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INSTALL.py
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INSTALL.py
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import os, sys, string, subprocess, distutils.util, site, glob, multiprocessing
def addEnvironmentVar(varName, newValue, sep = " "):
oldVal = ""
if varName in os.environ:
oldVal = os.environ[varName]
os.environ[varName] = newValue + sep + oldVal
else:
os.environ[varName] = newValue
return oldVal
def updateMakeFileForDarwin(fileName, addedCFlags, addedLDFlags, addFlagsToCompile=False):
if OSTYPE == "Darwin":
os.system("cp %s %s.orig"%(fileName, fileName))
numCF=utils.getCommandOutput("grep -c \"CFLAGS*=\" %s.orig"%(fileName), False).strip()
numCX=utils.getCommandOutput("grep -c \"CXXFLAGS*=\" %s.orig"%(fileName), False).strip()
numLD=utils.getCommandOutput("grep -c \"LDFLAGS*=\" %s.orig"%(fileName), False).strip()
numD=utils.getCommandOutput("grep -c \^DFLAGS*=\" %s.orig"%(fileName), False).strip()
addCF = False
addLD = False
if ((numCF == "" or int(numCF) == 0) and (numCX == "" or int(numCX) == 0)):
addCF = True
if ((numCF == "" or int(numCF) == 0) and (numD == "" or int(numD) == 0)):
addLD = True
os.system("cat %s.orig |awk '{if (match($0, \"^CFLAGS.*=\")) { print $0\" %s\"; } else if (match($0, \"^CXXFLAGS.*=\")) { print $0\" %s\"; } else if (match($0, \"^LDFLAGS.*=\")) { print $0\" %s\" } else if (match($0, \"^DFLAGS =\")) { print $0\" %s\"; } else { print $0; } }' >%s"%(fileName, addedCFlags, addedCFlags, addedLDFlags, addedLDFlags, fileName))
if addCF:
os.system("cp %s %s.orig"%(fileName, fileName))
os.system("cat %s.orig |awk '{if (NR == 1) { print \"CFLAGS=%s\\nCXXFLAGS=%s\\n\"$0; } else { print $0; } }' > %s"%(fileName, addedCFlags, addedCFlags, fileName))
if addLD:
os.system("cp %s %s.orig"%(fileName, fileName))
os.system("cat %s.orig |awk '{if (NR == 1) { print \"LDFLAGS=%s\\n\"$0; } else { print $0; } }' > %s"%(fileName, addedLDFlags, fileName))
if addFlagsToCompile:
os.system("cp %s %s.orig"%(fileName, fileName))
os.system("cat %s.orig |awk '{if (match($1, \"g++\")) { sub(/g\\+\\+/, \"g++ \\$(CXXFLAGS) \\$(LDFLAGS)\", $0) } print $0; }' > %s"%(fileName, fileName))
def copyPerlLib(pathToCopy, dest):
if pathToCopy != "":
pathsToCopy = pathToCopy.strip().split("\n")
for path in pathsToCopy:
pathToCopy = os.path.dirname(path)
os.system("mkdir -p %s"%(dest))
# copy one at a time in case of conflicts
for file in os.listdir("%s%s"%(pathToCopy, os.sep)):
toCopy = file
file = "%s%s%s"%(pathToCopy, os.sep, toCopy)
if os.path.exists("%s/%s"%(dest, toCopy)):
os.system("mv %s/* %s/%s/"%(file, dest, toCopy))
else:
os.system("mv %s %s/"%(file, dest))
user_home = os.environ["HOME"]
print "<<Welcome to metAMOS install>>"
#check for python version
if (sys.version_info[0] < 2) or (sys.version_info[0] == 2 and sys.version_info[1] < 6):
print "Python version is %s. metAMOS requires at least 2.6"%(sys.version)
sys.exit(1)
#add access to utils.py, for utils dir
METAMOS_ROOT = os.getcwd().strip()
INITIAL_SRC = "%s%ssrc"%(METAMOS_ROOT, os.sep)
sys.path.append(INITIAL_SRC)
import utils
import workflow
sys.path.append(utils.INITIAL_UTILS)
shellv = os.environ["SHELL"]
#add site dir
site.addsitedir(utils.INITIAL_UTILS+os.sep+"python"+os.sep+"lib"+os.sep+"python")
site.addsitedir(utils.INITIAL_UTILS+os.sep+"python"+os.sep+"lib64"+os.sep+"python")
if "PYTHONPATH" not in os.environ:
os.environ["PYTHONPATH"] = ""
os.environ["PYTHONPATH"]+=utils.INITIAL_UTILS+os.sep+"python"+os.pathsep
os.environ["PYTHONPATH"] += utils.INITIAL_UTILS+os.sep+"python"+os.sep+"lib"+os.pathsep
os.environ["PYTHONPATH"] += utils.INITIAL_UTILS+os.sep+"python"+os.sep+"lib"+os.sep+"python"+os.pathsep
os.environ["PYTHONPATH"] += utils.INITIAL_UTILS+os.sep+"python"+os.sep+"lib64"+os.pathsep
os.environ["PYTHONPATH"] += utils.INITIAL_UTILS+os.sep+"python"+os.sep+"lib64"+os.sep+"python"+os.pathsep
sys.path.append(utils.INITIAL_UTILS+os.sep+"python")
sys.path.append(utils.INITIAL_UTILS+os.sep+"python" + os.sep+"lib"+ os.sep+"python")
sys.path.append(utils.INITIAL_UTILS+os.sep+"python" + os.sep+"lib64"+ os.sep+"python")
if 'bash' in shellv or utils.cmdExists('export'):
os.system("export PYTHONPATH=%s:$PYTHONPATH"%(utils.INITIAL_UTILS+os.sep+"python"))
os.system("export PYTHONPATH=%s:$PYTHONPATH"%(utils.INITIAL_UTILS+os.sep+"python"+os.sep+"lib"+os.sep+"python"))
os.system("export PYTHONPATH=%s:$PYTHONPATH"%(utils.INITIAL_UTILS+os.sep+"python"+os.sep+"lib64"+os.sep+"python"))
elif utils.cmdExists('setenv'):
os.system("setenv PYTHONPATH %s:$PYTHONPATH"%(utils.INITIAL_UTILS+os.sep+"python"))
os.system("setenv PYTHONPATH %s:$PYTHONPATH"%(utils.INITIAL_UTILS+os.sep+"python"+os.sep+"lib"+os.sep+"python"))
os.system("setenv PYTHONPATH %s:$PYTHONPATH"%(utils.INITIAL_UTILS+os.sep+"python"+os.sep+"lib64"+os.sep+"python"))
else:
print "Cannot set PYTHONPATH variable, unknown shell %s\n"%(shellv)
if not os.path.exists("%s"%utils.INITIAL_UTILS+os.sep+"python"+os.sep+"lib"):
os.system("mkdir %s"%utils.INITIAL_UTILS+os.sep+"python"+os.sep+"lib")
if not os.path.exists("%s"%utils.INITIAL_UTILS+os.sep+"python"+os.sep+"lib64"):
os.system("mkdir %s"%utils.INITIAL_UTILS+os.sep+"python"+os.sep+"lib64")
if not os.path.exists("%s"%utils.INITIAL_UTILS+os.sep+"python"+os.sep+"lib"+os.sep+"python"):
os.system("mkdir %s"%utils.INITIAL_UTILS+os.sep+"python"+os.sep+"lib"+os.sep+"python")
if not os.path.exists("%s"%utils.INITIAL_UTILS+os.sep+"python"+os.sep+"lib64"+os.sep+"python"):
os.system("mkdir %s"%utils.INITIAL_UTILS+os.sep+"python"+os.sep+"lib64"+os.sep+"python")
ALLOW_FAST=True
HAVE_GCC42=False
HAVE_RT=False
HAVE_QUIET_HEAD=False
GCC_VERSION=0.0
try:
