Commit 47b11f60 authored by Thomas Van Parys's avatar Thomas Van Parys
Browse files

Launcher: use CEDALION_HOME env variable (fixes #58)

parent 219a1045
......@@ -244,15 +244,15 @@ def prompt(species_file):
def editProteome():
value = input("{} ({})> ".format(SpeciesEntry.contentNames['proteome'], thisEntry.proteome))
if value:
thisEntry.proteome = value if value!='-' else ''
thisEntry.proteome = value if value != '-' else ''
def editCds():
value = input("{} ({})> ".format(SpeciesEntry.contentNames['cds'], thisEntry.cds))
thisEntry.cds = value if value!='-' else ''
thisEntry.cds = value if value != '-' else ''
def editGff3():
value = input("{} ({})> ".format(SpeciesEntry.contentNames['gff3'], thisEntry.gff3))
thisEntry.gff3 = value if value!='-' else ''
thisEntry.gff3 = value if value != '-' else ''
editOptions = {
'i': editCedalionId,
......@@ -278,10 +278,14 @@ def prompt(species_file):
# Get main Nextflow pipeline script
main_nf = 'main.nf'
modpath, modfile = os.path.split(__file__)
cedpath, mod = os.path.split(modpath)
mainpath, mod = os.path.split(cedpath)
main_nf_path = os.path.join(mainpath, main_nf)
if 'CEDALION_HOME' in os.environ:
cedalion_home = os.environ['CEDALION_HOME']
else:
homeDirEntered = ''
while not homeDirEntered:
homeDirEntered = input("Cedalion installation folder> ")
cedalion_home = homeDirEntered
main_nf_path = os.path.join(cedalion_home, main_nf)
inputDir = '.'
inputDirEntered = input("Data input folder (default: .)> ")
......@@ -293,7 +297,7 @@ def prompt(species_file):
if outputDirEntered:
outputDir = outputDirEntered
workDir = os.path.join(os.getcwd(),'work')
workDir = os.path.join(os.getcwd(), 'work')
workDirEntered = input("Working and cache folder (default: ./work)> ")
if workDirEntered:
workDir = workDirEntered
......
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