--- a/data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.py	Thu Dec 08 03:43:26 2016 -0500
+++ b/data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.py	Thu Dec 21 13:51:22 2017 -0500
@@ -230,8 +230,8 @@
     print("NAME:\t%s" % data_table_entry['name'])
     print("PREFIX:\t%s" % data_table_entry['prefix'])
 
-    shutil.copyfile(stranded_index_name, os.path.join(target_directory, stranded_index_name))
-    shutil.copyfile(unstranded_index_name, os.path.join(target_directory, unstranded_index_name))
+    shutil.move(stranded_index_name, os.path.join(target_directory, stranded_index_name))
+    shutil.move(unstranded_index_name, os.path.join(target_directory, unstranded_index_name))
 
     cleanup_before_exit(tmp_dir)
 

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes_testchr.py	Thu Dec 21 13:51:22 2017 -0500
@@ -0,0 +1,272 @@
+#!/usr/bin/python
+
+import sys
+import shutil
+import re
+import urllib2
+import subprocess
+import gzip
+import os
+import tempfile
+from optparse import OptionParser
+from galaxy.util.json import from_json_string, to_json_string
+
+def get_arg():
+    parser = OptionParser()
+    parser.add_option("-e", "--ensembl", dest = 'ensembl_info', action = "store", nargs = 2, metavar = ("kingdom", "species_name"), type = "str")
+    parser.add_option("-o", "--output", dest='output_filename', action="store", nargs = 1, metavar = 'JSON_FILE')
+    parser.add_option("--log", dest='log_filename', action="store", nargs=1, metavar='log_report')
+    (options, args) = parser.parse_args()
+    return options, args
+
+def cleanup_before_exit(tmp_dir):
+    if tmp_dir and os.path.exists(tmp_dir):
+        shutil.rmtree(tmp_dir)
+
+def get_page_content(url):
+    req = urllib2.Request(url)
+    page = urllib2.urlopen(req)
+    return page.read()
+
+def download_file(link, local_file_name):
+    req = urllib2.Request(link)
+    src_file = urllib2.urlopen(req)
+    local_file = open(local_file_name, 'wb')
+    local_file.write(src_file.read())
+    local_file.close()
+
+def uncompress_gz(gz_file_name, uncompressed_file_name):
+    print("____________________________________________________________")
+    print("*** Uncompressing %s" % gz_file_name)
+    uncompressed_file = open(uncompressed_file_name, 'wb')
+    with gzip.open(gz_file_name, 'rb') as src_file:
+        uncompressed_file.write(src_file.read())
+    uncompressed_file.close()
+    print("-> Uncompressed !\n")
+
+def standardize_species_name(species_name):
+    #substitute all capital letters, replace every succession of chars that are not letters to one underscore
+    standard_species_name = re.sub(r'[)]$', '', species_name)
+    standard_species_name = re.sub(r'[ _),-.(=]+ *', '_', standard_species_name)
+    return standard_species_name.lower()
+
+def get_ensembl_url_root(kingdom):
+    print("____________________________________________________________")
+    print("*** Determining Ensembl ftp root url")
+    if kingdom == 'vertebrates':
+        root = 'ftp://ftp.ensembl.org/pub/current_gtf/'
+    else:
+        root = 'ftp://ftp.ensemblgenomes.org/pub/%s/current/' % kingdom
+    print("-> Determined !\n")
+    return root
+
+def test_ensembl_species_exists(kingdom, url, species_name):
+    """
+    Test if a species exist on the ftp & return the species name with the species_line if so.
