def installClustalw2OnWindows(tmpDirName, tmpFileName, guiParent=None):
"""
Run the msi installer.
"""
os.system(tmpFileName)
if not findOnSystem('clustalw2.exe'):
failiure(guiParent=guiParent, errorNr=6)
def installClustalw2OnWindows(tmpDirName, tmpFileName, guiParent=None):
"""
Run the msi installer.
"""
os.system(tmpFileName)
if not findOnSystem("clustalw2.exe"):
failiure(guiParent=guiParent, errorNr=6)
def assertBlastInstalled(guiParent=None):
"""
Checks if Blast is installed.
"""
# # First check if the user has wu-blast installed:
# if findOnSystem('blastn') and findOnSystem('xdformat'):
# return True
ftpURL = "ftp.ncbi.nlm.nih.gov"
ftpDir = "/blast/executables/blast+/LATEST"
found = False
if os.name in ("nt", "dos"):
name = "blastn.exe"
else:
name = "blastn"
msg = (
"This program depends on %s for searching databases. If you have an\ninternet connection SAP can download and install it for you.\nDo you want to do this now?"
% name
)
if findOnSystem(name):
return True
else:
if guiParent is None:
reply = prompt(msg + " Y/n:")
if reply == "n":
sys.exit()
else:
import wx
nResult = wx.MessageBox(msg, "Depency missing from your system!", wx.YES_NO | wx.ICON_QUESTION, guiParent)
if nResult == wx.NO:
msg = "You can download Blast yourself from:\nftp://%s/%s" % (ftpURL, ftpDir)
dlg = wx.MessageDialog(guiParent, msg, "Manual installation", wx.OK | wx.ICON_INFORMATION)
dlg.ShowModal()
dlg.Destroy()
sys.exit()
# packageRE = re.compile(r'ncbi-blast-[\d.]+\+-([^.]+)')
packageRE = re.compile(r"(ncbi-blast-.+)")
getPackage("blastn", packageRE, ftpURL, ftpDir, guiParent=guiParent)
return True
def assertBlastInstalled(guiParent=None):
"""
Checks if Blast is installed.
"""
# # First check if the user has wu-blast installed:
# if findOnSystem('blastn') and findOnSystem('xdformat'):
# return True
ftpURL = 'ftp.ncbi.nlm.nih.gov'
ftpDir = '/blast/executables/blast+/LATEST'
found = False
if os.name in ('nt', 'dos'):
name = 'blastn.exe'
else:
name = 'blastn'
msg = "This program depends on %s for searching databases. If you have an\ninternet connection SAP can download and install it for you.\nDo you want to do this now?" % name
if findOnSystem(name):
return True
else:
if guiParent is None:
reply = prompt(msg + ' Y/n:')
if reply == 'n':
sys.exit()
else:
import wx
nResult = wx.MessageBox(msg, "Depency missing from your system!",
wx.YES_NO | wx.ICON_QUESTION, guiParent)
if nResult == wx.NO:
msg = "You can download Blast yourself from:\nftp://%s/%s" % (
ftpURL, ftpDir)
dlg = wx.MessageDialog(guiParent, msg, 'Manual installation',
wx.OK | wx.ICON_INFORMATION)
dlg.ShowModal()
dlg.Destroy()
sys.exit()
#packageRE = re.compile(r'ncbi-blast-[\d.]+\+-([^.]+)')
packageRE = re.compile(r'(ncbi-blast-.+)')
getPackage('blastn', packageRE, ftpURL, ftpDir, guiParent=guiParent)
return True
def installBlastOnWindows(tmpDirName, tmpFileName, guiParent=None):
"""
Install downloaded package on a widows platform.
"""
z = zipfile.ZipFile(tmpFileName, "r")
for fileName in z.namelist():
if fileName == 'blastall.exe':
excecutable = z.read(fileName)
z.close()
installDir = 'C:\Program Files\Blast'
os.makedirs(installDir)
fh = open(os.path.join(installDir, 'blastall.exe'), 'wb')
fh.write(excecutable)
fh.close()
if not findOnSystem('blastall.exe'):
failiure(guiParent=guiParent, errorNr=4)
def installBlastOnWindows(tmpDirName, tmpFileName, guiParent=None):
"""
Install downloaded package on a widows platform.