GCC_VERSION=float(utils.getCommandOutput("gcc --version|grep gcc|awk '{print $NF}' |awk -F \".\" '{print $1\".\"$2}'", False))
except:
try:
GCC_VERSION=float(utils.getCommandOutput("gcc --version|grep gcc|awk '{print $3}' |awk -F \".\" '{print $1\".\"$2}'", False))
except:
print "Warning: cannot determine GCC version"
OSTYPE="Linux"
OSVERSION="1"
MACHINETYPE="x86_64"
kronaTools = "KronaTools-2.2"
#identify machine type
p = subprocess.Popen("echo `uname`", shell=True, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
(checkStdout, checkStderr) = p.communicate()
if checkStderr != "":
print "Warning: Cannot determine OS, defaulting to %s"%(OSTYPE)
else:
OSTYPE = checkStdout.strip()
p = subprocess.Popen("echo `uname -r`", shell=True, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
(checkStdout, checkStderr) = p.communicate()
if checkStderr != "":
print "Warning: Cannot determine OS version, defaulting to %s"%(OSVERSION)
else:
OSVERSION = checkStdout.strip()
p = subprocess.Popen("echo `uname -m`", shell=True, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
(checkStdout, checkStderr) = p.communicate()
if checkStderr != "":
print "Warning: Cannot determine system type, defaulting to %s"%(MACHINETYPE)
else:
MACHINETYPE = checkStdout.strip()
addedCFlags=""
addedLDFlags=""
oldCFlags = ""
oldCPPFlags = ""
oldCXXFlags = ""
oldLDFlags = ""
if OSTYPE == "Darwin":
p = subprocess.Popen("echo `gcc --version`", shell=True, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
(checkStdout, checkStderr) = p.communicate()
if "Apple" not in checkStdout:
ALLOW_FAST=False
gcc42 = utils.getCommandOutput("which g++-4.2", False)
if gcc42 == "":
HAVE_GCC42=False
else:
HAVE_GCC42=True
# global vars for building
libPath=""
clib=utils.getCommandOutput("g++ -print-file-name=libgcc.a", False)
if clib != "":
libPath="%s %s"%(libPath, clib)
cpplib=utils.getCommandOutput("g++ -print-file-name=libstdc++.a", False)
if cpplib != "":
libPath="%s %s"%(libPath, cpplib)
omplib=utils.getCommandOutput("g++ -print-file-name=libgomp.a", False)
if omplib != "":
libPath="%s %s"%(libPath, omplib)
commonFlags="-mmacosx-version-min=10.6 -static-libgcc -static-libstdc++ "
oldCFlags = addEnvironmentVar("CFLAGS", " %s "%(commonFlags))
oldCPPFlags = addEnvironmentVar("CPPFLAGS", " %s "%(commonFlags))
oldCXXFlags = addEnvironmentVar("CXXFLAGS", " %s "%(commonFlags))
oldLDFlags = addEnvironmentVar("LDFLAGS", " %s "%(libPath))
addedCFlags="%s %s"%(commonFlags, libPath)
addedLDFlags="-static-libgcc -static-libstdc++ %s"%(libPath)
libPaths = [ "/usr/lib", "/usr/lib64", "/usr/local/lib/", "/usr/local/lib64/", "/opt/local/lib/", "/opt/local/lib64/"]
for libPath in libPaths:
if os.path.exists(libPath + os.sep + "librt.a") or os.path.exists(libPath + os.sep + "librt.so"):
HAVE_RT=True
break
p = utils.getCommandOutput("head --help |grep \"\\-q\" |wc -l", False)
if int(p) >= 1:
HAVE_QUIET_HEAD=True
# get list of supported workflows
enabledWorkflows = set()
packagesToInstall = set()
knownPackages = set()
workflows = workflow.getAllWorkflows("%s/Utilities/workflows"%(METAMOS_ROOT))
for flow in workflows:
knownPackages.update(workflows[flow].programList)
manual = False
fail = False
nodbs = False
availableWf = workflow.getSupportedWorkflows("%s/Utilities/workflows"%(METAMOS_ROOT), False)
for wf in availableWf:
enabledWorkflows.update(wf.getDerivedName())
packagesToInstall.update(wf.programList)
if (len(sys.argv) > 1):
# should support tool list as well added
for i in range(1, len(sys.argv)):
arg = sys.argv[i]
if arg.lower() in workflows.keys():
packagesToInstall.update(workflows[arg.lower()].programList)
enabledWorkflows.update(workflows[arg.lower()].getDerivedName())
elif arg.lower() == "full":
for flow in workflows:
packagesToInstall.update(workflows[flow].programList)
enabledWorkflows.update(workflows[flow].getDerivedName())
print "Installing all available workflows"
elif arg.lower() == "manual":
manual = True
for flow in workflows:
enabledWorkflows.update(workflows[flow].getDerivedName())
elif arg.lower() == "nodbs":
nodbs = True
elif arg.lower() in knownPackages:
packagesToInstall.add(arg.lower())
for flow in workflows:
if arg.lower() in workflows[flow].programList:
enabledWorkflows.update(workflows[flow].getDerivedName())
break
else:
if arg != "help":
print "Unknown program or workflow %s specified."%(arg)
fail = True
if fail or help in sys.argv:
print "Available workflows: %s"%(" ".join(workflows.keys()))
print "Available packages: %s"%("\n\t".join(knownPackages))
exit(1)
if manual:
packagesToInstall = set()
for workflowName in enabledWorkflows:
print "Selected to install workflowName: %s."%(workflowName.upper())
print "Will automatically install:"
for p in packagesToInstall:
print "\t%s"%(p.title())
if not os.path.exists("./Utilities/config/usage.ok") and not os.path.exists("./Utilities/config/usage.no"):
print "MetAMOS would like to record anonymous usage statistics, is this ok ? "
dl = raw_input("Enter Y/N: ")
if dl == 'y' or dl == 'Y':
os.system("echo ok > ./Utilities/config/usage.ok")
else:
os.system("echo no > ./Utilities/config/usage.no")
# first the needed python packages
# make sure we have setuptools available
if 1:
fail = 0
try:
import setuptools
except ImportError:
fail = 1
if "setuptools" in packagesToInstall:
dl = 'y'
elif fail:
print "setuptools not found, required for install, download now?"
dl = raw_input("Enter Y/N: ")
if fail and (dl == 'y' or dl == "Y"):
os.system("curl -L https://bitbucket.org/pypa/setuptools/raw/0.7.4/ez_setup.py -o ez_setup.py")
os.system("python ez_setup.py --user")
if 1:
fail = 0
try:
import psutil
except ImportError:
fail = 1
if "psutil" in packagesToInstall:
dl = 'y'
elif fail:
print "psutil not found, required for memory usage estimation, download now?"
