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'