SYMBOL INDEX (940 symbols across 83 files)

FILE: cloudbio/biodata/galaxy.py
  class LocCols (line 37) | class LocCols(object):
    method __init__ (line 40) | def __init__(self, config, dbkey, file_path):
  function _get_tool_conf (line 51) | def _get_tool_conf(env, tool_name):
  function _build_galaxy_loc_line (line 66) | def _build_galaxy_loc_line(env, dbkey, file_path, config, prefix, tool_n...
  function update_loc_file (line 85) | def update_loc_file(env, ref_file, line_parts):
  function prep_locs (line 108) | def prep_locs(env, gid, indexes, config):
  function index_picard (line 129) | def index_picard(ref_file):
  function _finalize_index_seq (line 138) | def _finalize_index_seq(fname):
  function _finalize_index (line 149) | def _finalize_index(idx, fname):
  function rsync_genomes (line 158) | def rsync_genomes(genome_dir, genomes, genome_indexes):
  function _get_galaxy_genomes (line 169) | def _get_galaxy_genomes(gid, genome_dir, genomes, genome_indexes):
  function _rsync_genome_index (line 187) | def _rsync_genome_index(gid, idx, org_dir):

FILE: cloudbio/biodata/genomes.py
  class _DownloadHelper (line 37) | class _DownloadHelper:
    method __init__ (line 38) | def __init__(self):
    method ucsc_name (line 41) | def ucsc_name(self):
    method _exists (line 44) | def _exists(self, fname, seq_dir):
  class UCSCGenome (line 49) | class UCSCGenome(_DownloadHelper):
    method __init__ (line 50) | def __init__(self, genome_name, dl_name=None):
    method ucsc_name (line 58) | def ucsc_name(self):
    method _karyotype_sort (line 61) | def _karyotype_sort(self, xs):
    method _split_multifasta (line 88) | def _split_multifasta(self, fasta_file):
    method download (line 106) | def download(self, seq_dir):
    method _download_zip (line 142) | def _download_zip(self, seq_dir):
  class NCBIRest (line 153) | class NCBIRest(_DownloadHelper):
    method __init__ (line 156) | def __init__(self, name, refs, dl_name=None):
    method download (line 164) | def download(self, seq_dir):
  class VectorBase (line 178) | class VectorBase(_DownloadHelper):
    method __init__ (line 181) | def __init__(self, name, genus, species, strain, release, assembly_typ...
    method download (line 193) | def download(self, seq_dir):
  class EnsemblGenome (line 202) | class EnsemblGenome(_DownloadHelper):
    method __init__ (line 212) | def __init__(self, ensembl_section, release, organism, name, subsectio...
    method download (line 231) | def download(self, seq_dir):
  class BroadGenome (line 239) | class BroadGenome(_DownloadHelper):
    method __init__ (line 244) | def __init__(self, name, target_fasta, dl_name=None):
    method download (line 253) | def download(self, seq_dir):
  class GGDGenome (line 261) | class GGDGenome:
    method __init__ (line 264) | def __init__(self, name):
  function _check_version (line 319) | def _check_version(env):
  function install_data (line 324) | def install_data(config_source, approaches=None):
  function install_data_local (line 332) | def install_data_local(config_source, system_installdir, data_filedir,
  function install_data_s3 (line 357) | def install_data_s3(config_source):
  function install_data_rsync (line 370) | def install_data_rsync(config_source):
  function upload_s3 (line 383) | def upload_s3(config_source):
  function _install_additional_data (line 398) | def _install_additional_data(env, genomes, genome_indexes, config):
  function _get_genomes (line 407) | def _get_genomes(config_source):
  function _if_installed (line 437) | def _if_installed(pname):
  function _make_genome_dir (line 451) | def _make_genome_dir(data_filedir):
  function _make_genome_directories (line 456) | def _make_genome_directories(genomes, data_filedir):
  function _prep_genomes (line 463) | def _prep_genomes(env, genomes, genome_indexes, retrieve_fns, data_filed...
  function _get_ref_seq (line 504) | def _get_ref_seq(manager):
  function _prep_raw_index (line 514) | def _prep_raw_index(env, manager, gid, idx):
  function _data_ngs_genomes (line 521) | def _data_ngs_genomes(env, genomes, genome_indexes):
  function _index_to_galaxy (line 539) | def _index_to_galaxy(env, work_dir, ref_file, gid, genome_indexes, config):
  class CustomMaskManager (line 550) | class CustomMaskManager:
    method __init__ (line 553) | def __init__(self, custom, config):
    method download (line 558) | def download(self, seq_dir):
  function _prep_custom_genome (line 576) | def _prep_custom_genome(custom, genomes, genome_indexes, env):
  function _clean_genome_directory (line 592) | def _clean_genome_directory():
  function _move_seq_files (line 599) | def _move_seq_files(ref_file, base_zips, seq_dir):
  function _index_w_command (line 612) | def _index_w_command(env, dir_name, command, ref_file, pre=None, post=No...
  function _index_twobit (line 631) | def _index_twobit(env, ref_file):
  function _index_bowtie (line 638) | def _index_bowtie(env, ref_file):
  function _index_bowtie2 (line 643) | def _index_bowtie2(env, ref_file):
  function _index_bwa (line 654) | def _index_bwa(env, ref_file):
  function _index_bbmap (line 669) | def _index_bbmap(env, ref_file):
  function _index_bismark (line 681) | def _index_bismark(env, ref_file):
  function _index_maq (line 694) | def _index_maq(env, ref_file):
  function _index_minimap2 (line 705) | def _index_minimap2(env, ref_file):
  function _index_novoalign (line 716) | def _index_novoalign(env, ref_file):
  function _index_novoalign_cs (line 722) | def _index_novoalign_cs(env, ref_file):
  function _index_sam (line 727) | def _index_sam(env, ref_file):
  function _index_star (line 736) | def _index_star(env, ref_file):
  function _index_hisat2 (line 782) | def _index_hisat2(env, ref_file):
  function _index_snap (line 818) | def _index_snap(env, ref_file):
  function _get_path_export (line 829) | def _get_path_export(env):
  function _index_rtg (line 839) | def _index_rtg(env, ref_file):
  function _index_mosaik (line 854) | def _index_mosaik(env, ref_file):
  function _install_with_ggd (line 870) | def _install_with_ggd(env, manager, gid, recipe):
  function _download_s3_index (line 881) | def _download_s3_index(env, manager, gid, idx):
  function _download_genomes (line 891) | def _download_genomes(env, genomes, genome_indexes):
  function _upload_genomes (line 910) | def _upload_genomes(env, genomes, genome_indexes):
  function _upload_to_s3 (line 925) | def _upload_to_s3(tarball, bucket):
  function _tar_directory (line 937) | def _tar_directory(dir, tar_name):
  function _clean_directory (line 948) | def _clean_directory(dir, gid):
  function _data_liftover (line 967) | def _data_liftover(env, lift_over_genomes):
  function _data_uniref (line 996) | def _data_uniref(env):
  function _index_blast_db (line 1023) | def _index_blast_db(work_dir, base_file, db_type):
  function get_index_fn (line 1033) | def get_index_fn(index):
  function prepare_simple_reference (line 1042) | def prepare_simple_reference(ref_file, out_file):
  function is_alt (line 1056) | def is_alt(chrom):
  function is_decoy (line 1059) | def is_decoy(chrom):
  function is_HLA (line 1062) | def is_HLA(chrom):