"""
z = zipfile.ZipFile(tmpFileName, "r")
for fileName in z.namelist():
if fileName == "blastall.exe":
excecutable = z.read(fileName)
z.close()
installDir = "C:\Program Files\Blast"
os.makedirs(installDir)
fh = open(os.path.join(installDir, "blastall.exe"), "wb")
fh.write(excecutable)
fh.close()
if not findOnSystem("blastall.exe"):
failiure(guiParent=guiParent, errorNr=4)
def assertClustalw2Installed(guiParent=None):
"""
Checks if Clustalw2 is installed.
"""
ftpURL = 'ftp.ebi.ac.uk'
ftpDir = 'pub/software/clustalw2/2.0.8'
found = False
if os.name in ('nt', 'dos'):
name = 'clustalw2.exe'
else:
name = 'clustalw2'
msg = "This program depends on %s for aligning homologues. If you have an internet connection SAP\ncan download and install it for you. Do you want to do this now?" % name
if findOnSystem(name):
return True
else:
if guiParent is None:
reply = prompt(msg + ' Y/n:')
if reply == 'n':
sys.exit()
else:
import wx
nResult = wx.MessageBox(msg,
"Dependency missing from your system!",
wx.YES_NO | wx.ICON_QUESTION, guiParent)
if nResult == wx.NO:
msg = "You can download %s yourself from:\nftp://%s/%s" % (
name, ftpURL, ftpDir)
dlg = wx.MessageDialog(guiParent, msg, 'Manual installation',
wx.OK | wx.ICON_INFORMATION)
dlg.ShowModal()
dlg.Destroy()
sys.exit()
packageRE = re.compile(r'clustalw-[\d.]+-([^.]+)')
success = getPackage('clustalw2',
packageRE,
ftpURL,
ftpDir,
guiParent=guiParent)
return success
def installBlastOnPosix(tmpDirName, tmpFileName, guiParent=None):
"""
Install downloaded package on a posix platform.
"""
# Unpack the tarball:
tar = tarfile.open(tmpFileName, 'r:gz')
for item in tar:
tar.extract(item, tmpDirName)
tar.close()
os.unlink(tmpFileName)
# # Get content list:
# packageContent = glob.glob(os.path.join(tmpDirName, '*'))
# # Decend one dir level if tarball was unpacked to a dir:
# if len(packageContent) == 1 and os.path.isdir(packageContent[0]):
# packageContent = glob.glob(os.path.join(packageContent[0], '*'))
packageContent = glob.glob(os.path.join(tmpDirName, 'ncbi-blast-*', '*'))
installDir = getPossixInstallDir(guiParent=guiParent)
# Chop off the bin dir from the install path becauce we copy the
# bin dir and the data dir over when installing:
installDir = os.path.split(installDir)[0]
try:
if not os.access(installDir, os.W_OK):
if guiParent is None:
os.system("sudo cp -r %s %s" %
(" ".join(packageContent), installDir))
else:
os.system("echo '%s' | sudo -S cp -r %s %s" %
(passwDialog(guiParent), " ".join(packageContent),
installDir))
else:
os.system("cp -r %s %s" % (" ".join(packageContent), installDir))
except:
pass
if not findOnSystem('blastn'):
failiure(guiParent=guiParent, errorNr=7)
def installBlastOnPosix(tmpDirName, tmpFileName, guiParent=None):
"""
Install downloaded package on a posix platform.
"""
# Unpack the tarball:
tar = tarfile.open(tmpFileName, "r:gz")
for item in tar:
tar.extract(item, tmpDirName)
tar.close()
os.unlink(tmpFileName)
# # Get content list:
# packageContent = glob.glob(os.path.join(tmpDirName, '*'))
# # Decend one dir level if tarball was unpacked to a dir:
# if len(packageContent) == 1 and os.path.isdir(packageContent[0]):
# packageContent = glob.glob(os.path.join(packageContent[0], '*'))
packageContent = glob.glob(os.path.join(tmpDirName, "ncbi-blast-*", "*"))
installDir = getPossixInstallDir(guiParent=guiParent)
# Chop off the bin dir from the install path becauce we copy the
# bin dir and the data dir over when installing:
installDir = os.path.split(installDir)[0]
try:
if not os.access(installDir, os.W_OK):
if guiParent is None:
os.system("sudo cp -r %s %s" % (" ".join(packageContent), installDir))
else:
os.system(
"echo '%s' | sudo -S cp -r %s %s" % (passwDialog(guiParent), " ".join(packageContent), installDir)
)
else:
os.system("cp -r %s %s" % (" ".join(packageContent), installDir))
except:
pass
if not findOnSystem("blastn"):
failiure(guiParent=guiParent, errorNr=7)
def assertClustalw2Installed(guiParent=None):
"""
Checks if Clustalw2 is installed.
