assert_writable_dir(TEMPDIR)
TMPDIR = mk_dir(TEMPDIR+'/gn2/')
assert_writable_dir(TMPDIR)
CACHEDIR = mk_dir(TMPDIR+'/cache/')
# We can no longer write into the git tree:
GENERATED_IMAGE_DIR = mk_dir(TMPDIR+'generated/')
GENERATED_TEXT_DIR = mk_dir(TMPDIR+'generated_text/')
# Make sure we have permissions to access these
assert_writable_dir(CACHEDIR)
assert_writable_dir(GENERATED_IMAGE_DIR)
assert_writable_dir(GENERATED_TEXT_DIR)
# Flat file directories
GENODIR = flat_files('genotype')+'/'
assert_dir(GENODIR)
# JSON genotypes are OBSOLETE
JSON_GENODIR = flat_files('genotype/json')+'/'
if not valid_path(JSON_GENODIR):
# fall back on old location (move the dir, FIXME)
JSON_GENODIR = flat_files('json')
# Are we using the following...?
PORTADDR = "http://50.16.251.170"
INFOPAGEHREF = '/dbdoc/%s.html'
CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR'
SCRIPTFILE = 'main.py'
DBSNP = 'http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s'
UCSC_RUDI_TRACK_URL = " http://genome.cse.ucsc.edu/cgi-bin/hgTracks?org=%s&db=%s&hgt.customText=http://gbic.biol.rug.nl/~ralberts/tracks/%s/%s"
GENOMEBROWSER_URL = "http://ucscbrowser.genenetwork.org/cgi-bin/hgTracks?clade=mammal&org=Mouse&db=mm9&position=%s&hgt.suggest=&pix=800&Submit=submit"
ENSEMBLETRANSCRIPT_URL = "http://useast.ensembl.org/Mus_musculus/Lucene/Details?species=Mus_musculus;idx=Transcript;end=1;q=%s"
# The following paths are no longer in use!
# HTMLPATH is replaced by GENODIR
# IMGDIR is replaced by GENERATED_IMAGE_DIR
# Temporary storage (note that this TMPDIR is not the same directory
# as the UNIX TMPDIR)
TMPDIR = mk_dir(TEMPDIR + '/gn2/')
CACHEDIR = mk_dir(TMPDIR + '/cache/')
# We can no longer write into the git tree:
GENERATED_IMAGE_DIR = mk_dir(TMPDIR + '/generated/')
GENERATED_TEXT_DIR = mk_dir(TMPDIR + '/generated_text/')
# Flat file directories
GENODIR = flat_files('genotype') + '/'
JSON_GENODIR = flat_files('genotype/json') + '/'
if not valid_path(JSON_GENODIR):
# fall back on old location (move the dir, FIXME)
JSON_GENODIR = flat_files('json')
assert_dir(GENODIR)
PORTADDR = "http://50.16.251.170"
INFOPAGEHREF = '/dbdoc/%s.html'
CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR'
SCRIPTFILE = 'main.py'
TMPDIR = mk_dir(TEMPDIR + '/gn2/')
assert_writable_dir(TMPDIR)
CACHEDIR = mk_dir(TMPDIR + '/cache/')
# We can no longer write into the git tree:
GENERATED_IMAGE_DIR = mk_dir(TMPDIR + 'generated/')
GENERATED_TEXT_DIR = mk_dir(TMPDIR + 'generated_text/')
# Make sure we have permissions to access these
assert_writable_dir(CACHEDIR)
assert_writable_dir(GENERATED_IMAGE_DIR)
assert_writable_dir(GENERATED_TEXT_DIR)
# Flat file directories
GENODIR = flat_files('genotype') + '/'
assert_dir(GENODIR)
assert_dir(GENODIR + 'bimbam') # for gemma
# JSON genotypes are OBSOLETE
JSON_GENODIR = flat_files('genotype/json') + '/'
if not valid_path(JSON_GENODIR):
# fall back on old location (move the dir, FIXME)
JSON_GENODIR = flat_files('json')
# Are we using the following...?
PORTADDR = "http://50.16.251.170"
INFOPAGEHREF = '/dbdoc/%s.html'
CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR'
SCRIPTFILE = 'main.py'
UCSC_RUDI_TRACK_URL = " http://genome.cse.ucsc.edu/cgi-bin/hgTracks?org=%s&db=%s&hgt.customText=http://gbic.biol.rug.nl/~ralberts/tracks/%s/%s"
GENOMEBROWSER_URL="http://ucscbrowser.genenetwork.org/cgi-bin/hgTracks?clade=mammal&org=Mouse&db=mm9&position=%s&hgt.suggest=&pix=800&Submit=submit"
ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?species=Mus_musculus;idx=Transcript;end=1;q=%s"
# HTMLPATH = GNROOT + 'genotype_files/'
# PYLMM_PATH
# IMGDIR = GNROOT + '/wqflask/wqflask/static/output/'
# Temporary storage:
TMPDIR = mk_dir(TEMPDIR+'/gn2/')
CACHEDIR = mk_dir(TEMPDIR+'/cache/')
# We can no longer write into the git tree:
GENERATED_IMAGE_DIR = mk_dir(TMPDIR+'/generate/')
GENERATED_TEXT_DIR = mk_dir(TMPDIR+'/generate_text/')
# Flat file directories
GENODIR = flat_files('genotype')+'/'
JSON_GENODIR = assert_dir(GENODIR+'json/')
# SITENAME = 'GN'
# PORTADDR = "http://50.16.251.170"
# BASEHREF = '<base href="http://50.16.251.170/">'
INFOPAGEHREF = '/dbdoc/%s.html'
CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR'
SCRIPTFILE = 'main.py'
# GLOSSARYFILE = "/glossary.html"
# REFRESHSTR = '<meta http-equiv="refresh" content="5;url=%s' + SCRIPTFILE +'?sid=%s">'
# REFRESHDIR = '%s' + SCRIPTFILE +'?sid=%s'