FILE: cloudbio/biodata/ggd.py
  function install_recipe (line 17) | def install_recipe(base_dir, system_install, recipe_file, genome_build):
  function _has_required_programs (line 34) | def _has_required_programs(programs):
  function _run_recipe (line 54) | def _run_recipe(work_dir, recipe_cmds, recipe_type, system_install):
  function _move_files (line 64) | def _move_files(tmp_dir, final_dir, targets):
  function _read_recipe (line 82) | def _read_recipe(in_file):
  function version_uptodate (line 90) | def version_uptodate(base_dir, recipe):
  function add_version (line 98) | def add_version(base_dir, recipe):
  function _get_versions (line 105) | def _get_versions(base_dir):
  function _get_version_file (line 115) | def _get_version_file(base_dir):
  function tx_tmpdir (line 121) | def tx_tmpdir(base_dir):
  function chdir (line 131) | def chdir(new_dir):

FILE: cloudbio/biodata/rnaseq.py
  function finalize (line 8) | def finalize(genomes, data_filedir):
  function cleanup (line 23) | def cleanup(genomes, data_filedir):

FILE: cloudbio/cloudbiolinux.py
  function _freenx_scripts (line 9) | def _freenx_scripts(env):
  function _cleanup_space (line 27) | def _cleanup_space(env):
  function _configure_gnome (line 37) | def _configure_gnome(env):

FILE: cloudbio/cloudman.py
  function _configure_cloudman (line 36) | def _configure_cloudman(env, use_repo_autorun=False):
  function _configure_desktop (line 55) | def _configure_desktop(env):
  function _configure_novnc (line 74) | def _configure_novnc(env):
  function _configure_vncpasswd (line 111) | def _configure_vncpasswd(env):
  function _setup_env (line 121) | def _setup_env(env):
  function _configure_logrotate (line 157) | def _configure_logrotate(env):
  function _configure_ec2_autorun (line 168) | def _configure_ec2_autorun(env, use_repo_autorun=False):
  function _configure_sge (line 210) | def _configure_sge(env):
  function _configure_hadoop (line 232) | def _configure_hadoop(env):
  function _configure_nfs (line 250) | def _configure_nfs(env):
  function install_s3fs (line 298) | def install_s3fs(env):
  function _cleanup_ec2 (line 308) | def _cleanup_ec2(env):

