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setup.py
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#!/usr/bin/env python3
import subprocess, sys, os, argparse,shutil
from collections import namedtuple, defaultdict
sys.path.append(os.path.join(os.path.dirname(__file__), "scripts/pyUtils"))
sys.path.append(os.path.join(os.path.dirname(__file__), "scripts/setUpScripts"))
from utils import Utils
from genFuncs import genHelper
from color_text import ColorText as CT
import pickle, datetime, re, math
#tuples
BuildPaths = namedtuple("BuildPaths", 'url build_dir build_sub_dir local_dir')
LibNameVer = namedtuple("LibNameVer", 'name version')
GitRefs = namedtuple("GitRefs", "branches tags")
class LibDirMaster():
def __init__(self,externalLoc):
self.base_dir = os.path.abspath(externalLoc); #top dir to hold tars,build, local directories
self.ext_tars = os.path.join(self.base_dir, "tarballs") #location to keep tarballs of programs/libraries downloads
self.ext_build = os.path.join(self.base_dir, "build") #location for the building of programs/libraries
self.install_dir = os.path.join(self.base_dir, "local") #location for the final install of programs/libraries
self.cache_dir = os.path.join(self.base_dir, ".cache")
Utils.mkdir(self.ext_tars) #tar storage directory
Utils.mkdir(self.ext_build) #build directory
Utils.mkdir(self.install_dir) #local directory
Utils.mkdir(self.cache_dir) #cache directory
def joinNameVer(libNameVerTup):
return os.path.join(libNameVerTup.name, libNameVerTup.version, libNameVerTup.name)
class CPPLibPackageVersionR():
def __init__(self, name, url, version, dirMaster):
self.nameVer_ = LibNameVer(name, version)
build_dir = os.path.join(dirMaster.ext_build, name, version)
fn = os.path.basename(url)
fn_noex = fn.replace(".tar.gz", "").replace(".tar.bz2", "").replace(".git", "")
build_sub_dir = os.path.join(dirMaster.ext_build, name, version, fn_noex)
local_dir = os.path.join(dirMaster.install_dir, name, version, name)
self.bPaths_ = BuildPaths(url, build_dir, build_sub_dir, local_dir)
self.rInstallLoc_ = ""
self.rExecutable_ = ""
self.rHome_ = ""
self.depends_ = []
self.cmd_ = ""
def setExecutableLoc(self, localPath):
self.rInstallLoc_ = os.path.join(os.path.abspath(localPath), joinNameVer(self.nameVer_))
verSplit = self.nameVer_.version.split(".")
verNameStr = verSplit[0] + verSplit[1] + verSplit[2]
verNameInt = int(verNameStr)
#print verSplit
#print verNameStr
#print verNameInt
#sys.exit(1)
if Utils.isMac() and verNameInt < 330:
self.rExecutable_ = os.path.join(self.rInstallLoc_, "R.framework/Resources/bin/R")
else:
self.rExecutable_ = os.path.join(self.rInstallLoc_, "bin/R")
self.rHome_ = str(Utils.runAndCapture(self.rExecutable_ + " RHOME")).strip()
def getIncludeFlags(self, localPath):
self.setExecutableLoc(localPath)
ret = "-DSTRICT_R_HEADERS"
ret = ret + " " + Utils.runAndCapture(self.rExecutable_ + " CMD config --cppflags")
ret = ret + " " + Utils.runAndCapture("echo '.libPaths(.libPaths()[length(.libPaths() )] ); Rcpp:::CxxFlags()' | " + self.rExecutable_ + " --vanilla --slave")
ret = ret + " " + Utils.runAndCapture("echo '.libPaths(.libPaths()[length(.libPaths() )] ); RInside:::CxxFlags()' | " + self.rExecutable_ + " --vanilla --slave")
return ' '.join(ret.split())
def getLdFlags(self, localPath):
self.setExecutableLoc(localPath)
ret = ""
ret = ret + Utils.runAndCapture(self.rExecutable_ + " CMD config --ldflags")
ret = ret + " " + Utils.runAndCapture(self.rExecutable_ + " CMD config BLAS_LIBS")
ret = ret + " " + Utils.runAndCapture(self.rExecutable_ + " CMD config LAPACK_LIBS")
ret = ret + " " + "-Wl,-rpath," + self.rHome_ + "/lib"
ret = ret + " " + Utils.runAndCapture("echo '.libPaths(.libPaths()[length(.libPaths() )] ); Rcpp:::LdFlags()' | " + self.rExecutable_ + " --vanilla --slave")
ret = ret + " " + Utils.runAndCapture("echo '.libPaths(.libPaths()[length(.libPaths() )] ); RInside:::LdFlags()' | " + self.rExecutable_ + " --vanilla --slave")
return ' '.join(ret.split())
def getDownloadUrl(self):
return self.bPaths_.url
class CPPLibPackageVersion():
def __init__(self, name, version, bPaths, depends):
self.nameVer_ = LibNameVer(name, version)
self.depends_ = depends #should be a list of LibNameVer
self.bPaths_ = bPaths
self.includePath_ = os.path.join(joinNameVer(self.nameVer_), "include")
self.additionalIncludeFlags_ = []
self.additionalIncludePaths_ = []
self.libPath_ = os.path.join(joinNameVer(self.nameVer_), "lib")
self.additionalLdFlags_ = []
self.libName_ = name
self.altLibName_ = ""
self.cmd_ = ""
def getDownloadUrl(self):
ret = self.bPaths_.url
if str(self.bPaths_.url).endswith(".git"):
ret = self.bPaths_.url.replace(".git","/archive/" + str(self.nameVer_.version) + ".tar.gz").replace("[email protected]:", "https://github.com/")
return ret
def getIncludeFlags(self, localPath):
ret = ""
if(len(self.includePath_) > 0):
ret = "-isystem" + str(os.path.join(localPath, self.includePath_))
if len(self.additionalIncludePaths_) > 0:
for addPath in self.additionalIncludePaths_:
if len(ret) > 0:
ret = ret + " "
ret = ret + "-isystem" + str(os.path.join(localPath, addPath))
if len(self.additionalIncludeFlags_) > 0:
if len(ret)> 0:
ret = ret + " "
ret = ret + " ".join(self.additionalIncludeFlags_)
return ret
def getLdFlags(self, localPath):
ret = ""
retList = []
libPath = str(os.path.join(localPath,self.libPath_))
if(len(self.libPath_) > 0):
retList.append("-Wl,-rpath," + str(libPath))
retList.append("-L" + str(libPath))