"""
ftpURL = "ftp.ebi.ac.uk"
ftpDir = "pub/software/clustalw2/2.0.8"
found = False
if os.name in ("nt", "dos"):
name = "clustalw2.exe"
else:
name = "clustalw2"
msg = (
"This program depends on %s for aligning homologues. If you have an internet connection SAP\ncan download and install it for you. Do you want to do this now?"
% name
)
if findOnSystem(name):
return True
else:
if guiParent is None:
reply = prompt(msg + " Y/n:")
if reply == "n":
sys.exit()
else:
import wx
nResult = wx.MessageBox(
msg, "Dependency missing from your system!", wx.YES_NO | wx.ICON_QUESTION, guiParent
)
if nResult == wx.NO:
msg = "You can download %s yourself from:\nftp://%s/%s" % (name, ftpURL, ftpDir)
dlg = wx.MessageDialog(guiParent, msg, "Manual installation", wx.OK | wx.ICON_INFORMATION)
dlg.ShowModal()
dlg.Destroy()
sys.exit()
packageRE = re.compile(r"clustalw-[\d.]+-([^.]+)")
success = getPackage("clustalw2", packageRE, ftpURL, ftpDir, guiParent=guiParent)
return success
def installClustalw2OnPosix(tmpDirName, tmpFileName, guiParent=None):
installDir = getPossixInstallDir(guiParent=guiParent)
fail = False
if sys.platform == 'darwin':
# Unpack the disk image and move the executable to the install dir:
fail = os.system('open -g -a DiskImageMounter %s' % tmpFileName)
# Hack to for OSX 10.4 where open does not have the -g option:
if fail == 256:
fail = os.system('open -a DiskImageMounter %s' % tmpFileName)
if fail:
return False
while not glob.glob('/Volumes/clustalw-*/clustalw-*/clustalw2'):
time.sleep(1)
time.sleep(2)
executable = glob.glob('/Volumes/clustalw-*/clustalw-*/clustalw2')[0]
try:
if not os.access(installDir, os.W_OK):
if guiParent is None:
os.system("sudo cp %s %s" % (executable, installDir))
else:
os.system("echo '%s' | sudo -S cp %s %s" %
(passwDialog(guiParent), executable, installDir))
else:
os.system("cp %s %s" % (executable, installDir))
except:
return False
else:
# Unpack the tarball:
tar = tarfile.open(tmpFileName, 'r:gz')
for item in tar:
tar.extract(item, tmpDirName)
tar.close()
os.unlink(tmpFileName)
# Chop off the bin dir from the install path becauce we copy the
# bin dir and the data dir over when installing:
installDir = os.path.split(installDir)[0]
oldCWD = os.getcwd()
os.chdir(glob.glob(tmpDirName + '/clustalw-*')[0])
if installDir == '/usr/local':
if os.system("./configure"):
return False
else:
if os.system("./configure --prefix %s" % installDir):
return False
if os.system("make"):
return False
if not os.access(installDir, os.W_OK):
if guiParent is None:
os.system("sudo make install")
else:
os.system("echo '%s' | sudo -S make install")
else:
os.system("make install")
os.chdir(oldCWD)
if not findOnSystem('clustalw2'):
failiure(guiParent=guiParent, errorNr=8)
def sap():
try:
optionsParser = Options.Options()
options, args = optionsParser.postProcess()
if options.viewresults:
try:
webbrowser.open('file://' + os.path.abspath(
os.path.join(options.viewresults, 'html', 'index.html')),
new=2,
autoraise=1)
except:
if os.path.exists(options.viewresults):
print "The anlysis has not completed and no results are available."
else:
print "The spcified project folder does not exist."
sys.exit()
if options.compile:
if os.path.exists(options.database):
print "Database already exists. Delete old database or use other name."
sys.exit()
from CompileDatabase import compileDatabase
compileDatabase(options.compile, options.email, options.database)
sys.exit()
if options.installdependencies:
print "Checking that dependencies are installed on your system."