FILE: cloudbio/config_management/chef.py
  class ChefDict (line 36) | class ChefDict(_AttributeDict):
    method add_recipe (line 37) | def add_recipe(self, recipe):
    method add_role (line 40) | def add_role(self, role):
    method _get_json (line 43) | def _get_json(self):
  function omnibus (line 53) | def omnibus(env):
  function _chef_provision (line 67) | def _chef_provision(env, _omnibus=True):
  function _configure_chef (line 80) | def _configure_chef(env, chef):
  function _build_chef_properties (line 91) | def _build_chef_properties(env, config_file):
  function _parse_json (line 101) | def _parse_json(filename):

FILE: cloudbio/config_management/puppet.py
  function _puppet_provision (line 17) | def _puppet_provision(env, classes):
  function _build_node_def_body (line 28) | def _build_node_def_body(env, classes):
  function _build_class_include (line 37) | def _build_class_include(env, class_name):
  function _property_prefix (line 58) | def _property_prefix(class_name):

FILE: cloudbio/config_management/utils.py
  function config_dir (line 7) | def config_dir(relative_path):
  function build_properties (line 12) | def build_properties(env, prefix, overrides={}):
  function upload_config (line 37) | def upload_config(config, config_folder_names=[], config_files={}):

FILE: cloudbio/custom/bio_general.py
  function install_anaconda (line 12) | def install_anaconda(env):
  function install_emboss (line 42) | def install_emboss(env):
  function install_pgdspider (line 53) | def install_pgdspider(env):
  function install_bio4j (line 72) | def install_bio4j(env):

FILE: cloudbio/custom/bio_nextgen.py
  function install_ucsc_tools (line 23) | def install_ucsc_tools(env):
  function install_kent_tools (line 40) | def install_kent_tools(env):
  function _download_executables (line 52) | def _download_executables(env, base_url, tools):
  function install_featurecounts (line 65) | def install_featurecounts(env):
  function install_bowtie (line 83) | def install_bowtie(env):
  function install_bowtie2 (line 94) | def install_bowtie2(env):
  function install_bfast (line 105) | def install_bfast(env):
  function install_perm (line 118) | def install_perm(env):
  function install_snap (line 136) | def install_snap(env):
  function install_stampy (line 145) | def install_stampy(env):
  function install_gmap (line 165) | def install_gmap(env):
  function _wget_with_cookies (line 173) | def _wget_with_cookies(ref_url, dl_url):
  function install_novoalign (line 181) | def install_novoalign(env):
  function install_novosort (line 211) | def install_novosort(env):
  function install_lastz (line 229) | def install_lastz(env):
  function install_mosaik (line 243) | def install_mosaik(env):
  function install_samtools (line 254) | def install_samtools(env):
  function install_varianttools (line 283) | def install_varianttools(env):
  function install_dwgsim (line 293) | def install_dwgsim(env):
  function install_fastq_screen (line 311) | def install_fastq_screen(env):
  function install_bedtools (line 330) | def install_bedtools(env):
  function install_shrec (line 357) | def install_shrec(env):
  function install_echo (line 377) | def install_echo(env):
  function install_picard (line 388) | def install_picard(env):
  function install_alientrimmer (line 397) | def install_alientrimmer(env):
  function install_rnaseqc (line 407) | def install_rnaseqc(env):
  function install_varscan (line 421) | def install_varscan(env):
  function install_mutect (line 434) | def install_mutect(env):
  function install_bamutil (line 447) | def install_bamutil(env):
  function install_tabix (line 457) | def install_tabix(env):
  function install_disambiguate (line 466) | def install_disambiguate(env):
  function install_grabix (line 473) | def install_grabix(env):
  function install_pbgzip (line 491) | def install_pbgzip(env):
  function install_bamtools (line 505) | def install_bamtools(env):
  function install_ogap (line 522) | def install_ogap(env):
  function install_tophat (line 531) | def install_tophat(env):
  function install_abyss (line 553) | def install_abyss(env):
  function install_transabyss (line 570) | def install_transabyss(env):
  function install_velvet (line 580) | def install_velvet(env):
  function install_ray (line 597) | def install_ray(env):
  function install_trinity (line 609) | def install_trinity(env):
  function install_cortex_var (line 620) | def install_cortex_var(env):
  function install_bcbio_variation (line 653) | def install_bcbio_variation(env):
  function install_macs (line 670) | def install_macs(env):
  function install_hydra (line 682) | def install_hydra(env):
  function install_freec (line 693) | def install_freec(env):
  function install_crisp (line 708) | def install_crisp(env):
  function install_tassel (line 722) | def install_tassel(env):
  function install_stacks (line 747) | def install_stacks(env):
  function install_weblogo (line 757) | def install_weblogo(env):