dl = raw_input("Enter Y/N: ")
if fail and (dl == 'y' or dl == "Y"):
os.system("curl -L http://psutil.googlecode.com/files/psutil-0.6.1.tar.gz -o ./psutil.tar.gz")
os.system("tar -C ./Utilities/python -xvf psutil.tar.gz")
os.system("mv ./Utilities/python/psutil-0.6.1 ./Utilities/python/psutil")
os.chdir("./Utilities/python/psutil")
os.system("python setup.py install --home=%spython"%(utils.INITIAL_UTILS+os.sep))
os.chdir("%s"%(METAMOS_ROOT))
os.system("rm -rf psutil.tar.gz")
if 1:
fail = 0
try:
import cython
except ImportError:
fail = 1
if "cython" in packagesToInstall:
dl = 'y'
elif fail:
print "cython modules not found, necessary for c-compiling python code, download now?"
dl = raw_input("Enter Y/N: ")
if fail and (dl == 'y' or dl == "Y"):
os.system("curl -L https://github.com/cython/cython/archive/master.zip -o ./cython.zip")
os.system("unzip ./cython.zip")
os.system("mv ./cython-master ./Utilities/python/cython")
os.chdir("./Utilities/python/cython")
os.system("python setup.py install --home=%spython"%(utils.INITIAL_UTILS+os.sep))
os.chdir(METAMOS_ROOT)
os.system("rm -rf cython.zip")
if 1:
fail = 0
try:
import pysam
except ImportError:
fail = 1
if "pysam" in packagesToInstall:
dl = 'y'
elif fail:
print "pysam python modules not found, necessary for bowtie2 alignments, download now?"
dl = raw_input("Enter Y/N: ")
if fail and (dl == 'y' or dl == "Y"):
os.system("curl -L http://pysam.googlecode.com/files/pysam-0.6.tar.gz -o ./pysam.tar.gz")
os.system("tar -C ./Utilities/python -xvf pysam.tar.gz")
os.system("mv ./Utilities/python/pysam-0.6 ./Utilities/python/pysam")
doInstall = True
#for root install
#os.system("sudo python ./Utilities/python/pysam/setup.py install")
os.chdir("./Utilities/python/pysam")
if OSTYPE == "Darwin":
if utils.getFromPath("llvm-gcc-4.2", "LLVM GCC"):
os.system("export CC=llvm-gcc-4.2")
os.system("export CXX=llvm-g++-4.2")
else:
print "Warning: Cannot install pysam on your system. Please install LLVM compiler first."
doInstall=False
if doInstall:
os.system("python setup.py build_ext --inplace")
os.system("python setup.py build")
os.system("python setup.py install --home=%spython"%(utils.INITIAL_UTILS+os.sep))
os.chdir(METAMOS_ROOT)
os.system("rm -rf pysam.tar.gz")
#WARNING: matplotlib causes install issues for multiple users
fail = 0
try:
import numpy
except ImportError:
fail = 1
if "numpy" in packagesToInstall:
dl = 'y'
elif fail:
print "numpy python modules not found, necessary for html report, download now?"
dl = raw_input("Enter Y/N: ")
if fail and (dl == 'y' or dl == "Y"):
os.system("curl -L http://downloads.sourceforge.net/project/numpy/NumPy/1.7.1/numpy-1.7.1.tar.gz -o ./numpy.tar.gz")
os.system("tar -C ./Utilities/python -xvf numpy.tar.gz")
os.system("mv ./Utilities/python/numpy-1.7.1 ./Utilities/python/numpy")
os.chdir("./Utilities/python/numpy")
os.system("python setup.py install --home=%spython"%(utils.INITIAL_UTILS+os.sep))
os.chdir(METAMOS_ROOT)
os.system("rm -rf numpy.tar.gz")
if 1:
fail = 0
try:
import matplotlib
if (matplotlib.__version__ < "1.1.0"):
fail = 1
except ImportError:
fail = 1
if "matplotlib" in packagesToInstall:
dl = 'y'
elif fail:
print "Matplot lib version %s is incompatible with metAMOS. Need version 1.1.0+, download now?"%(matplotlib.__version__)
dl = raw_input("Enter Y/N: ")
if fail and (dl == 'y' or dl == "Y"):
os.system("curl -L http://downloads.sourceforge.net/project/matplotlib/matplotlib/matplotlib-1.1.0/matplotlib-1.1.0.tar.gz -o ./matplotlib.tar.gz")
os.system("tar -C ./Utilities/python -xvf matplotlib.tar.gz")
os.system("mv ./Utilities/python/matplotlib-1.1.0 ./Utilities/python/matplotlib")
os.chdir("./Utilities/python/matplotlib")
os.system("python setup.py install --home=%spython"%(utils.INITIAL_UTILS+os.sep))
os.chdir(METAMOS_ROOT)
os.system("rm -rf matplotlib.tar.gz")
# now software
if not os.path.exists("./AMOS") or 0:
if "amos" in packagesToInstall:
dl = 'y'
else:
print "AMOS binaries not found, needed for all steps, download now?"
dl = raw_input("Enter Y/N: ")
if dl == 'y' or dl == 'Y':
os.system("curl -L ftp://ftp.cbcb.umd.edu/pub/data/metamos/amos-3.2-BETA-%s-%s.binaries.tar.gz -o ./amos-binaries.tar.gz"%(OSTYPE, MACHINETYPE))
os.system("tar -xvf amos-binaries.tar.gz")
os.system("rm -rf amos-binaries.tar.gz")
# descriptive perl module
stat = utils.getCommandOutput("perl -MStatistics::Descriptive -e 0 && echo $?", True)
if stat == "":
os.system("curl -L http://search.cpan.org/CPAN/authors/id/C/CO/COLINK/Statistics-Descriptive-2.6.tar.gz -o stat.tar.gz")
os.system("tar -xvzf stat.tar.gz")
os.chdir("Statistics-Descriptive-2.6")
os.system("perl Makefile.PL PREFIX=`pwd`/build")
os.system("make install")
os.chdir("%s"%(METAMOS_ROOT))
pathToCopy = utils.getCommandOutput("find Statistics-Descriptive-2.6/build -type d -name \"Statistics\" |grep -v auto", False)
copyPerlLib(pathToCopy, "AMOS%s%s-%s%slib"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.system("rm -rf stat.tar.gz")
os.system("rm -rf Statistics-Descriptive-2.6")
if not os.path.exists("./Utilities/cpp%s%s-%s%skraken"%(os.sep, OSTYPE, MACHINETYPE, os.sep)):
if "kraken" in packagesToInstall:
dl = 'y'
else:
print "Kraken not found, optional for Annotate step, download now?"
dl = raw_input("Enter Y/N: ")
if dl == 'y' or dl == 'Y':
archive = "kraken.tar.gz"
os.system("curl -L ftp://ftp.cbcb.umd.edu/pub/data/metamos/kraken-0.10.3-beta.tgz -o %s"%(archive))
os.system("rm -rf ./Utilities/cpp%s%s-%s%skraken"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.system("tar -xvzf %s"%(archive))
os.system("mv kraken-0.10.3-beta ./Utilities/cpp/%s%s-%s%skraken"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.chdir("./Utilities/cpp/%s%s-%s%skraken"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.system("./install_kraken.sh `pwd`/bin")
os.chdir("%s"%(METAMOS_ROOT))
os.system("rm %s"%archive)
if not os.path.exists("./Utilities/DB/kraken"):
if "kraken" in packagesToInstall:
dl = 'y'
else:
print "Kraken DB not found, required for Kraken, download now?"
