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")