FILE: cloudbio/custom/bio_proteomics.py
  function install_transproteomic_pipeline (line 28) | def install_transproteomic_pipeline(env):
  function install_omssa (line 64) | def install_omssa(env):
  function install_openms (line 75) | def install_openms(env):
  function install_tint_proteomics_scripts (line 96) | def install_tint_proteomics_scripts(env):
  function install_ms2preproc (line 112) | def install_ms2preproc(env):
  function install_mzmine (line 129) | def install_mzmine(env):
  function install_searchgui (line 148) | def install_searchgui(env):
  function install_psm_eval (line 173) | def install_psm_eval(env):
  function install_peptide_shaker (line 189) | def install_peptide_shaker(env):
  function _get_gist_script (line 208) | def _get_gist_script(env, url):
  function install_mayu (line 215) | def install_mayu(env):
  function install_pride_inspector (line 231) | def install_pride_inspector(env):
  function install_pride_converter2 (line 248) | def install_pride_converter2(env):
  function _unzip_install (line 265) | def _unzip_install(pname, version, url, env, install_fn, dir_name="."):
  function install_superhirn (line 276) | def install_superhirn(env):
  function install_percolator (line 291) | def install_percolator(env):
  function install_pepnovo (line 307) | def install_pepnovo(env):
  function install_crux (line 324) | def install_crux(env):
  function install_fido (line 337) | def install_fido(env):
  function install_ipig (line 357) | def install_ipig(env):
  function install_peptide_to_gff (line 374) | def install_peptide_to_gff(env):
  function install_galaxy_protk (line 389) | def install_galaxy_protk(env):
  function install_myrimatch (line 458) | def install_myrimatch(env):
  function install_pepitome (line 464) | def install_pepitome(env):
  function install_directag (line 470) | def install_directag(env):
  function install_tagrecon (line 476) | def install_tagrecon(env):
  function install_idpqonvert (line 483) | def install_idpqonvert(env):
  function _install_tabb_tool (line 494) | def _install_tabb_tool(env, default_version, download_name, exec_names):

FILE: cloudbio/custom/bio_proteomics_wine.py
  function install_proteomics_wine_env (line 8) | def install_proteomics_wine_env(env):
  function install_multiplierz (line 15) | def install_multiplierz(env):
  function install_proteowizard (line 32) | def install_proteowizard(env):
  function install_morpheus (line 47) | def install_morpheus(env):
  function setup_wine_wrapper (line 60) | def setup_wine_wrapper(env, to):
  function _conf_wine (line 72) | def _conf_wine(env):
  function _get_wine_prefix (line 76) | def _get_wine_prefix(env):
  function _get_wine_user (line 81) | def _get_wine_user(env):

FILE: cloudbio/custom/cloudman.py
  function install_cloudman (line 20) | def install_cloudman(env):
  function install_ec2_autorun (line 33) | def install_ec2_autorun(env):
  function install_novnc (line 37) | def install_novnc(env):
  function install_nginx (line 42) | def install_nginx(env):
  function install_proftpd (line 46) | def install_proftpd(env):
  function install_sge (line 105) | def install_sge(env):

FILE: cloudbio/custom/distributed.py
  function install_pydoop (line 11) | def install_pydoop(env):
  function install_seal (line 21) | def install_seal(env):

FILE: cloudbio/custom/galaxy.py
  function install_galaxy_webapp (line 10) | def install_galaxy_webapp(env):
  function _prep_galaxy (line 16) | def _prep_galaxy(env):

FILE: cloudbio/custom/galaxy_tools.py
  function install_cbl_galaxy_tools (line 8) | def install_cbl_galaxy_tools(env):

FILE: cloudbio/custom/galaxyp.py
  function install_protvis (line 11) | def install_protvis(env):
  function _setup_protvis_env (line 45) | def _setup_protvis_env(env):
  function _setup_protvis_service (line 57) | def _setup_protvis_service(env):

FILE: cloudbio/custom/java.py
  function install_leiningen (line 12) | def install_leiningen(env):

FILE: cloudbio/custom/millstone.py
  function install_unafold (line 9) | def install_unafold(env):

FILE: cloudbio/custom/phylogeny.py
  function install_tracer (line 10) | def install_tracer(env):
  function install_beast (line 32) | def install_beast(env):

FILE: cloudbio/custom/python.py
  function install_bx_python (line 12) | def install_bx_python(env):
  function install_rpy (line 24) | def install_rpy(env):
  function install_netsa_python (line 42) | def install_netsa_python(env):