+    if the species_name matches a single string, then this string will be returned as the species name
+    if the species_name matches several strings, then an error is printed with all the possible species to enter for a new run
+    """
+    print("____________________________________________________________")
+    print ("*** Testing whether %s is referenced in Ensembl %s" % (species_name, kingdom))
+    list_species_file_name = 'species_Ensembl%s%s.txt' % (kingdom[0].upper(), kingdom[1:])
+    if kingdom=='vertebrates':
+        download_file(url, list_species_file_name)
+    else:
+        download_file(url + list_species_file_name, list_species_file_name)
+
+    grep_result = subprocess.Popen(['grep', species_name, list_species_file_name], stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+    species_lines_matched, grep_error = grep_result.communicate()
+    if grep_error != None or species_lines_matched == "":
+        msg = 'The species \'%s\' is not referenced on Ensembl (%s)' % (species_name, kingdom)
+        sys.exit(msg)
+
+    species_lines = species_lines_matched.split('\n')
+    del species_lines[-1]
+    nb_lines = len(species_lines)
+
+    if nb_lines == 1:
+        if kingdom == 'vertebrates':
+            fields = species_lines[0].split(' ')
+            columns = fields[-1].split('\r')
+            found_species_name = columns[0]
+        else:
+            columns = species_lines[0].split('\t')
+            found_species_name = columns[1]
+        if species_name != found_species_name:
+            print('-> \'%s\' has been replace with the complete species name \'%s\'' % (species_name, found_species_name))
+            return found_species_name, species_lines_matched
+        print("-> Referenced !\n")
+        return species_name, species_lines_matched
+    else:
+        list_species = [''] * nb_lines
+        for i in range(0, nb_lines):
+            if kingdom == 'vertebrates':
+                fields = species_lines[i].split(' ')
+                columns = fields[-1].split('\r')
+                list_species[i] = columns[0]
+            else:
+                columns = species_lines[i].split('\t')
+                list_species[i] = columns[1]
+            exact_match = re.search('^%s$' % species_name, list_species[i])
+            if exact_match:
+                print("-> Referenced !\n")
+                return species_name, species_lines[i]
+        msg = ("The string \'%s\' has been matched against the list of Ensembl Species but is not a complete species name.\n"
+                "Please retry with one of these following species names:\n" % species_name)
+        for s in list_species:
+            msg = ("%s- %s\n" % (msg, s))
+        sys.exit(msg)
+
+def get_ensembl_collection(kingdom, species_line):
+    print("*** Extracting the %s_collection of the species" % kingdom)
+    collection_regex = re.compile('%s_.+_collection' % kingdom.lower())
+    collection_match = re.search(collection_regex, species_line)
+    if not collection_match:
+        print("-> Skiped: this species is not classified in a Ensembl %s collection\n" % kingdom)
+        return None
+    print("-> Extracted !\n")
+    return collection_match.group(0)
+
+def get_ensembl_gtf_archive_name(url_dir, species_name):
+    print("____________________________________________________________")
+    print("*** Extracting the gtf archive name of %s" % species_name)
+    gtf_archive_regex = re.compile('%s\..*\.[0-9]+\.gtf\.gz' % species_name, flags = re.IGNORECASE)
+    chr_gtf_archive_regex = re.compile('%s\..*\.[0-9]+\.chr\.gtf\.gz' % species_name, flags = re.IGNORECASE)
+    dir_content = get_page_content(url_dir)
+    gtf_archive_match = re.search(gtf_archive_regex, dir_content)
+    chr_gtf_archive_match = re.search(chr_gtf_archive_regex, dir_content)
+    if not gtf_archive_match:
+        sys.exit('The species is referenced on Ensembl but error of nomenclature led to download failure')
+    if not chr_gtf_archive_match:
+        chr_gtf_archive_name = ""
+    else:
+        chr_gtf_archive_name = chr_gtf_archive_match.group(0)
+    gtf_archive_name = gtf_archive_match.group(0)
+    print("-> Extracted !\n")
+    return gtf_archive_name, chr_gtf_archive_name
+
+def get_ensembl_gtf_archive(kingdom, url, species_name, species_line):
+    if kingdom != 'vertebrates':
+        url = url + 'gtf/' 
+        if kingdom == 'bacteria' or kingdom == 'protists' or kingdom == 'fungi':
+            collection = get_ensembl_collection(kingdom, species_line)
+            if collection != None:
+                url = url + "%s/" % collection
+    final_url = url + species_name + '/'
+    gtf_archive_name, chr_gtf_archive_name = get_ensembl_gtf_archive_name(final_url, species_name)
+    print("____________________________________________________________")
+    print("*** Download the gtf archive of %s" % species_name)
+    download_file(final_url + gtf_archive_name, gtf_archive_name)
+    print("-> Downloaded !\n")
+    if chr_gtf_archive_name:
+        print("*** Download the chr gtf archive of %s" % species_name)
+        download_file(final_url + chr_gtf_archive_name, chr_gtf_archive_name)
+        print("-> Downloaded !\n")
+    return gtf_archive_name, chr_gtf_archive_name
+
+def generate_alfa_indexes(path_to_alfa, gtf_file_name):
+    print("____________________________________________________________")
+    print("*** Generating alfa indexes from %s" % gtf_file_name)
+    alfa_result = subprocess.Popen(['python', path_to_alfa, '-a',  gtf_file_name], stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+    alfa_out, alfa_err = alfa_result.communicate()
+    if alfa_err != None and not re.search('### End of program', alfa_err):
+        msg = 'Generation Failed due an alfa error: %s' % (alfa_err)
+        sys.exit(msg)
+    print("Alfa prompt:\n%s" % alfa_out)
+    print("-> Generated !\n")
+
+def get_data_table_new_entry(gtf_archive_name):
+    info_list = gtf_archive_name.split('.')
+    species = info_list[0]
+    version = info_list[1]
+    release = info_list[2]
+    value = '%s_%s_%s' % (species, version, release)
+    dbkey = value
+    name = '%s: %s (release %s)' % (species, version, release)
+    prefix = '%s.%s.%s' % (species, version, release)
+    entry_dict = { 'species': species, 'version': version, 'release': release, 'value': value, 'dbkey': dbkey, 'name': name, 'prefix': prefix }
+    return entry_dict
+
+def chr_get_data_table_new_entry(chr_gtf_archive_name):
+    info_list = chr_gtf_archive_name.split('.')