if len(self.altLibName_) > 0:
retList.append("-l" + self.altLibName_)
elif "" != self.libName_:
retList.append("-l" + self.libName_)
if len(self.additionalLdFlags_) > 0:
retList.extend(self.additionalLdFlags_)
if len(retList) > 0:
ret = " ".join(retList)
return ret
class CPPLibPackage():
def __init__(self, name, defaultBuildCmd, dirMaster, libType, defaultVersion):
self.name_ = name
self.defaultVersion_ = defaultVersion.replace("/", "__")
self.defaultBuildCmd_ = defaultBuildCmd
self.versions_ = {}
self.externalLibDir_ = dirMaster
if "git" != libType and "file" != libType and "git-headeronly" != libType:
raise Exception("libType should be 'git', 'git-headeronly', or 'file', not " + str(libType))
self.libType_ = libType #should be git, git-headeronly, or file
self.njhProject_ = False
def addVersion(self, url, verName, depends=[]):
verName = verName.replace("/", "__")
build_dir = os.path.join(self.externalLibDir_.ext_build, self.name_, verName)
fn = os.path.basename(url)
#fn_noex = fn.replace(".tar.gz", "").replace(".tar.bz2", "").replace(".git", "")
build_sub_dir = os.path.join(self.externalLibDir_.ext_build, self.name_, verName, self.name_)
local_dir = os.path.join(self.externalLibDir_.install_dir, self.name_, verName, self.name_)
self.versions_[verName] = CPPLibPackageVersion(self.name_, verName,BuildPaths(url, build_dir, build_sub_dir, local_dir), depends)
def addHeaderOnlyVersion(self, url, verName, depends=[]):
'''set up for header only libraries, these just need
the header copied no need for build_dir build_sub_dir '''
verName = verName.replace("/", "__")
local_dir = os.path.join(self.externalLibDir_.install_dir, self.name_, verName, self.name_)
self.versions_[verName] = CPPLibPackageVersion(self.name_, verName,BuildPaths(url, "", "", local_dir), depends)
self.versions_[verName].includePath_ = os.path.join(self.name_, verName)
#self.versions_[verName].includePath_ = joinNameVer(self.versions_[verName].nameVer_)
self.versions_[verName].libPath_ = ""
def hasVersion(self, version):
return version in self.versions_
def getVersions(self):
return sorted(self.versions_.keys())
def getLocalDir(self, version):
if self.hasVersion(version):
return self.versions_[version].bPaths_.local_dir
raise Exception("Error in getLocalDir" + self.name_ + " doesn't have version " + str(version))
def getBuildSubDir(self, version):
if self.hasVersion(version):
return self.versions_[version].bPaths_.build_sub_dir
raise Exception("Error in getBuildSubDir" + self.name_ + " doesn't have version " + str(version))
def getBuildDir(self, version):
if self.hasVersion(version):
return self.versions_[version].bPaths_.build_dir
raise Exception("Error in getBuildDir" + self.name_ + " doesn't have version " + str(version))
def getGitRefs(self, url):
if not self.libType_.startswith("git"):
raise Exception("Library " + self.name_ + " is not a git library, type is : " + self.libType_)
try:
cap = Utils.runAndCapture("git ls-remote {url}".format(url = url))
except Exception as inst:
try:
#if the first attempt fail, try doing https instead if that was reason
url = url.replace("[email protected]:", "https://github.com/")
cap = Utils.runAndCapture("git ls-remote {url}".format(url = url))
except Exception as instFallback:
raise instFallback
branches = []
tags = []
for line in cap.split("\n"):
if "" != line:
lineSplit = line.split()
if 2 == len(lineSplit):
if "heads" in lineSplit[1]:
branches.append(lineSplit[1][(lineSplit[1].find("heads/") + 6):])
elif "tags" in lineSplit[1] and not lineSplit[1].endswith("^{}"):
tags.append(lineSplit[1][(lineSplit[1].find("tags/") + 5):])
gRefs = GitRefs(branches, tags)
return (gRefs)
class Packages():
'''class to hold and setup all the necessary paths for
downloading, building, and then installing packages/libraries'''
def __init__(self, externalLoc, args, libsNeeded = []):
self.dirMaster_ = LibDirMaster(externalLoc); #top dir to hold tars, build, local directories
self.args = args
self.packages_ = {} #dictionary to hold path infos
self.setUpPackagesNeeded(libsNeeded);
def setUpPackagesNeeded(self, libsNeeded):
if "boost" in libsNeeded:
self.packages_["boost"] = self.__boost()
if "r" in libsNeeded:
self.packages_["r"] = self.__r()
if "cppcms" in libsNeeded:
self.packages_["cppcms"] = self.__cppcms()
if "dlib" in libsNeeded:
self.packages_["dlib"] = self.__dlib()
if "libsvm" in libsNeeded:
self.packages_["libsvm"] = self.__libsvm()
if "mathgl" in libsNeeded:
self.packages_["mathgl"] = self.__mathgl()
if "magic" in libsNeeded:
self.packages_["magic"] = self.__magic()
if "bowtie2" in libsNeeded:
self.packages_["bowtie2"] = self.__bowtie2()
if "pigz" in libsNeeded:
self.packages_["pigz"] = self.__pigz()
if "lastz" in libsNeeded:
self.packages_["lastz"] = self.__lastz()
if "samtools" in libsNeeded:
self.packages_["samtools"] = self.__samtools()
if "bcftools" in libsNeeded:
self.packages_["bcftools"] = self.__bcftools()
if "eigen" in libsNeeded:
self.packages_["eigen"] = self.__eigen()
if "glpk" in libsNeeded:
self.packages_["glpk"] = self.__glpk()
if "lapack" in libsNeeded:
self.packages_["lapack"] = self.__lapack()
if "atlas" in libsNeeded:
self.packages_["atlas"] = self.__atlas()
#git repos
if "adapterremoval" in libsNeeded:
self.packages_["adapterremoval"] = self.__adapterremoval()
if "curl" in libsNeeded:
self.packages_["curl"] = self.__curl()
if "mongoc" in libsNeeded:
self.packages_["mongoc"] = self.__mongoc()
if "mongocxx" in libsNeeded:
