--- a/directory_copier.py	Mon May 09 02:06:07 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,138 +0,0 @@
-import gzip
-import optparse  # using optparse as hydra still python 2.6
-import os.path
-import shutil
-import sys
-
-def report_error(*args):
-    sys.stderr.write(' '.join(map(str,args)) + '\n')
-    sys.stderr.flush()
-    sys.exit(1)
-
-
-def get_tool_data(name):
-    root_dir = os.path.dirname((os.path.realpath(__file__)))
-    path = os.path.join(root_dir,"tool-data",name)
-    if not(os.path.isfile(path)): 
-        report_error(name,"file not found in tool's tool-data folder. Please ask you galaxy admin to add it back")
-    return path
-
-
-def check_white_list(path_to_check):
-    white_list = get_tool_data("white-list.ini")
-    with open(white_list, 'r') as white_list_file:
-        for line in white_list_file:
-            line = line.strip()
-            if len(line) >= 1 and path_to_check.startswith(line):
-                return True
-    report_error(path_to_check,"has not been included in the white list. Please contact the local galaxy admin to add it.")
-
-
-def check_black_list(path_to_check):
-    black_list = get_tool_data("black-list.ini")
-    with open(black_list, 'r') as black_list_file:
-        for line in black_list_file:
-            line = line.strip()
-            if len(line) >= 1 and line in path_to_check:
-                report_error(line,"has been black list so",path_to_check,"is not allowed. Please contact the local galaxy admin to change that, or add a symlink.")
-    return True
-
-
-def check_pattern_get_new_name(a_file, ending, options):
-    if options.start:
-        if not(a_file.startswith(options.start)):
-            return None
-    if options.last:
-        if ending[0] == ".":
-            last = options.last + ending
-        else:
-            if options.last[-1] == ".":
-                last = options.last + ending
-            else:
-                last = options.last + "." + ending
-        if not(a_file.endswith(last)):
-            return None
-    if options.new_ending:
-        name = a_file[:-len(ending)]
-        if options.new_ending[0] ==".":
-            if name[-1] == ".":
-                name = name[:-1]
-        return name + options.new_ending
-    if options.decompress:
-        if a_file.endswith(".gz"):
-            return a_file[:-3]
-    return a_file
-
-
-def check_and_get_new_name(a_file, options):
-    for ending in options.endings:
-        if a_file.endswith(ending):
-            return check_pattern_get_new_name (a_file, ending, options)
-    return None
-
-
-def link(a_file, new_name, path):
-    file_path = os.path.join(os.path.realpath(path), a_file)
-    sym_path = os.path.join(os.path.realpath("output"), new_name)
-    #if not(os.path.exists(sym_path)):
-    os.link(file_path, sym_path)
-
-
-def decompress(a_file, new_name, path):
-    file_path = os.path.join(os.path.realpath(path), a_file)
-    target_path = os.path.join(os.path.realpath("output"), new_name)
-    with gzip.open(file_path, 'rb') as f_in, open(target_path, 'wb') as f_out:
-        shutil.copyfileobj(f_in, f_out)
-
-
-def copy_and_link(path, options):
-    os.mkdir("output")
-    with open(options.list, 'w') as list_file:
-        files = os.listdir(path)
-        files.sort()
-        for a_file in files:
-            new_name = check_and_get_new_name(a_file, options)
-            if new_name:
-                list_file.write(new_name)
-                list_file.write("\n")
-                if options.decompress:
-                    if a_file.endswith(".gz"):
-                        decompress(a_file, new_name,path)
-                    else:
-                        link(a_file, new_name, path)
-                elif options.link:
-                    link(a_file, new_name, path)
-
-
-if __name__ == '__main__':
-    parser = optparse.OptionParser()
-    parser.add_option("--path", action="store", type="string",
-                      help="Path of directory to check. ")
-    parser.add_option("--ending", action="append", type="string", dest="endings",
-                      help="Ending that can be listed and if requested linked or decompressed. ")
-    parser.add_option("--start", action="store", type="string",
-                      help="String that must be at the start of the file name ")
-    parser.add_option("--last", action="store", type="string",
-                      help="String that must be the last bit of the file name before the endings")
-    parser.add_option("--new_ending", action="store", type="string", 
-                      help="New ending to replace any previous ending in list and if required links or decompressions. Note: If not set decompression will auto remove the compressioned part of the ending")
-    #parser.add_option("--regex", action="store", type="string",
-    #                  help="Regex pattern the file name (less . ending) must match before the endings")
-    parser.add_option("--list", action="store", type="string",
-                      help="Path to where all files should be listed. ")
-    parser.add_option("--link", action="store_true", default=False,
-                      help="If set will cause links to be added in output directory. ")
-    parser.add_option("--decompress", action="store_true", default=False,
-                      help="If set will cause gz files to be decompressed or if not a supported decompression ending linked.")
-    (options, args) = parser.parse_args()
-
-
-    path = options.path.strip()
-    if path[-1] != '/':
-        path = path + "/"
-    check_white_list(path)
-    print path, "white listed"
-    check_black_list(path)
-    print path, "not black listed"
-    copy_and_link(path, options)
-