def CanRunDependencies(workingDir):
# FastME
testFN = workingDir + "SimpleTest.phy"
WriteTestDistancesFile(testFN)
outFN = workingDir + "SimpleTest.tre"
if os.path.exists(outFN): os.remove(outFN)
if not util.CanRunCommand("fastme -i %s -o %s" % (testFN, outFN),
qAllowStderr=False):
print("ERROR: Cannot run fastme")
print(
"Please check FastME is installed and that the executables are in the system path.\n"
)
return False
os.remove(testFN)
os.remove(outFN)
fastme_stat_fn = workingDir + "SimpleTest.phy_fastme_stat.txt"
if os.path.exists(fastme_stat_fn): os.remove(fastme_stat_fn)
# DLCPar
if not util.CanRunCommand("dlcpar_search --version", qAllowStderr=False):
print("ERROR: Cannot run dlcpar_search")
print(
"Please check DLCpar is installed and that the executables are in the system path.\n"
)
return False
return True
def CanRunOrthologueDependencies(workingDir, qMSAGeneTrees, qPhyldog,
qStopAfterTrees, qInferSpeciesTree):
# FastME
if (not qMSAGeneTrees) or qInferSpeciesTree:
testFN = workingDir + "SimpleTest.phy"
WriteTestDistancesFile(testFN)
outFN = workingDir + "SimpleTest.tre"
if os.path.exists(outFN): os.remove(outFN)
if not util.CanRunCommand("fastme -i %s -o %s" % (testFN, outFN),
qAllowStderr=False):
print("ERROR: Cannot run fastme")
print(
"Please check FastME is installed and that the executables are in the system path.\n"
)
return False
os.remove(testFN)
os.remove(outFN)
fastme_stat_fn = workingDir + "SimpleTest.phy_fastme_stat.txt"
if os.path.exists(fastme_stat_fn): os.remove(fastme_stat_fn)
# DLCPar
if not qStopAfterTrees:
if not util.CanRunCommand("dlcpar_search --version",
qAllowStderr=False):
print("ERROR: Cannot run dlcpar_search")
print(
"Please check DLCpar is installed and that the executables are in the system path.\n"
)
return False
# FastTree & MAFFT
if qMSAGeneTrees or qPhyldog:
testFN, temp_dir = msa.WriteTestFile(workingDir)
if not util.CanRunCommand("mafft %s" % testFN, qAllowStderr=True):
print("ERROR: Cannot run mafft")
print(
"Please check MAFFT is installed and that the executables are in the system path\n"
)
return False
if qMSAGeneTrees and not util.CanRunCommand("FastTree %s" % testFN,
qAllowStderr=True):
print("ERROR: Cannot run FastTree")
print(
"Please check FastTree is installed and that the executables are in the system path\n"
)
return False
try:
shutil.rmtree(temp_dir)
except OSError:
time.sleep(1)
shutil.rmtree(
temp_dir, True
) # shutil / NFS bug - ignore errors, it's less crucial that the files are deleted
return True
def CanRunOrthologueDependencies(workingDir, qMSAGeneTrees, qPhyldog, qStopAfterTrees, msa_method, tree_method, tree_options, qInferSpeciesTree, qStopAfterAlignments):
# FastME
if (not qMSAGeneTrees) or qInferSpeciesTree:
testFN = workingDir + "SimpleTest.phy"
WriteTestDistancesFile(testFN)
outFN = workingDir + "SimpleTest.tre"
if os.path.exists(outFN): os.remove(outFN)
if not util.CanRunCommand("fastme -i %s -o %s" % (testFN, outFN), qAllowStderr=False):
print("ERROR: Cannot run fastme")
print("Please check FastME is installed and that the executables are in the system path.\n")
return False
os.remove(testFN)
os.remove(outFN)
fastme_stat_fn = workingDir + "SimpleTest.phy_fastme_stat.txt"
if os.path.exists(fastme_stat_fn): os.remove(fastme_stat_fn)
# DLCPar
if not (qStopAfterTrees or qStopAfterAlignments):
if not util.CanRunCommand("dlcpar_search --version", qAllowStderr=False):
print("ERROR: Cannot run dlcpar_search")
print("Please check DLCpar is installed and that the executables are in the system path.\n")
return False
# FastTree & MAFFT
if qMSAGeneTrees or qPhyldog:
testFN, temp_dir = msa.WriteTestFile(workingDir)
if msa_method == "mafft":
if not util.CanRunCommand("mafft %s" % testFN, qAllowStderr=True):
print("ERROR: Cannot run mafft")
print("Please check MAFFT is installed and that the executables are in the system path\n")
return False
else:
if not tree_options.TestMSAMethod(temp_dir, msa_method):
print("ERROR: Cannot run user-configured MSA method '%s'" % msa_method)
print("Please check program is installed and that it is correctly configured in the ~/.orthofinder.config file\n")