self.packages_["mongocxx"] = self.__mongocxx()
if "flash" in libsNeeded:
self.packages_["flash"] = self.__flash()
if "libpca" in libsNeeded:
self.packages_["libpca"] = self.__libpca()
if "muscle" in libsNeeded:
self.packages_["muscle"] = self.__muscle()
if "armadillo" in libsNeeded:
self.packages_["armadillo"] = self.__armadillo()
if "cmake" in libsNeeded:
self.packages_["cmake"] = self.__cmake()
if "boost_filesystem" in libsNeeded:
self.packages_["boost_filesystem"] = self.__boost_filesystem()
if "zlib" in libsNeeded:
self.packages_["zlib"] = self.__zlib()
if "bamtools" in libsNeeded:
self.packages_["bamtools"] = self.__bamtools()
if "jsoncpp" in libsNeeded:
self.packages_["jsoncpp"] = self.__jsoncpp()
if "catch" in libsNeeded:
self.packages_["catch"] = self.__catch()
if "hts" in libsNeeded:
self.packages_["hts"] = self.__hts()
if "zi_lib" in libsNeeded:
self.packages_["zi_lib"] = self.__zi_lib()
if "pstreams" in libsNeeded:
self.packages_["pstreams"] = self.__pstreams()
if "cppitertools" in libsNeeded:
self.packages_["cppitertools"] = self.__cppitertools()
if "cppprogutils" in libsNeeded:
self.packages_["cppprogutils"] = self.__cppprogutils()
if "restbed" in libsNeeded:
self.packages_["restbed"] = self.__restbed()
if "zlib-ng" in libsNeeded:
self.packages_["zlib-ng"] = self.__zlibng()
if "openblas" in libsNeeded:
self.packages_["openblas"] = self.__openblas()
#njh setup
if "njhseq" in libsNeeded:
self.packages_["njhseq"] = self.__njhseq()
if "njhcpp" in libsNeeded:
self.packages_["njhcpp"] = self.__njhcpp()
if "seekdeep" in libsNeeded:
self.packages_["seekdeep"] = self.__SeekDeep()
if "seqserver" in libsNeeded:
self.packages_["seqserver"] = self.__seqserver()
if "njhrinside" in libsNeeded:
self.packages_["njhrinside"] = self.__njhRInside()
if "twobit" in libsNeeded:
self.packages_["twobit"] = self.__twobit()
if "sharedmutex" in libsNeeded:
self.packages_["sharedmutex"] = self.__sharedMutex()
if "bhtsne" in libsNeeded:
self.packages_["bhtsne"] = self.__bhtsne()
if "elucidator" in libsNeeded:
self.packages_["elucidator"] = self.__elucidator()
if "mipwrangler" in libsNeeded:
self.packages_["mipwrangler"] = self.__MIPWrangler()
#developer, private repos
if self.args.private:
if "elucidatorlab" in libsNeeded:
self.packages_["elucidatorlab"] = self.__elucidatorlab()
'''
self.packages_["mlpack"] = self.__mlpack()
self.packages_["liblinear"] = self.__liblinear()
'''
def package(self, name):
'''get package info if it exists'''
if name in self.packages_:
return self.packages_[name]
raise Exception(name + " not found in Packages")
def __zi_lib(self):
name = "zi_lib"
url = 'https://github.com/weng-lab/zi_lib.git'
buildCmd = ""
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "git-headeronly", "master")
if self.args.noInternet:
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
elif os.path.exists(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl')):
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
else:
refs = pack.getGitRefs(url)
for ref in [b.replace("/", "__") for b in refs.branches] + refs.tags:
pack.addHeaderOnlyVersion(url, ref)
pack.versions_[ref].includePath_ = os.path.join(name, ref, name)
if not Utils.isMac():
pack.versions_[ref].additionalLdFlags_ = ["-lrt"]
Utils.mkdir(os.path.join(self.dirMaster_.cache_dir, name))
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'wb') as output:
pickle.dump(pack, output, pickle.HIGHEST_PROTOCOL)
return pack
def __pstreams(self):
name = "pstreams"
url = 'https://github.com/nickjhathaway/pstreams.git'
buildCmd = ""
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "git-headeronly", "RELEASE_0_8_1")
if self.args.noInternet:
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
elif os.path.exists(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl')):
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
else:
refs = pack.getGitRefs(url)
for ref in [b.replace("/", "__") for b in refs.branches] + refs.tags:
pack.addHeaderOnlyVersion(url, ref)
Utils.mkdir(os.path.join(self.dirMaster_.cache_dir, name))
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'wb') as output:
pickle.dump(pack, output, pickle.HIGHEST_PROTOCOL)
return pack
def __bamtools(self):
url = 'https://github.com/nickjhathaway/bamtools.git'
name = "bamtools"
buildCmd = "mkdir -p build && cd build && ZLIBADDFLAGS CC={CC} CXX={CXX} cmake -DCMAKE_INSTALL_PREFIX:PATH={local_dir} .. && make -j {num_cores} install"
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "git", "v2.5.0")
defaultZlibVersion = "1.2.11";
zlibPack = self.__zlib()
if self.args.noInternet:
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
elif os.path.exists(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl')):
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
else:
refs = pack.getGitRefs(url)
for ref in [b.replace("/", "__") for b in refs.branches] + refs.tags:
pack.addVersion(url, ref, [LibNameVer("zlib", defaultZlibVersion)])
zlibLdFlags = zlibPack.versions_[defaultZlibVersion].getLdFlags(self.dirMaster_.install_dir)
zlibIncFlags = zlibPack.versions_[defaultZlibVersion].getIncludeFlags(self.dirMaster_.install_dir)
zlibAddFlags = "LDFLAGS=\""+ zlibLdFlags + "\" CXXFLAGS=\""+ zlibIncFlags + "\""
pack.versions_[ref].cmd_ = buildCmd.replace("ZLIBADDFLAGS", zlibAddFlags)
pack.versions_[ref].libPath_ = os.path.join(pack.versions_[ref].libPath_,name)
pack.versions_[ref].includePath_ = os.path.join(pack.versions_[ref].includePath_,name)
Utils.mkdir(os.path.join(self.dirMaster_.cache_dir, name))