+    species = info_list[0]
+    version = info_list[1]
+    release = info_list[2]
+    value = '%s_%s_%s.chr' % (species, version, release)
+    dbkey = value
+    name = '%s: %s (release %s) - Chr' % (species, version, release)
+    prefix = '%s.%s.%s.chr' % (species, version, release)
+    entry_dict = { 'species': species, 'version': version, 'release': release, 'value': value, 'dbkey': dbkey, 'name': name, 'prefix': prefix }
+    return entry_dict
+
+def main():
+    options, args = get_arg()
+    tool_dir = args[0]
+
+    path_to_alfa = os.path.join(tool_dir, 'ALFA.py')
+
+    if options.output_filename == None:
+        msg = 'No json output file specified'
+        sys.exit(msg)
+    output_filename = options.output_filename
+
+    # Interestingly the output file to return is not empty initially.
+    # it contains a dictionary, with notably the path to the dir where the alfa_indexes
+    # are expected to be found
+    params = from_json_string(open(output_filename).read())
+    target_directory = params['output_data'][0]['extra_files_path']
+    os.mkdir(target_directory)
+
+    tmp_dir = tempfile.mkdtemp(prefix='tmp', suffix='')
+    os.chdir(tmp_dir)
+
+    data_manager_dict = {}
+    data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
+    data_manager_dict['data_tables']['alfa_indexes'] = data_manager_dict['data_tables'].get('alfa_indexes', [])
+
+    if options.ensembl_info:
+        kingdom, species_name = options.ensembl_info
+        species_name = standardize_species_name(species_name)
+        url = get_ensembl_url_root(kingdom)
+        species_name, species_line = test_ensembl_species_exists(kingdom, url, species_name)
+        gtf_archive_name, chr_gtf_archive_name = get_ensembl_gtf_archive(kingdom, url, species_name, species_line)
+        data_table_entry = get_data_table_new_entry(gtf_archive_name)
+        gtf_file_name = '%s.gtf' % data_table_entry['prefix']
+        uncompress_gz(gtf_archive_name, gtf_file_name)
+        generate_alfa_indexes(path_to_alfa, gtf_file_name)
+        stranded_index_name = '%s.stranded.index' % data_table_entry['prefix']
+        unstranded_index_name = '%s.unstranded.index' % data_table_entry['prefix']
+        data_manager_dict['data_tables']['alfa_indexes'].append(data_table_entry)
+        if chr_gtf_archive_name:
+            data_table_entry = chr_get_data_table_new_entry(chr_gtf_archive_name)
+            chr_gtf_file_name = '%s.gtf' % data_table_entry['prefix']
+            uncompress_gz(chr_gtf_archive_name, chr_gtf_file_name)
+            generate_alfa_indexes(path_to_alfa, chr_gtf_file_name)
+            chr_stranded_index_name = '%s.stranded.index' % data_table_entry['prefix']
+            chr_unstranded_index_name = '%s.unstranded.index' % data_table_entry['prefix']
+            data_manager_dict['data_tables']['alfa_indexes'].append(data_table_entry)
+
+
+    print("____________________________________________________________")
+    print("*** General Info")
+    print("URL ROOT:\t%s" % url)
+    print("SPECIES:\t%s" % data_table_entry['species'])
+    print("VERSION:\t%s" % data_table_entry['version'])
+    print("RELEASE:\t%s" % data_table_entry['release'])
+    print("VALUE:\t%s" % data_table_entry['value'])
+    print("DBKEY:\t%s" % data_table_entry['dbkey'])
+    print("NAME:\t%s" % data_table_entry['name'])
+    print("PREFIX:\t%s" % data_table_entry['prefix'])
+
+    shutil.copyfile(stranded_index_name, os.path.join(target_directory, stranded_index_name))
+    shutil.copyfile(unstranded_index_name, os.path.join(target_directory, unstranded_index_name))
+
+    if chr_gtf_archive_name:
+        shutil.copyfile(chr_stranded_index_name, os.path.join(target_directory, stranded_index_name))
+        shutil.copyfile(chr_unstranded_index_name, os.path.join(target_directory, unstranded_index_name))
+
+
+    cleanup_before_exit(tmp_dir)
+
+    open(output_filename, 'wb').write(to_json_string(data_manager_dict))
+main()

--- a/data_manager_build_alfa_indexes/data_manager/tool_dependencies.xml	Thu Dec 08 03:43:26 2016 -0500
+++ b/data_manager_build_alfa_indexes/data_manager/tool_dependencies.xml	Thu Dec 21 13:51:22 2017 -0500
@@ -1,3 +1,4 @@
+<?xml version="1.0"?>
 <tool_dependency>
 	<package name="bedtools" version="2.24">
 		<repository changeset_revision="3416a1d4a582" name="package_bedtools_2_24" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
@@ -8,4 +9,4 @@
     <package name="matplotlib" version="1.4">
     	<repository changeset_revision="f7424e1cf115" name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-</tool_dependency>
\ No newline at end of file
+</tool_dependency>