from UtilityFunctions import findOnSystem
missing = False
if os.name in ('nt', 'dos'):
name = 'blastn.exe'
else:
name = 'blastn'
if not findOnSystem(name):
print "\nThis program depends on %s for searching databases. Automatic installation is not longer supported. You need to install this yourself from:\nftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST\n\n" % name
missing = True
if os.name in ('nt', 'dos'):
name = 'clustalw2.exe'
else:
name = 'clustalw2'
if not findOnSystem(name):
print "\nThis program depends on %s for aligning homologues. Automatic installation is not longer supported. You need to install this yourself from:\nftp.ebi.ac.uk/pub/software/clustalw2/2.0.8\n\n" % name
missing = True
if not missing:
print "You should be good to go."
# if assertClustalw2Installed() and assertBlastInstalled():
# print "All dependencies are installed"
# #sys.exit()
return None
if options.onlinehelp:
webbrowser.open(
'http://kaspermunch.wordpress.com/statistical-assignment-package-sap/',
new=2,
autoraise=1)
#sys.exit()
return None
# Make a string of all options except of the ones with a '_'
# prefix which are for internal use only:
optionStr = ''
for k, v in options.__dict__.items():
if not re.match('_', k):
if type(v) is ListType:
if len(v) > 0:
joinString = ' --%s ' % k
v = [str(x) for x in v]
optionStr += joinString + joinString.join(v)
elif v is True:
optionStr += ' --%s' % k
elif v is not False:
optionStr += ' --%s %s' % (k, v)
if options._align:
try:
plugin = findPlugin(options.alignment, 'sap.alignment')
except PluginNotFoundError, X:
raise AnalysisTerminated(
1, "The plugin or file %s was not found." % X.plugin)
aligner = plugin.Aligner(options)
for fastaFileName in args:
aligner.align(fastaFileName)
elif options._sample:
try:
plugin = findPlugin(options.assignment, 'sap.assignment')
except PluginNotFoundError, X:
raise AnalysisTerminated(
1, "The plugin or file %s was not found." % X.plugin)
# #######################################
# if options.ghostpopulation:
# ima = IMa.Assignment(options)
# ima.run(args)
# #######################################
else:
# Check that netblast and clustalw2 are installed:
from UtilityFunctions import findOnSystem
missing = False
if os.name in ('nt', 'dos'):
name = 'blastn.exe'
else:
name = 'blastn'
if not findOnSystem(name):
print "\nThis program depends on %s for searching databases. Automatic installation is not longer supported. You need to install this yourself from:\nftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST\n\n" % name
missing = True
if os.name in ('nt', 'dos'):
name = 'clustalw2.exe'
else:
name = 'clustalw2'
if not findOnSystem(name):
print "\nThis program depends on %s for aligning homologues. Automatic installation is not longer supported. You need to install this yourself from:\nftp.ebi.ac.uk/pub/software/clustalw2/2.0.8\n\n" % name
missing = True
if missing:
return None
#
# print "Locating dependencies"
# assertClustalw2Installed()
# assertBlastInstalled()
def installClustalw2OnPosix(tmpDirName, tmpFileName, guiParent=None):
installDir = getPossixInstallDir(guiParent=guiParent)
fail = False
if sys.platform == "darwin":
# Unpack the disk image and move the executable to the install dir:
fail = os.system("open -g -a DiskImageMounter %s" % tmpFileName)
# Hack to for OSX 10.4 where open does not have the -g option:
if fail == 256:
fail = os.system("open -a DiskImageMounter %s" % tmpFileName)
if fail:
return False
while not glob.glob("/Volumes/clustalw-*/clustalw-*/clustalw2"):
time.sleep(1)
time.sleep(2)
executable = glob.glob("/Volumes/clustalw-*/clustalw-*/clustalw2")[0]
try:
if not os.access(installDir, os.W_OK):
if guiParent is None:
os.system("sudo cp %s %s" % (executable, installDir))
else:
os.system("echo '%s' | sudo -S cp %s %s" % (passwDialog(guiParent), executable, installDir))
else:
os.system("cp %s %s" % (executable, installDir))
except:
return False
else:
# Unpack the tarball:
tar = tarfile.open(tmpFileName, "r:gz")
for item in tar:
tar.extract(item, tmpDirName)
tar.close()
os.unlink(tmpFileName)
# Chop off the bin dir from the install path becauce we copy the
# bin dir and the data dir over when installing:
installDir = os.path.split(installDir)[0]
oldCWD = os.getcwd()
os.chdir(glob.glob(tmpDirName + "/clustalw-*")[0])
if installDir == "/usr/local":
if os.system("./configure"):
return False
else:
if os.system("./configure --prefix %s" % installDir):
return False
if os.system("make"):
return False
if not os.access(installDir, os.W_OK):
if guiParent is None:
os.system("sudo make install")
else:
os.system("echo '%s' | sudo -S make install")
else:
os.system("make install")
os.chdir(oldCWD)
if not findOnSystem("clustalw2"):
failiure(guiParent=guiParent, errorNr=8)
def sap():
try:
optionsParser = Options.Options()
options, args = optionsParser.postProcess()
if options.viewresults:
try:
webbrowser.open('file://' + os.path.abspath(os.path.join(options.viewresults, 'html', 'index.html')), new=2, autoraise=1)
except:
if os.path.exists(options.viewresults):
print "The anlysis has not completed and no results are available."
