cp -r ${TBB_SOURCE_DIR}/include/* ${TBB_INSTALL_DIR}/include"
     BUILD_IN_SOURCE 1
 )
 
@@ -543,6 +549,9 @@ ExternalProject_Add_Step(libtbb reconfigure
 )
 
 set (FETCHED_TBB TRUE)
+if (${FETCHED_BOOST})
+	add_dependencies(libtbb libboost)
+endif()
 endif()
 
 ##

cmake/TestSalmonQuasi.cmake

@@ -1,3 +1,12 @@
+execute_process(COMMAND tar xzvf sample_data.tgz
+                WORKING_DIRECTORY ${TOPLEVEL_DIR}
+                RESULT_VARIABLE TAR_RESULT
+               )
+
+if (TAR_RESULT)
+    message(FATAL_ERROR "Error untarring sample_data.tgz")
+endif()
+
 set(SALMON_QUASI_INDEX_CMD ${CMAKE_BINARY_DIR}/salmon index -t transcripts.fasta -i sample_salmon_quasi_index --type quasi)
 execute_process(COMMAND ${SALMON_QUASI_INDEX_CMD}
                 WORKING_DIRECTORY ${TOPLEVEL_DIR}/sample_data

current_version.txt

@@ -0,0 +1,3 @@
+VERSION_MAJOR 0
+VERSION_MINOR 11
+VERSION_PATCH 1

doc/source/alevin.rst

@@ -1,7 +1,7 @@
 Alevin
 ================
 
-Aleivn is a tool --- integrated with the salmon software --- that introduces a family of algorithms for quantification and analysis of 3' tagged-end single-cell sequencing data. Currently alevin supports the following two major droplet based single-cell protocols:
+Alevin is a tool --- integrated with the salmon software --- that introduces a family of algorithms for quantification and analysis of 3' tagged-end single-cell sequencing data. Currently alevin supports the following two major droplet based single-cell protocols:
 
 1. Drop-seq
 2. 10x-Chromium v1/2

doc/source/conf.py

@@ -55,9 +55,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.8.1'
+version = '0.11'
 # The full version, including alpha/beta/rc tags.
-release = '0.8.1'
+release = '0.11.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docker/Dockerfile

@@ -6,7 +6,7 @@ MAINTAINER [email protected]
 
 ENV PACKAGES git gcc make g++ cmake libboost-all-dev liblzma-dev libbz2-dev \
     ca-certificates zlib1g-dev curl unzip autoconf
-ENV SALMON_VERSION 0.11.0
+ENV SALMON_VERSION 0.11.1
 
 # salmon binary will be installed in /home/salmon/bin/salmon
 

include/AlevinTypes.hpp

@@ -0,0 +1,15 @@
+#ifndef __ALEVIN_TYPES_HPP__
+#define __ALEVIN_TYPES_HPP__
+
+#include "rapmap/Kmer.hpp"
+
+namespace alevin {
+namespace types {
+
+  using AlevinUMIKmer = combinelib::kmers::Kmer<32,2>;
+
+}
+}
+
+#endif//__ALEVIN_TYPES_HPP__
+

include/Dedup.hpp

@@ -7,7 +7,6 @@
 #include "SalmonOpts.hpp"
 #include "CollapsedEMOptimizer.hpp"
 #include "GZipWriter.hpp"
-#include "AlevinKmer.hpp"
 #include "RapMapUtils.hpp"
 #include "AlevinUtils.hpp"
 

include/GZipWriter.hpp

@@ -14,7 +14,6 @@
 #include "SalmonOpts.hpp"
 #include "SalmonSpinLock.hpp"
 #include "AlevinOpts.hpp"
-#include "AlevinKmer.hpp"
 
 class GZipWriter {
 public:

include/ProgramOptionsGenerator.hpp

@@ -4,10 +4,6 @@
 #include <boost/program_options.hpp>
 #include "SalmonOpts.hpp"
 
-extern "C" {
-#include "bwamem.h"
-}
-
 namespace salmon {
 namespace po = boost::program_options;
 class ProgramOptionsGenerator{
@@ -18,11 +14,9 @@ class ProgramOptionsGenerator{
   po::options_description getBasicOptions(SalmonOpts& sopt);
 
   po::options_description getMappingSpecificOptions(SalmonOpts& sopt);
-  po::options_description getFMDOptions(mem_opt_t* memOpt, SalmonOpts& sopt);
   po::options_description getAlignmentSpecificOptions(SalmonOpts& sopt);
   po::options_description getAlevinBasicOptions();
   po::options_description getAlevinDevsOptions();
-
   po::options_description getAdvancedOptions(int32_t& numBiasSamples, SalmonOpts& sopt);
   po::options_description getHiddenOptions(SalmonOpts& sopt);
   po::options_description getTestingOptions(SalmonOpts& sopt);