FILE: cloudbio/custom/shared.py
  function chdir (line 31) | def chdir(new_dir):
  function safe_makedir (line 55) | def safe_makedir(dname):
  function which (line 74) | def which(program, env=None):
  function _if_not_installed (line 94) | def _if_not_installed(pname):
  function _all_cbl_paths (line 112) | def _all_cbl_paths(env, ext):
  function _executable_not_on_path (line 117) | def _executable_not_on_path(pname):
  function _galaxy_tool_install (line 126) | def _galaxy_tool_install(args):
  function _galaxy_tool_present (line 133) | def _galaxy_tool_present(args):
  function _if_not_python_lib (line 137) | def _if_not_python_lib(library):
  function make_tmp_dir_local (line 155) | def make_tmp_dir_local(ext, work_dir):
  function _make_tmp_dir (line 163) | def _make_tmp_dir(ext=None, work_dir=None):
  function __work_dir (line 193) | def __work_dir():
  function _get_expected_file (line 208) | def _get_expected_file(url, dir_name=None, safe_tar=False, tar_file_name...
  function _safe_dir_name (line 227) | def _safe_dir_name(dir_name, need_dir=True):
  function _remote_fetch (line 250) | def _remote_fetch(env, url, out_file=None, allow_fail=False, fix_fn=None...
  function _fetch_and_unpack (line 284) | def _fetch_and_unpack(url, need_dir=True, dir_name=None, revision=None,
  function _configure_make (line 305) | def _configure_make(env):
  function _ac_configure_make (line 313) | def _ac_configure_make(env):
  function _make_copy (line 317) | def _make_copy(find_cmd=None, premake_cmd=None, do_make=True):
  function _get_install (line 330) | def _get_install(url, env, make_command, post_unpack_fn=None, revision=N...
  function _apply_patch (line 343) | def _apply_patch(env, url):
  function _get_install_local (line 348) | def _get_install_local(url, env, make_command, dir_name=None,
  function _symlinked_install_dir (line 378) | def _symlinked_install_dir(pname, version, env, extra_dir=None):
  function _symlinked_dir_exists (line 385) | def _symlinked_dir_exists(pname, version, env, extra_dir=None):
  function _symlinked_shared_dir (line 395) | def _symlinked_shared_dir(pname, version, env, extra_dir=None):
  function _symlinked_java_version_dir (line 419) | def _symlinked_java_version_dir(pname, version, env):
  function _java_install (line 423) | def _java_install(pname, version, url, env, install_fn=None,
  function _python_cmd (line 446) | def _python_cmd(env):
  function _pip_cmd (line 462) | def _pip_cmd(env):
  function _conda_cmd (line 483) | def _conda_cmd(env):
  function _is_anaconda (line 497) | def _is_anaconda(env):
  function _python_make (line 511) | def _python_make(env):
  function _get_installed_file (line 521) | def _get_installed_file(env, local_file):
  function _get_installed_file_contents (line 536) | def _get_installed_file_contents(env, local_file):
  function _write_to_file (line 540) | def _write_to_file(contents, path, mode):
  function _get_bin_dir (line 556) | def _get_bin_dir(env):
  function _get_include_dir (line 564) | def _get_include_dir(env):
  function _get_lib_dir (line 568) | def _get_lib_dir(env):
  function _get_install_subdir (line 572) | def _get_install_subdir(env, subdir):
  function _set_default_config (line 579) | def _set_default_config(env, install_dir, sym_dir_name="default"):
  function _setup_simple_service (line 600) | def _setup_simple_service(service_name):
  function _render_config_file_template (line 614) | def _render_config_file_template(env, name, defaults={}, overrides={}, d...
  function _extend_env (line 657) | def _extend_env(env, defaults={}, overrides={}):
  function _setup_conf_file (line 673) | def _setup_conf_file(env, dest, name, defaults={}, overrides={}, default...
  function _add_to_profiles (line 678) | def _add_to_profiles(line, profiles=[], use_sudo=True):
  function install_venvburrito (line 691) | def install_venvburrito():
  function _create_python_virtualenv (line 703) | def _create_python_virtualenv(env, venv_name, reqs_file=None, reqs_url=N...
  function _create_local_python_virtualenv (line 735) | def _create_local_python_virtualenv(env, venv_name, reqs_file, reqs_url):
  function _create_global_python_virtualenv (line 749) | def _create_global_python_virtualenv(env, venv_name, reqs_file, reqs_url):
  function _get_bitbucket_download_url (line 771) | def _get_bitbucket_download_url(revision, default_repo):
  function _read_boolean (line 779) | def _read_boolean(env, name, default):

FILE: cloudbio/custom/system.py
  function install_homebrew (line 12) | def install_homebrew(env):
  function _linuxbrew_origin_problem (line 64) | def _linuxbrew_origin_problem(brewcmd):
  function install_s3fs (line 75) | def install_s3fs(env):