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'wb') as output:
pickle.dump(pack, output, pickle.HIGHEST_PROTOCOL)
return pack
def __jsoncpp(self):
url = "https://github.com/open-source-parsers/jsoncpp.git"
name = "jsoncpp"
buildCmd = "mkdir -p build && cd build && CC={CC} CXX={CXX} cmake -DCMAKE_CXX_FLAGS=-fPIC -DCMAKE_EXE_LINKER_FLAGS=-fPIC -DCMAKE_INSTALL_PREFIX:PATH={local_dir} .. && make -j {num_cores} install"
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "git", "1.8.3")
if self.args.noInternet:
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
elif os.path.exists(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl')):
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
else:
refs = pack.getGitRefs(url)
for ref in [b.replace("/", "__") for b in refs.branches] + refs.tags:
pack.addVersion(url, ref)
Utils.mkdir(os.path.join(self.dirMaster_.cache_dir, name))
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'wb') as output:
pickle.dump(pack, output, pickle.HIGHEST_PROTOCOL)
return pack
def __mongoc(self):
url = "https://github.com/mongodb/mongo-c-driver.git"
name = "mongoc"
#
# if Utils.isMac():
# buildCmd = "sed -i.bak s/git:/http:/g .gitmodules && CC={CC} CXX={CXX} PKG_CONFIG_PATH=/usr/local/opt/openssl/lib/pkgconfig:$PKG_CONFIG_PATH ./autogen.sh --enable-ssl --enable-sasl --prefix={local_dir}&& make -j {num_cores} && make install"
# else:
# buildCmd = "sed -i.bak s/git:/http:/g .gitmodules && CC={CC} CXX={CXX} ./autogen.sh --enable-ssl --enable-sasl --prefix={local_dir} && make -j {num_cores} && make install"
#
if Utils.isMac():
buildCmd = """sed -i.bak s/git:/http:/g .gitmodules && CC={CC} CXX={CXX} PKG_CONFIG_PATH=/usr/local/opt/openssl/lib/pkgconfig:$PKG_CONFIG_PATH LDFLAGS="$(echo $(pkg-config openssl --libs) | sed 's/-L/-Wl,-rpath,/g' | sed 's/lib\ .*/lib/g')" ./autogen.sh --enable-ssl --enable-sasl --prefix={local_dir}&& make -j {num_cores} && make install"""
else:
buildCmd = """sed -i.bak s/git:/http:/g .gitmodules && CC={CC} CXX={CXX} LDFLAGS="$(echo $(pkg-config openssl --libs) | sed 's/-L/-Wl,-rpath,/g' | sed 's/lib\ .*/lib/g')" ./autogen.sh --enable-ssl --enable-sasl --prefix={local_dir} && make -j {num_cores} && make install"""
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "git", "1.3.3")
pack.addVersion(url, "1.3.3")
pack.versions_["1.3.3"].additionalIncludePaths_.append(pack.versions_["1.3.3"].includePath_ + "/libmongoc-1.0")
pack.versions_["1.3.3"].includePath_ = pack.versions_["1.3.3"].includePath_ + "/libbson-1.0"
pack.versions_["1.3.3"].altLibName_ = "ssl" #a trick to control order of -l flags for libs
pack.versions_["1.3.3"].additionalLdFlags_ = ["-lcrypto","-lmongoc-1.0", "-lbson-1.0"]
if not Utils.isMac():
pack.versions_["1.3.3"].additionalLdFlags_.append("-lrt")
pack.addVersion(url, "1.3.4")
pack.versions_["1.3.4"].additionalIncludePaths_.append(pack.versions_["1.3.4"].includePath_ + "/libmongoc-1.0")
pack.versions_["1.3.4"].includePath_ = pack.versions_["1.3.4"].includePath_ + "/libbson-1.0"
pack.versions_["1.3.4"].altLibName_ = "ssl" #a trick to control order of -l flags for libs
pack.versions_["1.3.4"].additionalLdFlags_ = ["-lcrypto","-lmongoc-1.0", "-lbson-1.0"]
if not Utils.isMac():
pack.versions_["1.3.4"].additionalLdFlags_.append("-lrt")
pack.addVersion(url, "1.4.1")
pack.versions_["1.4.1"].additionalIncludePaths_.append(pack.versions_["1.4.1"].includePath_ + "/libmongoc-1.0")
pack.versions_["1.4.1"].includePath_ = pack.versions_["1.4.1"].includePath_ + "/libbson-1.0"
pack.versions_["1.4.1"].altLibName_ = "ssl" #a trick to control order of -l flags for libs
pack.versions_["1.4.1"].additionalLdFlags_ = ["-lcrypto","-lmongoc-1.0", "-lbson-1.0"]
if not Utils.isMac():
pack.versions_["1.4.1"].additionalLdFlags_.append("-lrt")
pack.addVersion(url, "1.5.0")
pack.versions_["1.5.0"].additionalIncludePaths_.append(pack.versions_["1.5.0"].includePath_ + "/libmongoc-1.0")
pack.versions_["1.5.0"].includePath_ = pack.versions_["1.5.0"].includePath_ + "/libbson-1.0"
pack.versions_["1.5.0"].altLibName_ = "ssl" #a trick to control order of -l flags for libs
pack.versions_["1.5.0"].additionalLdFlags_ = ["-lcrypto","-lmongoc-1.0", "-lbson-1.0"]
if not Utils.isMac():
pack.versions_["1.5.0"].additionalLdFlags_.append("-lrt")
return pack#
def __mongocxx(self):
url = "https://github.com/mongodb/mongo-cxx-driver.git"
name = "mongocxx"
buildCmd = "cd build && PKG_CONFIG_PATH={external}/local/mongoc/{mongoc_ver}/mongoc/lib/pkgconfig/:PKG_CONFIG_PATH CC={CC} CXX={CXX} cmake -DCMAKE_BUILD_TYPE=Release -DLIBBSON_DIR={external}/local/mongoc/{mongoc_ver}/mongoc/ -DLIBMONGOC_DIR={external}/local/mongoc/{mongoc_ver}/mongoc/ -DCMAKE_INSTALL_PREFIX={local_dir} .. && make -j {num_cores} && make install"
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "git", "r3.0.1")
pack.addVersion(url, "r3.0.0", [LibNameVer("mongoc", "1.3.3")])
pack.versions_["r3.0.0"].additionalIncludePaths_.append(pack.versions_["r3.0.0"].includePath_ + "/mongocxx/v_noabi")
pack.versions_["r3.0.0"].includePath_ = pack.versions_["r3.0.0"].includePath_ + "/bsoncxx/v_noabi"
pack.versions_["r3.0.0"].additionalLdFlags_ = ["-lbsoncxx"]
pack.addVersion(url, "r3.0.1", [LibNameVer("mongoc", "1.3.4")])
pack.versions_["r3.0.1"].additionalIncludePaths_.append(pack.versions_["r3.0.1"].includePath_ + "/mongocxx/v_noabi")
pack.versions_["r3.0.1"].includePath_ = pack.versions_["r3.0.1"].includePath_ + "/bsoncxx/v_noabi"
