dummy = {}
execfile(confName, dummy, newVars)
for key, value in newVars.iteritems():
locals()[key] = value
# GENERAL SETTINGS ================================================
# baseDir for internal data, accessible from cluster
# used for data created during pipeline runs
# Preference is given to a locally defined directory
if "pubsDataDir" not in locals():
pubsDataDir = "."
# static data, accessible from cluster, but part of distribution
# these are basic files like gene lists, marker lists, journal lists
# Some of it can be updated with pubPrepXXX commands
staticDataDir = join(getAppDir(), "data")
# scripts only used at UCSC
ucscScriptDir = normpath(join(dirname(__file__), "..", "ucscScripts"))
# external tools
extToolDir = normpath(join(dirname(__file__), "..", "ext"))
# a directory with files that associate publishers with journals
# one of them is the NLM Catalog, others we got from publishers or created them semi-
# manually
#journalListDir = join(staticDataDir, "journalLists")
#journalListDir = join(staticDataDir, "journalLists")
journalListDir = "/hive/data/inside/pubs/journalLists/"
# base dir for anything journal related in the repo data dir
exec(fh.read(), {}, newVars)
for key, value in newVars.items():
locals()[key] = value
# GENERAL SETTINGS ================================================
# baseDir for internal data, accessible from cluster
# used for data created during pipeline runs
# Preference is given to a locally defined directory
if "pubsDataDir" not in locals():
pubsDataDir = "."
# static data, accessible from cluster, but part of distribution
# these are basic files like gene lists, marker lists, journal lists
# Some of it can be updated with pubPrepXXX commands
if "staticDataDir" not in locals():
staticDataDir = join(getAppDir(), "data")
# scripts only used at UCSC
ucscScriptDir = normpath(join(dirname(__file__), "..", "ucscScripts"))
# a directory with files that associate publishers with journals
# one of them is the NLM Catalog, others we got from publishers or created them semi-
# manually
#journalListDir = join(staticDataDir, "journalLists")
#journalListDir = join(staticDataDir, "journalLists")
journalListDir = "/hive/data/inside/pubs/journalLists/"
# base dir for anything journal related in the repo data dir
journalInfoDir = join(staticDataDir, "journals")
# the lists are reformatted into this table. It is created by pubJournals and used by pubPrepCrawl