return False
if tree_method == "fasttree":
if qMSAGeneTrees and (not qStopAfterAlignments) and not util.CanRunCommand("FastTree %s" % testFN, qAllowStderr=True):
print("ERROR: Cannot run FastTree")
print("Please check FastTree is installed and that the executables are in the system path\n")
return False
else:
if not tree_options.TestTreeMethod(temp_dir, tree_method):
print("ERROR: Cannot run user-configured tree method '%s'" % tree_method)
print("Please check program is installed and that it is correctly configured in the ~/.orthofinder.config file\n")
return False
try:
shutil.rmtree(temp_dir)
except OSError:
time.sleep(1)
shutil.rmtree(temp_dir, True) # shutil / NFS bug - ignore errors, it's less crucial that the files are deleted
return True
def CanRunOrthologueDependencies(workingDir, qMSAGeneTrees, qPhyldog, qStopAfterTrees, msa_method, tree_method, recon_method, program_caller, qStopAfterAlignments):
# FastME
if (not qMSAGeneTrees):
testFN = workingDir + "SimpleTest.phy"
WriteTestDistancesFile(testFN)
outFN = workingDir + "SimpleTest.tre"
if os.path.exists(outFN): os.remove(outFN)
if not util.CanRunCommand("fastme -i %s -o %s" % (testFN, outFN), qAllowStderr=False):
print("ERROR: Cannot run fastme")
print("Please check FastME is installed and that the executables are in the system path.\n")
return False
os.remove(testFN)
os.remove(outFN)
fastme_stat_fn = workingDir + "SimpleTest.phy_fastme_stat.txt"
if os.path.exists(fastme_stat_fn): os.remove(fastme_stat_fn)
# DLCPar
if ("dlcpar" in recon_method) and not (qStopAfterTrees or qStopAfterAlignments):
if not util.CanRunCommand("dlcpar_search --version", qAllowStderr=False):
print("ERROR: Cannot run dlcpar_search")
print("Please check DLCpar is installed and that the executables are in the system path.\n")
return False
if recon_method == "dlcpar_convergedsearch":
capture = subprocess.Popen("dlcpar_search --version", shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, env=my_env)
stdout = "".join([x for x in capture.stdout])
version = stdout.split()[-1]
major, minor, release = map(int, version.split("."))
# require 1.0.1 or above
actual = (major, minor, release)
required = [1,0,1]
versionOK = True
for r, a in zip(required, actual):
if a > r:
versionOK = True
break
elif a < r:
versionOK = False
break
else:
pass
# need to check next level down
if not versionOK:
print("ERROR: dlcpar_convergedsearch requires dlcpar_search version 1.0.1 or above")
return False
# FastTree & MAFFT
if qMSAGeneTrees or qPhyldog:
testFN, temp_dir = trees_msa.WriteTestFile(workingDir)
if msa_method == "mafft":
if not util.CanRunCommand("mafft %s" % testFN, qAllowStderr=True):
print("ERROR: Cannot run mafft")
print("Please check MAFFT is installed and that the executables are in the system path\n")
return False
elif msa_method != None:
if not program_caller.TestMSAMethod(temp_dir, msa_method):
print("ERROR: Cannot run user-configured MSA method '%s'" % msa_method)
print("Please check program is installed and that it is correctly configured in the orthofinder/config.json file\n")
return False
if tree_method == "fasttree":
if qMSAGeneTrees and (not qStopAfterAlignments) and not util.CanRunCommand("FastTree %s" % testFN, qAllowStderr=True):
print("ERROR: Cannot run FastTree")
print("Please check FastTree is installed and that the executables are in the system path\n")
return False
elif tree_method != None:
if not program_caller.TestTreeMethod(temp_dir, tree_method):
print("ERROR: Cannot run user-configured tree method '%s'" % tree_method)
print("Please check program is installed and that it is correctly configured in the orthofinder/config.json file\n")
return False
try:
shutil.rmtree(temp_dir)
except OSError:
time.sleep(1)
shutil.rmtree(temp_dir, True) # shutil / NFS bug - ignore errors, it's less crucial that the files are deleted
if qPhyldog:
if not util.CanRunCommand("mpirun -np 1 phyldog", qAllowStderr=False):
print("ERROR: Cannot run mpirun -np 1 phyldog")
print("Please check phyldog is installed and that the executable is in the system path\n")
return False
return True