FILE: cloudbio/custom/vcr.py
  function install_galaxy_vcr (line 20) | def install_galaxy_vcr(env):
  function install_viralassembly (line 62) | def install_viralassembly(env):
  function install_viralassembly_cleanall (line 71) | def install_viralassembly_cleanall(env):
  function _initialize_area_viral (line 81) | def _initialize_area_viral():
  function _add_tools_viral (line 113) | def _add_tools_viral():
  function _add_refs (line 133) | def _add_refs():
  function _initialize_bio_linux (line 138) | def _initialize_bio_linux():
  function install_viralvigor (line 157) | def install_viralvigor(env):
  function install_viralvigor_test (line 166) | def install_viralvigor_test(env):
  function install_viralvigor_validate (line 180) | def install_viralvigor_validate(env):
  function install_viralvigor_cleanall (line 192) | def install_viralvigor_cleanall(env):
  function _initialize_area_vigor (line 203) | def _initialize_area_vigor():
  function _initialize_host (line 246) | def _initialize_host():
  function _add_vigor (line 251) | def _add_vigor():
  function _add_tools_vigor (line 263) | def _add_tools_vigor():
  function _fix_etc_hosts (line 271) | def _fix_etc_hosts():
  function _create_vigor_tempspace_dir (line 277) | def _create_vigor_tempspace_dir():
  function _create_vigor_scratch_dir (line 283) | def _create_vigor_scratch_dir():
  function _create_tools_dir (line 289) | def _create_tools_dir():
  function _add_blast (line 294) | def _add_blast():
  function _add_clustalw (line 304) | def _add_clustalw():
  function install_vicvb (line 314) | def install_vicvb(env):
  function install_vicvb_cleanall (line 337) | def install_vicvb_cleanall(env):
  function _initialize_env (line 351) | def _initialize_env(pipeline):
  function _add_package (line 369) | def _add_package(download_url, filename, install_dir, type):
  function _remove_dir (line 388) | def _remove_dir(dirspec):
  function _unlock_dir (line 395) | def _unlock_dir(dirspec):
  function _apt_get_install (line 401) | def _apt_get_install(tool):
  function _path_exists (line 404) | def _path_exists(path):
  function _path_is_dir (line 411) | def _path_is_dir(path):
  function _set_pre_VCR (line 418) | def _set_pre_VCR(filename,user,group):
  function _get_file_string (line 422) | def _get_file_string(filename,directory):

FILE: cloudbio/custom/versioncheck.py
  function _parse_from_stdoutflag (line 13) | def _parse_from_stdoutflag(out, flag, stdout_index=-1):
  function _clean_version (line 27) | def _clean_version(x):
  function up_to_date (line 38) | def up_to_date(env, cmd, version, args=None, stdout_flag=None,
  function is_version (line 47) | def is_version(env, cmd, version, args=None, stdout_flag=None,
  function get_installed_version (line 56) | def get_installed_version(env, cmd, version, args=None, stdout_flag=None,

FILE: cloudbio/deploy/__init__.py
  function deploy (line 35) | def deploy(options):
  class LocalVmLauncher (line 66) | class LocalVmLauncher:
    method __init__ (line 69) | def __init__(self, options):
    method get_ip (line 72) | def get_ip(self):
    method get_key_file (line 77) | def get_key_file(self):
    method boot_and_connect (line 80) | def boot_and_connect(self):
    method destroy (line 83) | def destroy(self):
    method get_user (line 86) | def get_user(self):
    method list (line 89) | def list(self):
  function _setup_vm (line 93) | def _setup_vm(options, vm_launcher, actions):
  function _expand_actions (line 137) | def _expand_actions(actions):
  function _possible_actions (line 150) | def _possible_actions():
  function _do_perform_action (line 175) | def _do_perform_action(action, action_list):
  function _setup_fabric (line 182) | def _setup_fabric(vm_launcher, ip, options):
  function _setup_cloudbiolinux (line 189) | def _setup_cloudbiolinux(options):
  function _setup_cloudbiolinux_fabric_properties (line 200) | def _setup_cloudbiolinux_fabric_properties(env, options):
  function _setup_image_user_data (line 221) | def _setup_image_user_data(env, options):
  function purge_genomes (line 226) | def purge_genomes():
  function configure_ssh_key (line 230) | def configure_ssh_key(options):
  function setup_biodata (line 242) | def setup_biodata(options):
  function configure_instance (line 256) | def configure_instance(options, actions):
  function install_custom (line 274) | def install_custom(options):
  function install_biolinux (line 279) | def install_biolinux(options):
  function _interactive_ssh (line 285) | def _interactive_ssh(vm_launcher):
  function transfer_files (line 295) | def transfer_files(options):
  function _build_transfer_options (line 300) | def _build_transfer_options(options, destination, user):
  function _do_transfer (line 314) | def _do_transfer(transfer_options, files, compressed_files=[]):
  function purge_tools (line 320) | def purge_tools():
  function install_tools (line 324) | def install_tools(tools_conf):
  function get_boolean_option (line 330) | def get_boolean_option(options, name, default=False):
  function get_main_options_string (line 337) | def get_main_options_string(options, key, default=''):
  function __invoke_plugin_actions (line 344) | def __invoke_plugin_actions(env, actions, action_type, provided_args):
  function __invoke_plugin_action (line 352) | def __invoke_plugin_action(env, action_function, provided_args):
  function __get_plugin_actions (line 358) | def __get_plugin_actions(env, action_type):
  function __get_plugin_modules (line 367) | def __get_plugin_modules(env):
  function __get_plugin_module_names (line 388) | def __get_plugin_module_names():

FILE: cloudbio/deploy/config.py
  function parse_settings (line 6) | def parse_settings(name="deploy/settings.yaml"):
  function _path_from_root (line 10) | def _path_from_root(name):
  function _read_yaml (line 16) | def _read_yaml(yaml_file):

FILE: cloudbio/deploy/main.py
  function main (line 34) | def main():
  function _copy_arg_to_options (line 49) | def _copy_arg_to_options(options, args, property):
  function parse_args (line 55) | def parse_args():
  function parse_settings (line 87) | def parse_settings(name):
  function _read_yaml (line 97) | def _read_yaml(yaml_file):