dl = raw_input("Enter Y/N: ")
if dl == 'y' or dl == 'Y':
settings = utils.Settings(1, 1, "", "")
settings.OSTYPE = OSTYPE
mem = utils.getAvailableMemory(settings)
if (mem < 100) and not nodbs:
print "Insufficient memory to build full Kraken database. Requires at least 100GB of memory, using mini DB"
archive = "minikraken.tgz"
os.system("curl -L ftp://ftp.cbcb.umd.edu/pub/data/metamos/%s -o %s"%(archive, archive))
os.system("tar xvzf %s"%(archive))
os.system("mv minikraken_* ./Utilities/DB/kraken")
os.system("rm %s"%(archive))
elif not nodbs:
# first we need jellyfish which is used to build DB
# kraken needs jellyfish, if we don't find it build it and add to path
jellyfish = utils.getFromPath("jellyfish", "Jellyfish", False)
if jellyfish == "":
archive = "jellyfish.tar.gz"
os.system("curl -L http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz -o %s"%(archive))
os.system("tar xvzf %s"%(archive))
os.system("mv jellyfish-1.1.11 ./Utilities/cpp%s%s-%s%s/jellyfish"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.chdir("./Utilities/cpp%s%s-%s%s/jellyfish"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.system("./configure --prefix=`pwd`")
os.system("make")
os.system("make install")
os.chdir("%s"%(METAMOS_ROOT))
pathUpdate = "%s/Utilities/cpp%s%s-%s%sjellyfish/bin/"%(METAMOS_ROOT, os.sep, OSTYPE, MACHINETYPE, os.sep)
if "PATH" in os.environ:
pathUpdate = "%s%s%s"%(os.environ["PATH"], os.pathsep, pathUpdate)
os.environ["PATH"]=pathUpdate
os.chdir("./Utilities/cpp/%s%s-%s%skraken"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.system("./bin/kraken-build --standard --threads %d --db %s/Utilities/DB/kraken"%(multiprocessing.cpu_count() - 1, METAMOS_ROOT))
os.chdir("%s"%(METAMOS_ROOT))
if not os.path.exists("./LAP"):
if "lap" in packagesToInstall:
dl = 'y'
else:
print "LAP tool not found, needed for multiple assembly pipeline, download now?"
dl = raw_input("Enter Y/N: ")
if dl == 'y' or dl == 'Y':
os.system("curl -L http://www.cbcb.umd.edu/~cmhill/files/lap_release_1.1.zip -o lap_release_1.1.zip")
os.system("unzip lap_release_1.1.zip")
os.system("mv ./lap_release_1.1 ./LAP")
os.system("rm -rf lap_release_1.1.zip")
if not os.path.exists("KronaTools") or 0:
if "kronatools" in packagesToInstall:
dl = 'y'
else:
print "KronaTools not found, needed for Postprocess, download now?"
dl = raw_input("Enter Y/N: ")
if dl == 'y' or dl == 'Y':
# TODO: KronaTools should be on the FTP site for robustness to URL changes
os.system("curl -L 'ftp://ftp.cbcb.umd.edu/pub/data/metamos/" + kronaTools + ".tar' -o %s.tar"%(kronaTools))
os.system("tar -xvf %s.tar"%(kronaTools))
os.system("rm -rf %s.tar"%(kronaTools))
os.system("mv %s KronaTools"%(kronaTools))
os.system("cd KronaTools && ./install.pl --prefix=.")
if not os.path.exists("KronaTools/taxonomy/taxonomy.tab") or 0:
if "kronatools" in packagesToInstall:
dl = 'y'
else:
print "KronaTools taxonomy data not found, needed for Postprocess, download now (will take around 20 minutes)?"
dl = raw_input("Enter Y/N: ")
if (dl == 'y' or dl == 'Y') and not nodbs:
os.system("cd KronaTools && ./updateTaxonomy.sh")
os.chdir("%s"%(METAMOS_ROOT))
os.system("cat KronaTools/taxonomy/taxonomy.tab |awk -F \"\\t\" '{print $1\"\\t\"$NF}' > ./Utilities/DB/tax_key.tab")
if not os.path.exists("./FastQC"):
if "fastqc" in packagesToInstall:
dl = 'y'
else:
print "FastQC not found, optional for Preprocess, download now?"
dl = raw_input("Enter Y/N: ")
if dl == 'y' or dl == 'Y':
archive = "fastqc_v0.10.0.zip"
os.system("curl -L http://www.bioinformatics.babraham.ac.uk/projects/fastqc/%s -o %s" % (archive,archive))
os.system("unzip %s" % archive)
os.system("rm %s" % archive)
os.system("chmod u+x FastQC/fastqc")
if not os.path.exists("./Utilities/DB/uniprot_sprot.fasta"):
if "uniprot" in packagesToInstall:
dl = 'y'
else:
print "Uniprot/Swissprot DB not found, optional for Functional Annotation, download now?"
dl = raw_input("Enter Y/N: ")
if (dl == 'y' or dl == 'Y') and not nodbs:
archive = "uniprot.tar.gz"
os.system("curl -L ftp://ftp.cbcb.umd.edu/pub/data/metamos/%s -o %s" %(archive, archive))
os.system("tar -C ./Utilities/DB/ -xvf %s" % archive)
os.system("rm %s"%archive)
# velvet
if not os.path.exists("./Utilities/cpp%s%s-%s%svelvet"%(os.sep, OSTYPE, MACHINETYPE, os.sep)):
if "velvet" in packagesToInstall:
dl = 'y'
else:
print "Velvet not found, optional for Assemble step, download now?"
dl = raw_input("Enter Y/N: ")
if dl == 'y' or dl == 'Y':
archive = "velvet.tar.gz"
os.system("curl -L ftp://ftp.cbcb.umd.edu/pub/data/metamos/velvet_1.2.10.tgz -o %s"%(archive))
os.system("rm -rf ./Utilities/cpp%s%s-%s%svelvet"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.system("tar -xvzf %s"%(archive))
os.system("mv velvet_1.2.10 ./Utilities/cpp/%s%s-%s%svelvet"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.chdir("./Utilities/cpp/%s%s-%s%svelvet"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
updateMakeFileForDarwin("Makefile", addedCFlags, addedLDFlags)
os.system("make clean")
os.system("make CATEGORIES=16 MAXKMERLENGTH=127 OPENMP=1 BUNDLEDZLIB=1")
os.chdir("%s"%(METAMOS_ROOT))
os.system("rm %s"%archive)
# velvet-sc
if not os.path.exists("./Utilities/cpp%s%s-%s%svelvet-sc"%(os.sep, OSTYPE, MACHINETYPE, os.sep)):
if "velvet-sc" in packagesToInstall:
dl = 'y'
else:
print "Velvet-SC not found, optional for Assemble step, download now?"