pack.versions_["r3.0.1"].additionalLdFlags_ = ["-lbsoncxx"]
pack.addVersion(url, "r3.0.2", [LibNameVer("mongoc", "1.4.1")])
pack.versions_["r3.0.2"].additionalIncludePaths_.append(pack.versions_["r3.0.2"].includePath_ + "/mongocxx/v_noabi")
pack.versions_["r3.0.2"].includePath_ = pack.versions_["r3.0.2"].includePath_ + "/bsoncxx/v_noabi"
pack.versions_["r3.0.2"].additionalLdFlags_ = ["-lbsoncxx"]
pack.addVersion(url, "r3.1.0-rc0", [LibNameVer("mongoc", "1.5.0")])
pack.versions_["r3.1.0-rc0"].additionalIncludePaths_.append(pack.versions_["r3.1.0-rc0"].includePath_ + "/mongocxx/v_noabi")
pack.versions_["r3.1.0-rc0"].includePath_ = pack.versions_["r3.1.0-rc0"].includePath_ + "/bsoncxx/v_noabi"
pack.versions_["r3.1.0-rc0"].additionalLdFlags_ = ["-lbsoncxx"]
return pack
def __cppitertools(self):
url = 'https://github.com/ryanhaining/cppitertools.git'
name = "cppitertools"
buildCmd = ""
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "git-headeronly", "v0.1")
if self.args.noInternet:
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
elif os.path.exists(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl')):
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
else:
refs = pack.getGitRefs(url)
for ref in [b.replace("/", "__") for b in refs.branches] + refs.tags:
pack.addHeaderOnlyVersion(url, ref)
Utils.mkdir(os.path.join(self.dirMaster_.cache_dir, name))
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'wb') as output:
pickle.dump(pack, output, pickle.HIGHEST_PROTOCOL)
return pack
def __catch(self):
url = 'https://github.com/philsquared/Catch.git'
name = "catch"
buildCmd = ""
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "git-headeronly", "v1.3.3")
if self.args.noInternet:
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
elif os.path.exists(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl')):
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
else:
refs = pack.getGitRefs(url)
for ref in [b.replace("/", "__") for b in refs.branches] + refs.tags:
pack.addHeaderOnlyVersion(url, ref)
pack.versions_[ref].includePath_ = os.path.join(joinNameVer(pack.versions_[ref].nameVer_), "single_include")
Utils.mkdir(os.path.join(self.dirMaster_.cache_dir, name))
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'wb') as output:
pickle.dump(pack, output, pickle.HIGHEST_PROTOCOL)
return pack
def __r(self):
name = "R"
rHomeLoc = "bin/R RHOME"
if Utils.isMac():
rHomeLoc = "R.framework/Resources/bin/R RHOME"
#&& echo 'install.packages(c(\"gridExtra\", \"ape\", \"ggplot2\", \"seqinr\",\"Rcpp\", \"RInside\",\"devtools\"),
buildCmd = """./configure --prefix={local_dir} --enable-R-shlib --with-x=no CC={CC} CXX={CXX} OBJC={CC}
&& make -j {num_cores}
&& make install
&& echo '.libPaths(.libPaths()[length(.libPaths() )] ); install.packages(c(\"tidyverse\", \"gridExtra\", \"ape\", \"ggplot2\", \"seqinr\",\"Rcpp\", \"RInside\"),
repos=\"http://cran.us.r-project.org\", Ncpus = {num_cores}, lib =.libPaths()[length(.libPaths() )] )' | $({local_dir}/""" + rHomeLoc + """)/bin/R --slave --vanilla
"""
buildCmd = " ".join(buildCmd.split())
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "file", "3.4.0")
pack.versions_["3.4.0"] = CPPLibPackageVersionR("R", "http://baileylab.umassmed.edu/sourceCodes/R/R-3.4.0.tar.gz", "3.4.0", self.dirMaster_)
pack.versions_["3.3.3"] = CPPLibPackageVersionR("R", "http://baileylab.umassmed.edu/sourceCodes/R/R-3.3.3.tar.gz", "3.3.3", self.dirMaster_)
pack.versions_["3.3.2"] = CPPLibPackageVersionR("R", "http://baileylab.umassmed.edu/sourceCodes/R/R-3.3.2.tar.gz", "3.3.2", self.dirMaster_)
pack.versions_["3.3.0"] = CPPLibPackageVersionR("R", "http://baileylab.umassmed.edu/sourceCodes/R/R-3.3.0.tar.gz", "3.3.0", self.dirMaster_)
pack.versions_["3.2.4"] = CPPLibPackageVersionR("R", "http://baileylab.umassmed.edu/sourceCodes/R/R-3.2.4.tar.gz", "3.2.4", self.dirMaster_)
pack.versions_["3.2.3"] = CPPLibPackageVersionR("R", "http://baileylab.umassmed.edu/sourceCodes/R/R-3.2.3.tar.gz", "3.2.3", self.dirMaster_)
pack.versions_["3.2.2"] = CPPLibPackageVersionR("R", "http://baileylab.umassmed.edu/sourceCodes/R/R-3.2.2.tar.gz", "3.2.2", self.dirMaster_)
pack.versions_["3.2.1"] = CPPLibPackageVersionR("R", "http://baileylab.umassmed.edu/sourceCodes/R/R-3.2.1.tar.gz", "3.2.1", self.dirMaster_)
pack.versions_["3.2.0"] = CPPLibPackageVersionR("R", "http://baileylab.umassmed.edu/sourceCodes/R/R-3.2.0.tar.gz", "3.2.0", self.dirMaster_)
pack.versions_["3.1.3"] = CPPLibPackageVersionR("R", "http://baileylab.umassmed.edu/sourceCodes/R/R-3.1.3.tar.gz", "3.1.3", self.dirMaster_)
return pack
def __armadillo(self):
name = "armadillo"
buildCmd = "mkdir -p build && cd build && CC={CC} CXX={CXX} cmake -DDETECT_HDF5=false -DCMAKE_CXX_FLAGS=\"-std=c++11\" -DCMAKE_INSTALL_PREFIX:PATH={local_dir} .. && make -j {num_cores} install"
url = "https://github.com/nickjhathaway/armadillo.git"
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "git", "8.200.0")
if self.args.noInternet:
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
elif os.path.exists(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl')):
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
else:
refs = pack.getGitRefs(url)
for ref in [b.replace("/", "__") for b in refs.branches] + refs.tags:
pack.addVersion(url, ref)
Utils.mkdir(os.path.join(self.dirMaster_.cache_dir, name))
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'wb') as output:
pickle.dump(pack, output, pickle.HIGHEST_PROTOCOL)