FILE: cloudbio/deploy/plugins/cloudman.py
  function bundle_cloudman (line 22) | def bundle_cloudman(vm_launcher, options):
  function cloudman_launch (line 53) | def cloudman_launch(vm_launcher, options):
  function sync_cloudman_bucket (line 84) | def sync_cloudman_bucket(vm_launcher, options):
  function _save_file_to_bucket (line 97) | def _save_file_to_bucket(conn, bucket_name, remote_filename, local_file,...
  function __get_bucket_default (line 127) | def __get_bucket_default(options):
  function _prepare_user_data (line 134) | def _prepare_user_data(vm_launcher, cloudman_options):
  function _set_property_if_needed (line 151) | def _set_property_if_needed(user_data, property, value):
  function _get_bucket (line 156) | def _get_bucket(s3_conn, bucket_name):

FILE: cloudbio/deploy/plugins/galaxy.py
  function install_tool (line 4) | def install_tool(options):

FILE: cloudbio/deploy/plugins/gvl.py
  function setup_genomes (line 26) | def setup_genomes(options):
  function setup_taxonomy_data (line 44) | def setup_taxonomy_data():
  function stash_genomes (line 69) | def stash_genomes(where):
  function upload_genomes (line 84) | def upload_genomes(options):
  function purge_genomes (line 94) | def purge_genomes():
  function _cd_indices_parent (line 98) | def _cd_indices_parent():
  function _indices_parent (line 102) | def _indices_parent():
  function _indices_dir_name (line 107) | def _indices_dir_name():
  function galaxy_transfer (line 115) | def galaxy_transfer(vm_launcher, options):
  function create_data_library_for_uploads (line 128) | def create_data_library_for_uploads(options):
  function _seed_at_configure_time (line 140) | def _seed_at_configure_time(options):
  function copy_runtime_properties (line 147) | def copy_runtime_properties(vm_launcher, options):
  function _transfer_genomes (line 162) | def _transfer_genomes(options):
  function wait_for_galaxy (line 170) | def wait_for_galaxy():
  function purge_galaxy (line 178) | def purge_galaxy():
  function setup_galaxy (line 190) | def setup_galaxy(options):
  function _setup_galaxy (line 197) | def _setup_galaxy(options, seed=True):
  function _migrate_galaxy_database (line 211) | def _migrate_galaxy_database():
  function seed_database (line 216) | def seed_database(galaxy_data):
  function seed_workflows (line 223) | def seed_workflows(options):
  function _setup_database_seed_file (line 238) | def _setup_database_seed_file(galaxy_data):
  function _import_histories (line 298) | def _import_histories(user_object, histories):
  function _import_history (line 305) | def _import_history(user_object, history_name):
  function _seed_append (line 311) | def _seed_append(text):
  function _start_galaxy (line 315) | def _start_galaxy():
  function refresh_galaxy (line 321) | def refresh_galaxy(target_galaxy_repo):
  function _setup_galaxy_log_dir (line 326) | def _setup_galaxy_log_dir():
  function _setup_shed_tools_dir (line 330) | def _setup_shed_tools_dir():
  function _make_dir_for_galaxy (line 334) | def _make_dir_for_galaxy(path):
  function _update_galaxy (line 339) | def _update_galaxy(target_galaxy_repo):
  function refresh_galaxy_action (line 346) | def refresh_galaxy_action(vm_launcher, options):
  function setup_image (line 350) | def setup_image(options):
  function _configure_package_holds (line 357) | def _configure_package_holds(options):
  function configure_smtp (line 365) | def configure_smtp(options):
  function configure_sudoers (line 384) | def configure_sudoers(options):
  function configure_MI (line 390) | def configure_MI(env):
  function _required_programs (line 400) | def _required_programs(env):
  function _ensure_export (line 421) | def _ensure_export(command):
  function _start_nginx (line 426) | def _start_nginx(env):
  function _deploy_setup_postgresql (line 433) | def _deploy_setup_postgresql(env):

FILE: cloudbio/deploy/util.py
  function setup_install_dir (line 9) | def setup_install_dir():
  function eval_template (line 19) | def eval_template(env, template_str):
  function ensure_can_sudo_into (line 28) | def ensure_can_sudo_into(user):
  function sudoers_append (line 32) | def sudoers_append(line):
  function start_service (line 36) | def start_service(service_name):
  function wget (line 42) | def wget(url, install_command=sudo, file_name=None):