dl = raw_input("Enter Y/N: ")
if dl == 'y' or dl == 'Y':
archive = "velvet-sc.tar.gz"
os.system("curl -L ftp://ftp.cbcb.umd.edu/pub/data/metamos/velvet-sc.tar.gz -o %s"%(archive))
os.system("rm -rf ./Utilities/cpp%s%s-%s%svelvet-sc"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.system("tar -xvzf %s"%(archive))
os.system("mv velvet-sc ./Utilities/cpp/%s%s-%s%svelvet-sc"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.chdir("./Utilities/cpp/%s%s-%s%svelvet-sc"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
updateMakeFileForDarwin("Makefile", addedCFlags, addedLDFlags)
os.system("make clean")
os.system("make CATEGORIES=16 MAXKMERLENGTH=127 OPENMP=1")
os.chdir("%s"%(METAMOS_ROOT))
os.system("rm %s"%archive)
# metavelvet
if not os.path.exists("./Utilities/cpp%s%s-%s%sMetaVelvet"%(os.sep, OSTYPE, MACHINETYPE, os.sep)):
if "metavelvet" in packagesToInstall:
dl = 'y'
else:
print "MetaVelvet not found, optional for Assemble step, download now?"
dl = raw_input("Enter Y/N: ")
if dl == 'y' or dl == 'Y':
archive = "MetaVelvet-1.2.02.tgz"
os.system("curl -L ftp://ftp.cbcb.umd.edu/pub/data/metamos/MetaVelvet-1.2.02.tgz -o %s"%(archive))
os.system("rm -rf ./Utilities/cpp%s%s-%s%sMetaVelvet"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.system("tar -xvzf %s"%(archive))
os.system("mv MetaVelvet-1.2.02 ./Utilities/cpp/%s%s-%s%sMetaVelvet"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.chdir("./Utilities/cpp/%s%s-%s%sMetaVelvet"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
if OSTYPE == "Darwin":
os.system("cp Utils/Utils.hh Utils/Utils.hh.orig")
os.system("cat Utils/Utils.hh.orig |awk '{if (match($0, \"#define MAX_STRING_LENGTH\")) { print \"#include <sys/types.h>\\n\"$0; } else { print $0; }}' > Utils/Utils.hh")
updateMakeFileForDarwin("Makefile", addedCFlags, addedLDFlags)
os.system("make clean")
os.system("make CATEGORIES=16 MAXKMERLENGTH=127")
os.chdir("%s"%(METAMOS_ROOT))
os.system("rm %s"%archive)
if "viritas" in enabledWorkflows or manual:
if not os.path.exists("./Utilities/cpp%s%s-%s%strnascan"%(os.sep, OSTYPE, MACHINETYPE, os.sep)):
if "trnascan" in packagesToInstall:
dl = 'y'
else:
print "tRNAscan not found, optional for Annotate step, download now?"
dl = raw_input("Enter Y/N: ")
if dl == 'y' or dl == 'Y':
os.system("curl -L http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -o trnascan.tar")
os.system("tar xvf trnascan.tar")
os.system("mv tRNAscan-SE-1.3.1 ./Utilities/cpp/%s%s-%s%strnascan"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.chdir("./Utilities/cpp/%s%s-%s%strnascan"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
updateMakeFileForDarwin("Makefile", addedCFlags, addedLDFlags)
os.system("make")
os.chdir("%s"%(METAMOS_ROOT))
os.system("rm -rf trnascan.tar")
# now workflow specific tools
if "optional" in enabledWorkflows or manual:
if not os.path.exists("./Utilities/cpp/%s-%s/metaphylerClassify"%(OSTYPE, MACHINETYPE)) or not os.path.exists("./Utilities/perl/metaphyler/markers/markers.protein") or not os.path.exists("./Utilities/perl/metaphyler/markers/markers.dna"):
if "metaphyler" in packagesToInstall:
dl = 'y'
else:
print "Metaphyler (latest version) not found, optional for Annotate, download now?"
dl = raw_input("Enter Y/N: ")
if dl == 'y' or dl == 'Y':
os.system("curl -L http://metaphyler.cbcb.umd.edu/MetaPhylerV1.25.tar.gz -o metaphyler.tar.gz")
os.system("tar -C ./Utilities/perl/ -xvf metaphyler.tar.gz")
os.system("mv ./Utilities/perl/MetaPhylerV1.25 ./Utilities/perl/metaphyler")
os.system("mv ./Utilities/perl/metaphyler/installMetaphyler.pl ./Utilities/perl/metaphyler/installMetaphylerFORMATDB.pl");
os.system("cat ./Utilities/perl/metaphyler/installMetaphylerFORMATDB.pl |sed 's/formatdb/\.\/Utilities\/cpp\/%s-%s\/formatdb/g' > ./Utilities/perl/metaphyler/installMetaphyler.pl"%(OSTYPE, MACHINETYPE));
os.system("perl ./Utilities/perl/metaphyler/installMetaphyler.pl")
os.system("cp ./Utilities/perl/metaphyler/metaphylerClassify ./Utilities/cpp/%s-%s/metaphylerClassify"%(OSTYPE, MACHINETYPE))
if not os.path.exists("./Utilities/models") or not os.path.exists("./Utilities/DB/blast_data"):
if "fcp" in packagesToInstall:
dl = 'y'
else:
print "Genome models not found, optional for FCP/NB, download now?"
dl = raw_input("Enter Y/N: ")
if (dl == 'y' or dl == 'Y') and not nodbs:
archive = "fcp_models.tar.gz"
os.system("curl -L ftp://ftp.cbcb.umd.edu/pub/data/metamos/%s -o %s" %(archive, archive))
os.system("rm -rf ./Utilities/DB/blast_data")
os.system("rm -rf ./Utilities/models")
os.system("tar -C ./Utilities/ -xvf %s" % archive)
os.system("rm %s"%archive)
if not os.path.exists("./phylosift") or not os.path.exists("./phylosift/lib/version.pm") or not os.path.exists("./phylosift/lib/Params"):
if "phylosift" in packagesToInstall:
dl = 'y'
else:
print "PhyloSift binaries not found, optional for Annotate step, download now?"
dl = raw_input("Enter Y/N: ")
if dl == 'y' or dl == 'Y':
if not os.path.exists("./phylosift"):
#phylosift OSX binaries included inside Linux X86_64 tarball..