return pack
def __libpca(self):
name = "libpca"
#the version will get overridden by setting pack.defaultBuildCmd_ latter, but the dependency check needs to install it first
armPack = self.__armadillo()
buildCmd = """CC={CC} CXX={CXX} autoreconf -f -i && ./configure --prefix {local_dir} && make -j {num_cores} install"""
defaultArmVer = "8.200.0"
url = "https://github.com/nickjhathaway/libpca.git"
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "git", "1.3.3")
if self.args.noInternet:
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
elif os.path.exists(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl')):
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
else:
refs = pack.getGitRefs(url)
for ref in [b.replace("/", "__") for b in refs.branches] + refs.tags:
pack.addVersion(url, ref, [LibNameVer("armadillo", defaultArmVer)] )
armLdFlags = armPack.versions_[defaultArmVer].getLdFlags(self.dirMaster_.install_dir)
armIncFlags = armPack.versions_[defaultArmVer].getIncludeFlags(self.dirMaster_.install_dir)
pack.versions_[ref].cmd_ = "CC={CC} CXX={CXX} LDFLAGS=\"" + armLdFlags + "\" CXXFLAGS=\"" + armIncFlags + "\" autoreconf -f -i && " + "CC={CC} CXX={CXX} LDFLAGS=\"" + armLdFlags + "\" CXXFLAGS=\"" + armIncFlags + "\" ./configure --prefix {local_dir} && make -j {num_cores} install"
pack.versions_[ref].cmd_ = " ".join(pack.versions_[ref].cmd_.split())
pack.versions_[ref] .altLibName_ = "pca"
Utils.mkdir(os.path.join(self.dirMaster_.cache_dir, name))
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'wb') as output:
pickle.dump(pack, output, pickle.HIGHEST_PROTOCOL)
return pack
def __eigen(self):
name = "eigen"
buildCmd = """mkdir build && cd build && CC={CC} CXX={CXX} cmake -DCMAKE_INSTALL_PREFIX={local_dir} .. && make install -j {num_cores}"""
buildCmd = " ".join(buildCmd.split())
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "file", "3.3.1")
pack.addVersion("http://baileylab.umassmed.edu/sourceCodes/eigen/eigen-3.3.1.tar.bz2", "3.3.1")
pack.versions_["3.3.1"].libPath_ = "";
pack.versions_["3.3.1"].includePath_ = os.path.join(joinNameVer(pack.versions_["3.3.1"].nameVer_), "include", "eigen3")
return pack
def __lapack(self):
name = "lapack"
buildCmd = """mkdir build && cd build && CC={CC} CXX={CXX} cmake -DCMAKE_INSTALL_PREFIX={local_dir} .. && make install -j {num_cores}"""
buildCmd = " ".join(buildCmd.split())
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "file", "3.7.0")
pack.addVersion("http://baileylab.umassmed.edu/sourceCodes/lapack/lapack-3.7.0.tar.gz", "3.7.0")
return pack
def __glpk(self):
name = "glpk"
buildCmd = """CC={CC} CXX={CXX} ./configure
--prefix={local_dir}
&& make -j {num_cores}
&& make -j {num_cores} install"""
buildCmd = " ".join(buildCmd.split())
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "file", "4.61")
pack.addVersion("http://baileylab.umassmed.edu/sourceCodes/glpk/glpk-4.61.tar.gz", "4.61")
return pack
def __cmake(self):
name = "cmake"
buildCmd = """CC={CC} CXX={CXX} ./configure
--prefix={local_dir}
&& make -j {num_cores}
&& make -j {num_cores} install"""
buildCmd = " ".join(buildCmd.split())
url = "https://github.com/nickjhathaway/cmake.git"
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "git", "3.7.2")
if self.args.noInternet:
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
elif os.path.exists(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl')):
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
else:
refs = pack.getGitRefs(url)
for ref in [b.replace("/", "__") for b in refs.branches] + refs.tags:
pack.addVersion(url, ref)
Utils.mkdir(os.path.join(self.dirMaster_.cache_dir, name))
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'wb') as output:
pickle.dump(pack, output, pickle.HIGHEST_PROTOCOL)
return pack
def __curl(self):
name = "curl"
url = "https://github.com/curl/curl.git"
extraFlags = ""
#curl library doesn't link to the openssl library at run time as it finds at configure so need to add the following to
#make the openssl library directory found to be set as run time path
if Utils.hasProgram("pkg-config"):
pkgconfgOutput = Utils.runAndCapture("pkg-config --libs openssl")
if "-L" in pkgconfgOutput:
pkgconfgOutput_splits = pkgconfgOutput.split()
extraFlags = "LDFLAGS=" + "\""
for pkgconfgOutput_split in pkgconfgOutput_splits:
if pkgconfgOutput_split.startswith("-L"):
extraFlags = extraFlags + " -Wl,-rpath," + pkgconfgOutput_split[2:]
extraFlags = extraFlags + " $LDFLAGS\""
buildCmd = """./buildconf && CC={CC} CXX={CXX} """ + extraFlags + """ ./configure
--prefix={local_dir}
&& make -j {num_cores}
&& make -j {num_cores} install"""
buildCmd = " ".join(buildCmd.split())
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "git", "curl-7_56_1")
if self.args.noInternet:
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
elif os.path.exists(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl')):
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
else:
refs = pack.getGitRefs(url)
for ref in [b.replace("/", "__") for b in refs.branches] + refs.tags:
pack.addVersion(url, ref)
Utils.mkdir(os.path.join(self.dirMaster_.cache_dir, name))
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'wb') as output:
pickle.dump(pack, output, pickle.HIGHEST_PROTOCOL)
return pack
def __atlas(self):
name = "atlas"
buildCmd = """mkdir build && cd build && CC={CC} CXX={CXX} ../configure
--prefix={local_dir}
&& make -j {num_cores}
&& make -j {num_cores} install"""