else:
print "The spcified project folder does not exist."
sys.exit()
if options.compile:
if os.path.exists(options.database):
print "Database already exists. Delete old database or use other name."
sys.exit()
from CompileDatabase import compileDatabase
compileDatabase(options.compile, options.email, options.database)
sys.exit()
if options.installdependencies:
print "Checking that dependencies are installed on your system."
from UtilityFunctions import findOnSystem
missing = False
if os.name in ('nt', 'dos'):
name = 'blastn.exe'
else:
name = 'blastn'
if not findOnSystem(name):
print "\nThis program depends on %s for searching databases. Automatic installation is not longer supported. You need to install this yourself from:\nftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST\n\n" % name
missing = True
if os.name in ('nt', 'dos'):
name = 'clustalw2.exe'
else:
name = 'clustalw2'
if not findOnSystem(name):
print "\nThis program depends on %s for aligning homologues. Automatic installation is not longer supported. You need to install this yourself from:\nftp.ebi.ac.uk/pub/software/clustalw2/2.0.8\n\n" % name
missing = True
if not missing:
print "You should be good to go."
# if assertClustalw2Installed() and assertBlastInstalled():
# print "All dependencies are installed"
# #sys.exit()
return None
if options.onlinehelp:
webbrowser.open('http://kaspermunch.wordpress.com/statistical-assignment-package-sap/', new=2, autoraise=1)
#sys.exit()
return None
# Make a string of all options except of the ones with a '_'
# prefix which are for internal use only:
optionStr = ''
for k, v in options.__dict__.items():
if not re.match('_', k):
if type(v) is ListType:
if len(v) > 0:
joinString = ' --%s ' % k
v = [str(x) for x in v]
optionStr += joinString + joinString.join(v)
elif v is True:
optionStr += ' --%s' % k
elif v is not False:
optionStr += ' --%s %s' % (k, v)
if options._align:
try:
plugin = findPlugin(options.alignment, 'sap.alignment')
except PluginNotFoundError, X:
raise AnalysisTerminated(1, "The plugin or file %s was not found." % X.plugin)
aligner = plugin.Aligner(options)
for fastaFileName in args:
aligner.align(fastaFileName)
elif options._sample:
try:
plugin = findPlugin(options.assignment, 'sap.assignment')
except PluginNotFoundError, X:
raise AnalysisTerminated(1, "The plugin or file %s was not found." % X.plugin)
# #######################################
# if options.ghostpopulation:
# ima = IMa.Assignment(options)
# ima.run(args)
# #######################################
else:
# Check that netblast and clustalw2 are installed:
from UtilityFunctions import findOnSystem
missing = False
if os.name in ('nt', 'dos'):
name = 'blastn.exe'
else:
name = 'blastn'
if not findOnSystem(name):
print "\nThis program depends on %s for searching databases. Automatic installation is not longer supported. You need to install this yourself from:\nftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST\n\n" % name
missing = True
if os.name in ('nt', 'dos'):
name = 'clustalw2.exe'
else:
name = 'clustalw2'
if not findOnSystem(name):
print "\nThis program depends on %s for aligning homologues. Automatic installation is not longer supported. You need to install this yourself from:\nftp.ebi.ac.uk/pub/software/clustalw2/2.0.8\n\n" % name
missing = True
if missing:
return None
#
# print "Locating dependencies"
# assertClustalw2Installed()
# assertBlastInstalled()