os.system("curl -L http://edhar.genomecenter.ucdavis.edu/~koadman/phylosift/devel/phylosift_20130829.tar.bz2 -o ./phylosift.tar.bz2")
os.system("tar -xvjf phylosift.tar.bz2")
os.system("rm -rf phylosift.tar.bz2")
os.system("mv phylosift_20130829 phylosift")
if not os.path.exists("./phylosift/legacy/version.pm"):
#phylosift needs version but doesn't include it
os.system("curl -L http://www.cpan.org/authors/id/J/JP/JPEACOCK/version-0.9903.tar.gz -o version.tar.gz")
os.system("tar xvzf version.tar.gz")
os.chdir("./version-0.9903/")
os.system("perl Makefile.PL")
os.system("make")
os.system("cp -r blib/lib/* ../phylosift/lib")
os.chdir(METAMOS_ROOT)
os.system("rm -rf version.tar.gz")
os.system("rm -rf version-0.9903")
if not os.path.exists("./phylosift/lib/Params"):
os.system("curl -L ftp://ftp.cbcb.umd.edu/pub/data/metamos/params-validate.tar.gz -o ./params-validate.tar.gz")
os.system("tar xvzf params-validate.tar.gz")
os.system("rm -rf params-validate.tar.gz")
# download markers dbs
if not os.path.exists("./phylosift/share"):
markerUrl = utils.getCommandOutput("cat phylosift/phylosiftrc |grep marker_base |awk '{print $NF}' |sed s/\;//g", False)
ncbiUrl = utils.getCommandOutput("cat phylosift/phylosiftrc |grep ncbi_url |awk '{print $NF}' |sed s/\;//g", False)
os.system("mkdir -p ./phylosift/share/phylosift")
os.chdir("./phylosift/share/phylosift")
os.system("curl -L %s/markers.tgz -o marker.tgz"%(markerUrl))
os.system("tar xvzf marker.tgz")
os.system("rm marker.tgz")
os.system("curl -L %s -o ncbi.tgz"%(ncbiUrl))
os.system("tar xvzf ncbi.tgz")
os.system("rm ncbi.tgz")
os.chdir(METAMOS_ROOT)
# check the number of files the DB currently is and see if we have the expected number
dbResult = ""
if not nodbs:
dbResult = utils.getCommandOutput("perl ./Utilities/perl/update_blastdb.pl refseq_protein --numpartitions", False)
if not nodbs and dbResult == "":
print "Error: could not connect to NCBI, will not be installing refseq protein DB"
elif not nodbs:
(dbName, numPartitions) = dbResult.split("\t", 1)
print "Checking whether %s is complete. Expecting %d partitions.\n"%(dbName, int(numPartitions))
numPartitions = int(numPartitions) - 1
if not os.path.exists("./Utilities/DB/refseq_protein.pal") or not os.path.exists("./Utilities/DB/refseq_protein.%02d.psq"%(int(numPartitions))) or not os.path.exists("./Utilities/DB/allprots.faa"):
if "phmmer" in packagesToInstall:
dl = 'y'
else:
print "refseq protein DB not found or incomplete, needed for Annotate step, download now?"
dl = raw_input("Enter Y/N: ")
if dl == 'y' or dl == 'Y':
print "Download and install refseq protein DB.."
os.system("perl ./Utilities/perl/update_blastdb.pl refseq_protein")
os.system("mv refseq_protein.*.tar.gz ./Utilities/DB/")
fileList = glob.glob("./Utilities/DB/refseq_protein.*.tar.gz")
for file in fileList:
os.system("tar -C ./Utilities/DB/ -xvf %s"%(file))
print " running fastacmd (might take a few min)..."
os.system(".%sUtilities%scpp%s%s-%s%sfastacmd -d ./Utilities/DB/refseq_protein -p T -a T -D 1 -o ./Utilities/DB/allprots.faa"%(os.sep, os.sep, os.sep, OSTYPE, MACHINETYPE, os.sep))
# sra toolkit
if not os.path.exists("./Utilities/cpp%s%s-%s%ssra"%(os.sep, OSTYPE, MACHINETYPE, os.sep)):
sra = utils.getFromPath("srapath", "SRA PATH", False)
if sra == "":
if "sra" in packagesToInstall:
dl = 'y'
else:
print "SRA binaries not found, optional for initPipeline step, download now?"
dl = raw_input("Enter Y/N: ")
if dl == 'y' or dl == 'Y':
if OSTYPE == 'Linux' and MACHINETYPE == "x86_64":
os.system("curl -L http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.3.3-3/sratoolkit.2.3.3-3-centos_linux64.tar.gz -o sra.tar.gz")
elif OSTYPE == "Darwin" and MACHINETYPE == "x86_64":
os.system("curl -L http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.3.3-3/sratoolkit.2.3.3-3-mac64.tar.gz -o sra.tar.gz")
os.system("tar xvzf sra.tar.gz")
os.system("mv sratoolkit.2.3.3-3-* ./Utilities/cpp%s%s-%s%ssra"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.system("rm -rf sra.tar.gz")
if "isolate" in enabledWorkflows or "imetamos" in enabledWorkflows or manual:
# check for cmake
if not os.path.exists("./Utilities/cpp%s%s-%s%scmake"%(os.sep, OSTYPE, MACHINETYPE, os.sep)):
cmake = utils.getFromPath("cmake", "CMAKE", False)
if cmake == "":
if "cmake" in packagesToInstall:
dl = 'y'
else:
print "cmake binaries not found, optional for initPipeline step, download now?"
dl = raw_input("Enter Y/N: ")
if dl == 'y' or dl == 'Y':
os.system("curl -L http://www.cmake.org/files/v2.8/cmake-2.8.12.tar.gz -o cmake.tar.gz")
os.system("tar xvzf cmake.tar.gz")
os.system("mv cmake-2.8.12 ./Utilities/cpp%s%s-%s%scmake"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.chdir("./Utilities/cpp%s%s-%s%scmake"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.system("./bootstrap --prefix=`pwd`/build;make;make install")
os.chdir("%s"%(METAMOS_ROOT))
os.system("rm cmake.tar.gz")
if os.path.exists("./Utilities/cpp%s%s-%s%scmake"%(os.sep, OSTYPE, MACHINETYPE, os.sep)):
pathUpdate = "%s/Utilities/cpp%s%s-%s%scmake/build/bin"%(METAMOS_ROOT, os.sep, OSTYPE, MACHINETYPE, os.sep)
if "PATH" in os.environ:
pathUpdate = "%s%s%s"%(os.environ["PATH"], os.pathsep, pathUpdate)
os.environ["PATH"]=pathUpdate
os.chdir("%s"%(METAMOS_ROOT))
if not os.path.exists("./CA"):
if "ca" in packagesToInstall:
dl = 'y'
else:
print "Celera Assembler binaries not found, optional for Assemble step, download now?"
dl = raw_input("Enter Y/N: ")
if dl == 'y' or dl == 'Y':
os.system("curl -L https://downloads.sourceforge.net/project/wgs-assembler/wgs-assembler/wgs-8.1/wgs-8.1.tar.bz2 -o wgs-8.1.tar.bz2")
os.system("tar xvjf wgs-8.1.tar.bz2")
os.system("rm -rf wgs-8.1.tar.bz2")
os.system("mv wgs-8.1 CA")
# patch CA to support PacBio sequences and non-apple compilers on OSX
if not ALLOW_FAST:
os.system("cd CA/kmer/ && cp configure.sh configure.original")
os.system("cd CA/kmer/ && cat configure.original |sed s/\-fast//g > configure.sh")
os.system("cd CA/src/ && cp c_make.as c_make.original")
os.system("cd CA/src/ && cat c_make.original |sed s/\-fast//g > c_make.as")
if not HAVE_GCC42:
os.system("cd CA/src/ && cp c_make.as c_make.original")
os.system("cd CA/src/ && cat c_make.original |sed s/\-4.2//g > c_make.as")
if GCC_VERSION >= 4.7:
os.system("cd CA/src/ && cp c_make.as c_make.original")
os.system("cd CA/src/ && cat c_make.original |sed s/\-rdynamic//g > c_make.as")
updateMakeFileForDarwin("CA/kmer/Makefile", addedCFlags, addedLDFlags)
updateMakeFileForDarwin("CA/samtools/Makefile", addedCFlags, addedLDFlags)
updateMakeFileForDarwin("CA/src/c_make.as", addedCFlags, addedLDFlags)
os.system("cd CA/samtools && make")
os.system("cd CA/kmer && ./configure.sh && gmake install")
os.system("cd CA/src && gmake")
if not os.path.exists("./Utilities/cpp%s%s-%s%sRay"%(os.sep, OSTYPE, MACHINETYPE, os.sep)):
if "ray" in packagesToInstall:
dl = 'y'
else:
print "Ray binaries not found, optional for Assemble step, download now?"