buildCmd = " ".join(buildCmd.split())
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "file", "3.10.3")
pack.addVersion("http://baileylab.umassmed.edu/sourceCodes/atlas/atlas3.10.3.tar.gz", "3.10.3")
return pack
def __muscle(self):
name = "muscle"
buildCmd = "CC={CC} CXX={CXX} make -j {num_cores} && mkdir -p {local_dir}/bin && cp muscle {local_dir}/bin/"
url = "https://github.com/nickjhathaway/muscle.git"
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "git", "3.8.31")
if self.args.noInternet:
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
elif os.path.exists(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl')):
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
else:
refs = pack.getGitRefs(url)
for ref in [b.replace("/", "__") for b in refs.branches] + refs.tags:
pack.addVersion(url, ref)
Utils.mkdir(os.path.join(self.dirMaster_.cache_dir, name))
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'wb') as output:
pickle.dump(pack, output, pickle.HIGHEST_PROTOCOL)
return pack
def __adapterremoval(self):
name = "adapterremoval"
buildCmd = "CC={CC} CXX={CXX} make -j {num_cores} && make -j {num_cores} install PREFIX={local_dir}"
url = "https://github.com/MikkelSchubert/adapterremoval.git"
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "git", "v2.2.2")
if self.args.noInternet:
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
elif os.path.exists(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl')):
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
else:
refs = pack.getGitRefs(url)
for ref in [b.replace("/", "__") for b in refs.branches] + refs.tags:
pack.addVersion(url, ref)
Utils.mkdir(os.path.join(self.dirMaster_.cache_dir, name))
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'wb') as output:
pickle.dump(pack, output, pickle.HIGHEST_PROTOCOL)
return pack
def __bowtie2(self):
name = "bowtie2"
url = "https://github.com/BenLangmead/bowtie2.git"
buildCmd = "CC={CC} CXX={CXX} make -j {num_cores} && mkdir -p {local_dir}/bin && cp -r bowtie2* {local_dir}/bin/"
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "git", "v2.3.4.1")
if self.args.noInternet:
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
elif os.path.exists(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl')):
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
else:
refs = pack.getGitRefs(url)
for ref in [b.replace("/", "__") for b in refs.branches] + refs.tags:
pack.addVersion(url, ref)
Utils.mkdir(os.path.join(self.dirMaster_.cache_dir, name))
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'wb') as output:
pickle.dump(pack, output, pickle.HIGHEST_PROTOCOL)
return pack
def __flash(self):
name = "flash"
buildCmd = "CC={CC} CXX={CXX} ZLIBADDFLAGS make -j {num_cores} && mkdir -p {local_dir}/bin && cp flash {local_dir}/bin/"
url = "https://github.com/nickjhathaway/flash.git"
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "git", "1.2.11")
defaultZlibVersion = "1.2.11";
zlibPack = self.__zlib()
if self.args.noInternet:
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
elif os.path.exists(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl')):
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
else:
refs = pack.getGitRefs(url)
for ref in [b.replace("/", "__") for b in refs.branches] + refs.tags:
pack.addVersion(url, ref)
zlibLdFlags = zlibPack.versions_[defaultZlibVersion].getLdFlags(self.dirMaster_.install_dir)
zlibIncFlags = zlibPack.versions_[defaultZlibVersion].getIncludeFlags(self.dirMaster_.install_dir)
zlibAddFlags = "LDFLAGS=\""+ zlibLdFlags + "\" CXXFLAGS=\""+ zlibIncFlags + "\""
pack.versions_[ref].cmd_ = buildCmd.replace("ZLIBADDFLAGS", zlibAddFlags)
Utils.mkdir(os.path.join(self.dirMaster_.cache_dir, name))
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'wb') as output:
pickle.dump(pack, output, pickle.HIGHEST_PROTOCOL)
return pack
def __pigz(self):
name = "pigz"
buildCmd = "CC={CC} CXX={CXX} make -j {num_cores} && mkdir -p {local_dir}/bin && cp pigz unpigz {local_dir}/bin/"
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "file", "2.3.4")
pack.addVersion("http://baileylab.umassmed.edu/sourceCodes/pigz/pigz-2.3.4.tar.gz", "2.3.4")
return pack
def __lastz(self):
name = "lastz"
buildCmd = "sed -i.bak 's/-Werror//g' src/Makefile && CC={CC} CXX={CXX} make -j {num_cores} && mkdir -p {local_dir}/bin && cp src/lastz src/lastz_D {local_dir}/bin/"
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "file", "1.03.73")
pack.addVersion("http://baileylab.umassmed.edu/sourceCodes/lastz/lastz-1.03.73.tar.gz", "1.03.73")
return pack
def __samtools(self):
name = "samtools"
url = "https://github.com/samtools/samtools.git"
buildCmd = "git clone https://github.com/samtools/htslib.git && cd htslib && git checkout SAMVERSION && CC={CC} CXX={CXX} autoheader && autoconf && cd .. && CC={CC} CXX={CXX} autoheader && autoconf && ./configure --prefix={local_dir} && make -j {num_cores} && make install "
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "git", "1.8")
if self.args.noInternet:
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
elif os.path.exists(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl')):
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
else:
refs = pack.getGitRefs(url)
for ref in [b.replace("/", "__") for b in refs.branches] + refs.tags:
pack.addVersion(url, ref)
pack.versions_[ref].cmd_ = buildCmd.replace("SAMVERSION", ref)
Utils.mkdir(os.path.join(self.dirMaster_.cache_dir, name))
