if not fail or silentInstall:
dl = 'y'
elif lightInstall:
dl = 'n'
else:
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")
#os.system("ln -s %s/Utilities/python/taxonomy.txt %s/Utilities/models/taxonomy.txt"%(sys.path[0], sys.path[0]))
#WARNING: matplotlib causes install issues for multiple users
fail = 0
if "FINDORFS" in skipsteps or "FindORFS" in skipsteps or "findorfs" in skipsteps:
pass
else:
tasks_to_run.append("findorfs.FindORFS")
tasks_to_run.append("postprocess.Postprocess")
#pipeline_printout(sys.stdout,tasks_to_run,verbose=2)
pipeline_printout(sys.stdout,[preprocess.Preprocess,assemble.Assemble, \
mapreads.MapReads, \
findorfs.FindORFS, findreps.FindRepeats, annotate.Annotate, \
abundance.Abundance, fannotate.FunctionalAnnotation, scaffold.Scaffold, \
findscforfs.FindScaffoldORFS, propagate.Propagate, \
classify.Classify, postprocess.Postprocess], verbose=1)
if not utils.getFromPath("dot", "Graphviz") == "":
pipeline_printout_graph ( 'flowchart.svg',
'svg',
[postprocess.Postprocess],
no_key_legend = True)
if 1 or not utils.Settings.BINARY_DIST:
printConfiguration()
printConfiguration("%s/pipeline.run"%(settings.rundir))
updateCounter()
forcetasks = []
for item in forcesteps:
if "ASSEMBLE" in string.upper(item):
forcetasks.append("assemble.Assemble")
elif "FINDORFS" in string.upper(item):
else:
tasks_to_run.append("findorfs.FindORFS")
tasks_to_run.append("postprocess.Postprocess")
#pipeline_printout(sys.stdout,tasks_to_run,verbose=2)
if len(wf.stepList) != 0:
pipeline_printout(sys.stdout, wf.stepList, verbose=1)
else:
pipeline_printout(sys.stdout,[preprocess.Preprocess,assemble.Assemble, \
mapreads.MapReads, \
findorfs.FindORFS, findreps.FindRepeats, classify.Classify, \
abundance.Abundance, fannotate.FunctionalAnnotation, scaffold.Scaffold, \
findscforfs.FindScaffoldORFS, propagate.Propagate, \
bin.Bin, postprocess.Postprocess], verbose=1)
if not utils.getFromPath("dot", "Graphviz") == "":
pipeline_printout_graph('flowchart.svg',
'svg', [postprocess.Postprocess],
no_key_legend=True)
if 1 or not utils.Settings.BINARY_DIST:
printConfiguration()
printConfiguration("%s/pipeline.run" % (settings.rundir))
updateCounter()
forcetasks = []
for item in forcesteps:
if "ASSEMBLE" in string.upper(item):
forcetasks.append("assemble.Assemble")
elif "FINDORFS" in string.upper(item):
forcetasks.append("findorfs.FindORFS")