dl = raw_input("Enter Y/N: ")
if dl == 'y' or dl == 'Y':
# check for mpi which is required
command="mpicxx"
mpi=utils.getFromPath(command, "MPI", False)
if not os.path.exists("%s%s%s"%(mpi, os.sep, command)):
command="openmpicxx"
mpi=utils.getFromPath(command, "MPI", False)
if not os.path.exists("%s%s%s"%(mpi, os.sep, command)):
mpi = command = ""
print "Error: cannot find MPI, required to build Ray. Please add it to your path."
if command != "":
os.system("curl -L http://downloads.sourceforge.net/project/denovoassembler/Ray-v2.2.0.tar.bz2 -o Ray-v2.2.0.tar.bz2")
os.system("tar xvjf Ray-v2.2.0.tar.bz2")
os.system("mv Ray-v2.2.0 ./Utilities/cpp/%s%s-%s%sRay"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.chdir("./Utilities/cpp/%s%s-%s%sRay"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.system("make PREFIX=bin MPICXX=%s%s%s MAXKMERLENGTH=128 MPI_IO=y DEBUG=n ASSERT=n EXTRA=\" -march=native\""%(mpi, os.sep, command))
os.system("make install")
os.chdir("%s"%(METAMOS_ROOT))
os.system("rm -rf Ray-v2.2.0.tar.bz2")
if not os.path.exists("./Utilities/cpp%s%s-%s%skmergenie"%(os.sep, OSTYPE, MACHINETYPE, os.sep)):
kmerGenie = utils.getFromPath("kmergenie", "Kmer Genie", False)
if kmerGenie == "":
if "kmergenie" in packagesToInstall:
dl = 'y'
else:
print "Kmer Genie was not found, optional for Assemble step, download now?"
dl = raw_input("Enter Y/N: ")
if dl == 'y' or dl == 'Y':
os.system("curl -L ftp://ftp.cbcb.umd.edu/pub/data/metamos/kmergenie-1.5692.tar.gz -o kmer.tar.gz")
os.system("tar xvzf kmer.tar.gz")
os.system("mv kmergenie-1.5692 ./Utilities/cpp%s%s-%s%skmergenie"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.chdir("./Utilities/cpp%s%s-%s%skmergenie"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
updateMakeFileForDarwin("makefile", addedCFlags, addedLDFlags)
os.system("make k=300")
os.chdir("%s"%(METAMOS_ROOT))
os.system("rm -rf kmer.tar.gz")
if not os.path.exists("./Utilities/cpp%s%s-%s%sspades"%(os.sep, OSTYPE, MACHINETYPE, os.sep)):
spades = utils.getFromPath("spades.py", "SPAdes", False)
if spades == "":
if "spades" in packagesToInstall:
dl = 'y'
else:
print "SPAdes was not found, optional for Assemble step, download now?"
dl = raw_input("Enter Y/N: ")
if dl == 'y' or dl == 'Y':
if OSTYPE == "Darwin":
if GCC_VERSION < 4.7:
print "Error: SPAdes requires gcc at least version 4.7, found version %s. Please update and try again"%(GCC_VERSION)
else:
os.system("curl -L http://spades.bioinf.spbau.ru/release3.0.0/SPAdes-3.0.0.tar.gz -o spades.tar.gz")
os.system("tar xvzf spades.tar.gz")
os.system("mv SPAdes-3.0.0 ./Utilities/cpp%s%s-%s%sspades"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.chdir("./Utilities/cpp%s%s-%s%sspades"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.system("export CC=`which gcc` && bash spades_compile.sh")
os.chdir("%s"%(METAMOS_ROOT))
else:
os.system("curl -L http://spades.bioinf.spbau.ru/release3.0.0/SPAdes-3.0.0-Linux.tar.gz -o spades.tar.gz")
os.system("tar xvzf spades.tar.gz")
os.system("mv SPAdes-3.0.0-Linux ./Utilities/cpp%s%s-%s%sspades"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.system("rm -rf spades.tar.gz")
if not os.path.exists("./Utilities/cpp%s%s-%s%sprokka"%(os.sep, OSTYPE, MACHINETYPE, os.sep)):
prokaBin = utils.getFromPath("prokka", "Prokka", False)
dl = 'n'
if prokaBin == "":
if "prokka" in packagesToInstall:
dl = 'y'
else:
print "Prokka binaries not found, optional for Assemble step, download now?"
dl = raw_input("Enter Y/N: ")
if dl == 'y' or dl == 'Y':
signalp = utils.getFromPath("signalp", "SignalP", False)
if signalp == "":
print "Warning: SignalP is not installed and is required for Prokka's gram option. Please download it and add it to your path."
os.system("curl -L ftp://ftp.cbcb.umd.edu/pub/data/metamos/prokka-1.7.tar.gz -o prokka-1.7.tar.gz")
os.system("tar xvzf prokka-1.7.tar.gz")
os.system("mv prokka-1.7 ./Utilities/cpp%s%s-%s%sprokka"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.system("rm prokka-1.7.tar.gz")
bioperl = utils.getCommandOutput("perl -MBio::Seq -e 0 && echo $?", True)
perltime = utils.getCommandOutput("perl -MTime::Piece -e 0 && echo $?", True)
xmlsimple = utils.getCommandOutput("perl -MXML::Simple -e 0 && echo $?", True)
storable = utils.getCommandOutput("perl -MStorable -e 0 && echo $?", True)
xmlparser = utils.getCommandOutput("perl -MXML:Parser -e 0 && echo $?", True)
# always install bioperl, otherwise parts may be missing or it may be the wrong version
# phylosift comes with BioPerl, use it
os.system("curl -L http://edhar.genomecenter.ucdavis.edu/~koadman/phylosift/devel/phylosift_20130829.tar.bz2 -o ./phylosift.tar.bz2")
os.system("tar -xvjf phylosift.tar.bz2")
os.system("rm -rf phylosift.tar.bz2")
os.system("mv phylosift_20130829/lib ./Utilities/cpp%s%s-%s%sprokka"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.system("rm -rf phylosift_20130829")
if perltime == "":
os.system("curl -L http://search.cpan.org/CPAN/authors/id/M/MS/MSERGEANT/Time-Piece-1.08.tar.gz -o time.tar.gz")
os.system("tar -xvzf time.tar.gz")
os.chdir("Time-Piece-1.08")
os.system("perl Makefile.PL PREFIX=`pwd`/build")
os.system("make install")
os.chdir("%s"%(METAMOS_ROOT))
pathToCopy = utils.getCommandOutput("find Time-Piece-1.08/build -type d -name \"Time\" |grep -v auto", False)