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'wb') as output:
pickle.dump(pack, output, pickle.HIGHEST_PROTOCOL)
return pack
def __bcftools(self):
name = "bcftools"
buildCmd = "CC={CC} CXX={CXX} && make prefix={local_dir} -j {num_cores} && make prefix={local_dir} install "
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "file", "1.3.1")
pack.addVersion("http://baileylab.umassmed.edu/sourceCodes/bcftools/bcftools-1.3.1.tar.bz2", "1.3.1")
return pack
def __hts(self):
name = "hts"
url = "https://github.com/samtools/htslib.git"
buildCmd = "CC={CC} CXX={CXX} && autoheader && autoconf && ./configure --prefix={local_dir} && make -j {num_cores} && make install -j {num_cores}"
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "git", "1.3.1")
if self.args.noInternet:
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
elif os.path.exists(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl')):
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
else:
refs = pack.getGitRefs(url)
for ref in [b.replace("/", "__") for b in refs.branches] + refs.tags:
pack.addVersion(url, ref)
pack.versions_[ref].additionalLdFlags_ = ["-lz -lm -lpthread"]
Utils.mkdir(os.path.join(self.dirMaster_.cache_dir, name))
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'wb') as output:
pickle.dump(pack, output, pickle.HIGHEST_PROTOCOL)
return pack
def __zlibng(self):
name = "zlib-ng"
url = "https://github.com/Dead2/zlib-ng"
buildCmd = "CC={CC} CXX={CXX} && ./configure --prefix={local_dir} && make -j {num_cores} && make install -j {num_cores}"
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "git", "develop")
if self.args.noInternet:
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
elif os.path.exists(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl')):
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
else:
refs = pack.getGitRefs(url)
for ref in [b.replace("/", "__") for b in refs.branches] + refs.tags:
pack.addVersion(url, ref)
pack.versions_[ref].altLibName_ = "z"
Utils.mkdir(os.path.join(self.dirMaster_.cache_dir, name))
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'wb') as output:
pickle.dump(pack, output, pickle.HIGHEST_PROTOCOL)
return pack
def __openblas(self):
name = "openblas"
url = "https://github.com/xianyi/OpenBLAS.git"
buildCmd = "CC={CC} CXX={CXX} && make PREFIX={local_dir} -j {num_cores} && make install PREFIX={local_dir} -j {num_cores}"
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "git", "develop")
if self.args.noInternet:
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
elif os.path.exists(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl')):
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
else:
refs = pack.getGitRefs(url)
for ref in [b.replace("/", "__") for b in refs.branches] + refs.tags:
pack.addVersion(url, ref)
pack.versions_[ref].altLibName_ = "z"
Utils.mkdir(os.path.join(self.dirMaster_.cache_dir, name))
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'wb') as output:
pickle.dump(pack, output, pickle.HIGHEST_PROTOCOL)
return pack
def __restbed(self):
name = "restbed"
url = "https://github.com/Corvusoft/restbed.git"
if not Utils.isMac():
buildCmd = """git submodule init && git submodule update && sed -i 's/CMAKE_CXX_FLAGS}} -stdlib=libc++/CMAKE_CXX_FLAGS}}/g' cmake/build_configuration.cmake && mkdir build && cd build && CC={CC} CXX={CXX} cmake -DBUILD_TESTS=NO -DBUILD_EXAMPLES=NO -DBUILD_SSL=NO -DBUILD_SHARED=YES -DCMAKE_INSTALL_PREFIX={local_dir} .. && make install -j {num_cores}"""
else:
buildCmd = """git submodule init && git submodule update && mkdir build && cd build && CC={CC} CXX={CXX} cmake -DBUILD_TESTS=NO -DBUILD_EXAMPLES=NO -DBUILD_SSL=NO -DBUILD_SHARED=YES -DCMAKE_INSTALL_PREFIX={local_dir} .. && make install -j {num_cores}"""
pack = CPPLibPackage(name, buildCmd, self.dirMaster_, "git", "4.0")
if self.args.noInternet:
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
elif os.path.exists(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl')):
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'rb') as inputPkl:
pack = pickle.load(inputPkl)
pack.defaultBuildCmd_ = buildCmd
else:
refs = pack.getGitRefs(url)
for ref in [b.replace("/", "__") for b in refs.branches] + refs.tags:
pack.addVersion(url, ref)
pack.versions_[ref].libPath_ = pack.versions_[ref].libPath_ + "rary"
allFloats = re.findall(r"[+-]? *(?:\d+(?:\.\d*)?|\.\d+)(?:[eE][+-]?\d+)?", ref)
if len(allFloats) >= 1 and float(allFloats[0]) >= 4.5:
pack.versions_[ref].cmd_ = """git submodule init && git submodule update && mkdir build && cd build && CC={CC} CXX={CXX} cmake -DBUILD_TESTS=NO -DBUILD_EXAMPLES=NO -DBUILD_SSL=NO -DBUILD_SHARED=YES -DCMAKE_INSTALL_PREFIX={local_dir} .. && make install -j {num_cores}"""
Utils.mkdir(os.path.join(self.dirMaster_.cache_dir, name))
with open(os.path.join(self.dirMaster_.cache_dir, name, name + '.pkl'), 'wb') as output:
pickle.dump(pack, output, pickle.HIGHEST_PROTOCOL)
#pack.addVersion("https://github.com/Corvusoft/restbed.git", "4.0")
#pack.versions_["4.0"].additionalLdFlags_ = ["-lz -lm -lpthread"]
return pack
'''
def __mlpack(self):
url = "http://www.mlpack.org/files/mlpack-1.0.8.tar.gz"
armadillo_dir = Utils.shellquote(i.local_dir).replace("mlpack", "armadillo")
boost_dir = Utils.shellquote(i.local_dir).replace("mlpack", "boost")
cmd = """
mkdir -p build
&& cd build
&& CC={CC} CXX={CXX} cmake -D DEBUG=OFF -D PROFILE=OFF
-D ARMADILLO_LIBRARY={armadillo_dir}/lib/libarmadillo.so.4.0.2