copyPerlLib(pathToCopy, "./Utilities/cpp%s%s-%s%sprokka/lib/"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.system("rm -rf time.tar.gz")
os.system("rm -rf Time-Piece-1.08")
if xmlparser == "":
os.system("curl -L http://search.cpan.org/CPAN/authors/id/M/MS/MSERGEANT/XML-Parser-2.36.tar.gz -o parse.tar.gz")
os.system("tar -xvzf parse.tar.gz")
os.chdir("XML-Parser-2.36")
os.system("perl Makefile.PL PREFIX=`pwd`/build")
os.system("make install")
os.chdir("%s"%(METAMOS_ROOT))
pathToCopy = utils.getCommandOutput("find XML-Parser-2.36/build -type d -name \"XML\" |grep -v auto", False)
copyPerlLib(pathToCopy, "./Utilities/cpp%s%s-%s%sprokka/lib/"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
libUpdate = "%s/Utilities/cpp%s%s-%s%sprokka/lib/"%(METAMOS_ROOT, os.sep, OSTYPE, MACHINETYPE, os.sep)
if "PERL5LIB" in os.environ:
libUpdate = "%s%s%s"%(os.environ["PERL5LIB"], os.pathsep, libUpdate)
os.environ["PERL5LIB"]=libUpdate
os.system("rm -rf parse.tar.gz")
os.system("rm -rf XML-Parser-2.36")
if xmlsimple == "":
os.system("curl -L http://search.cpan.org/CPAN/authors/id/G/GR/GRANTM/XML-Simple-1.08.tar.gz -o xml.tar.gz")
os.system("tar -xvzf xml.tar.gz")
os.chdir("XML-Simple-1.08")
os.system("perl Makefile.PL PREFIX=`pwd`/build")
os.system("make install")
os.chdir("%s"%(METAMOS_ROOT))
pathToCopy = utils.getCommandOutput("find XML-Simple-1.08/build -type d -name \"XML\" |grep -v auto", False)
copyPerlLib(pathToCopy, "./Utilities/cpp%s%s-%s%sprokka/lib/"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.system("rm -rf xml.tar.gz")
os.system("rm -rf XML-Simple-1.08")
if os.path.exists("./Utilities/cpp%s%s-%s%sprokka/lib"%(os.sep, OSTYPE, MACHINETYPE, os.sep)):
os.chdir("./Utilities/cpp%s%s-%s%sprokka/bin"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.system("cp prokka prokka.original")
os.system("cat prokka.original |awk '{if (match($0, \"use strict\")) { print \"use lib \\\"%s/Utilities/cpp%s%s-%s%sprokka/lib\\\";\"; print $0; } else { print $0}}' > prokka"%(METAMOS_ROOT, os.sep, OSTYPE, MACHINETYPE, os.sep))
os.chdir("%s"%(METAMOS_ROOT))
# for some reason prokka adds its binaries to the end of path, not beginning so if your path has the wrong version of a program, it will crash. Update
os.chdir("./Utilities/cpp%s%s-%s%sprokka/bin"%(os.sep, OSTYPE, MACHINETYPE, os.sep))
os.system("cp prokka prokka.original")
os.system("cat prokka.original |awk '{if (match($0, \"ENV{PATH}\")) { print \"$ENV{PATH} = $BINDIR . \\\":\\\" . $ENV{PATH};\"; } else { print $0}}' > prokka")
os.chdir("%s"%(METAMOS_ROOT))
aragorn = utils.getFromPath("aragorn", "aragorn", False)
aragornVersion = ""
if aragorn != "":
aragornVersion = utils.getCommandOutput("%s/aragorn -h 2>&1 | grep -i '^ARAGORN v' |sed s/v//g |awk '{printf(\"%%2.2f\n\", $2)}'", True)
if float(aragornVersion) < 1.2:
aragorn = ""
if aragorn == "":
print "Aragorn missing, will install"
os.system("curl -L http://130.235.46.10/ARAGORN/Downloads/aragorn1.2.36.tgz -o aragorn.tar.gz")
os.system("tar xvzf aragorn.tar.gz")
os.chdir("aragorn1.2.36")
os.system("gcc -O3 -ffast-math -finline-functions %s %s -o aragorn aragorn1.2.36.c"%(addedCFlags, addedLDFlags))
os.chdir("%s"%(METAMOS_ROOT))
os.system("mv aragorn1.2.36/aragorn ./Utilities/cpp%s%s-%s%sprokka/binaries%s%s"%(os.sep, OSTYPE, MACHINETYPE, os.sep, os.sep, OSTYPE.lower()))
os.system("rm -rf aragorn1.2.36")
os.system("rm aragorn.tar.gz")
infernal = utils.getFromPath("cmscan", "Infernal", False)
if infernal == "" and not os.path.exists("./Utilities/cpp%s%s-%s%sprokka/binaries/%s/infernal"%(os.sep, OSTYPE, MACHINETYPE, os.sep, OSTYPE.lower())):
print "Infernal missing, will install"
if OSTYPE == "Darwin":
os.system("curl -L http://selab.janelia.org/software/infernal/infernal-1.1rc4-macosx-intel.tar.gz -o infernal.tar.gz")
else:
os.system("curl -L http://selab.janelia.org/software/infernal/infernal-1.1rc4-linux-intel-gcc.tar.gz -o infernal.tar.gz")
os.system("tar xvzf infernal.tar.gz")
os.system("mv infernal*/binaries/* ./Utilities/cpp%s%s-%s%sprokka/binaries%s%s"%(os.sep, OSTYPE, MACHINETYPE, os.sep, os.sep, OSTYPE.lower()))
os.system("rm -rf infernal*")
barrnap = utils.getFromPath("barrnap", "barrnap", False)
if barrnap == "" and not os.path.exists("./Utilities/cpp%s%s-%s%sprokka/binaries/%s/barrnap"%(os.sep, OSTYPE, MACHINETYPE, os.sep, OSTYPE.lower())):
print "Barrnap missing, will install"
os.system("curl -L http://www.vicbioinformatics.com/barrnap-0.1.tar.gz -o barrnap.tar.gz")
os.system("tar xvzf barrnap.tar.gz")
os.system("mv barrnap-0.1/barrnap ./Utilities/cpp%s%s-%s%sprokka/binaries%s%s"%(os.sep, OSTYPE, MACHINETYPE, os.sep, os.sep, OSTYPE.lower()))
os.system("mv barrnap-0.1/db ./Utilities/cpp%s%s-%s%sprokka/binaries%s%s"%(os.sep, OSTYPE, MACHINETYPE, os.sep, os.sep, OSTYPE.lower()))
if os.path.exists("./Utilities/cpp%s%s-%s%sprokka/lib"%(os.sep, OSTYPE, MACHINETYPE, os.sep)):
os.chdir("./Utilities/cpp%s%s-%s%sprokka/binaries%s%s"%(os.sep, OSTYPE, MACHINETYPE, os.sep, os.sep, OSTYPE.lower()))
os.system("cp barrnap barrnap.original")
os.system("cat barrnap.original |awk '{if (match($0, \"use strict\")) { print \"use lib \\\"%s/Utilities/cpp%s%s-%s%sprokka/lib\\\";\"; print $0; } else { print $0}}' > barrnap"%(METAMOS_ROOT, os.sep, OSTYPE, MACHINETYPE, os.sep))
os.chdir("%s"%(METAMOS_ROOT))
os.system("rm -rf barrnap-0.1")
os.system("rm barrnap.tar.gz")
hmmscan = utils.getFromPath("hmmscan", "HMMER3", False)