FILE: cloudbio/deploy/vmlauncher/__init__.py
  class VmLauncher (line 19) | class VmLauncher:
    method __init__ (line 21) | def __init__(self, driver_options_key, options):
    method __set_and_verify_key (line 26) | def __set_and_verify_key(self):
    method _get_driver_options (line 35) | def _get_driver_options(self, driver_option_keys):
    method _driver_options (line 42) | def _driver_options(self):
    method get_key_file (line 45) | def get_key_file(self):
    method boot_and_connect (line 48) | def boot_and_connect(self):
    method _connect_driver (line 56) | def _connect_driver(self):
    method _wait_for_node_info (line 61) | def _wait_for_node_info(self, f):
    method _parse_node_info (line 72) | def _parse_node_info(self, value):
    method _find_node (line 78) | def _find_node(self):
    method destroy (line 85) | def destroy(self, node=None):
    method __get_ssh_client (line 91) | def __get_ssh_client(self):
    method get_user (line 100) | def get_user(self):
    method get_ssh_port (line 103) | def get_ssh_port(self):
    method connect (line 106) | def connect(self, conn, tries=5):
    method list (line 116) | def list(self):
    method _boot (line 120) | def _boot(self):
    method _image_from_id (line 146) | def _image_from_id(self, image_id=None):
    method _get_image_id (line 150) | def _get_image_id(self, image_id=None):
    method _default_image_id (line 158) | def _default_image_id(self):
    method _get_default_size_id (line 161) | def _get_default_size_id(self):
    method _get_size_id_option (line 164) | def _get_size_id_option(self):
    method _size_from_id (line 167) | def _size_from_id(self, size_id):
    method _get_size_id (line 171) | def _get_size_id(self, size_id=None):
    method _boot_new (line 180) | def _boot_new(self, conn):
    method access_id (line 185) | def access_id(self):
    method secret_key (line 188) | def secret_key(self):
    method package_image_name (line 191) | def package_image_name(self):
    method package_image_description (line 195) | def package_image_description(self, default=""):
  class VagrantConnection (line 200) | class VagrantConnection:
    method _ssh_client_connect (line 203) | def _ssh_client_connect(self, ssh_client):
    method destroy_node (line 206) | def destroy_node(self, node=None):
    method list_nodes (line 209) | def list_nodes(self):
  class VagrantNode (line 213) | class VagrantNode:
    method __init__ (line 215) | def __init__(self):
  class VagrantVmLauncher (line 220) | class VagrantVmLauncher(VmLauncher):
    method _get_connection (line 223) | def _get_connection():
    method __init__ (line 226) | def __init__(self, driver_options_key, options):
    method _boot (line 232) | def _boot(self):
    method get_ip (line 236) | def get_ip(self):
    method get_user (line 239) | def get_user(self):
    method package (line 242) | def package(self, **kwds):
  class OpenstackVmLauncher (line 246) | class OpenstackVmLauncher(VmLauncher):
    method get_ip (line 249) | def get_ip(self):
    method _get_size_id_option (line 252) | def _get_size_id_option(self):
    method create_node (line 255) | def create_node(self, hostname, image_id=None, size_id=None, **kwds):
    method _get_connection (line 269) | def _get_connection(self):
    method package (line 288) | def package(self, **kwds):
    method attach_public_ip (line 292) | def attach_public_ip(self, public_ip=None):
  class EucalyptusVmLauncher (line 298) | class EucalyptusVmLauncher(VmLauncher):
    method get_ip (line 300) | def get_ip(self):
    method _get_connection (line 303) | def _get_connection(self):
    method create_node (line 316) | def create_node(self, hostname, image_id=None, size_id=None, **kwds):
  class Ec2VmLauncher (line 330) | class Ec2VmLauncher(VmLauncher):
    method get_ip (line 332) | def get_ip(self):
    method boto_connection (line 335) | def boto_connection(self):
    method boto_s3_connection (line 345) | def boto_s3_connection(self):
    method _default_image_id (line 351) | def _default_image_id(self):
    method package (line 354) | def package(self, **kwds):
    method _create_image (line 361) | def _create_image(self, **kwds):
    method _default_package (line 379) | def _default_package(self, **kwds):
    method _install_ec2_tools (line 386) | def _install_ec2_tools(self):
    method _install_packaging_scripts (line 391) | def _install_packaging_scripts(self):
    method _write_script (line 408) | def _write_script(self, path, contents):
    method _copy_keys (line 413) | def _copy_keys(self):
    method _availability_zone (line 419) | def _availability_zone(self):
    method _get_default_size_id (line 426) | def _get_default_size_id(self):
    method _get_location (line 429) | def _get_location(self):
    method create_node (line 437) | def create_node(self, hostname, image_id=None, size_id=None, location=...
    method attach_public_ip (line 459) | def attach_public_ip(self, public_ip=None):
    method _get_connection (line 464) | def _get_connection(self):
  function build_vm_launcher (line 472) | def build_vm_launcher(options):

FILE: cloudbio/deploy/vmlauncher/transfer.py
  class FileSplitter (line 16) | class FileSplitter:
    method __init__ (line 24) | def __init__(self, chunk_size, destination_directory, callback):
    method split_file (line 29) | def split_file(self, path, compress, transfer_target):
  class TransferTarget (line 59) | class TransferTarget:
    method __init__ (line 61) | def __init__(self, file, precompressed, transfer_manager):
    method should_compress (line 73) | def should_compress(self):
    method split_up (line 76) | def split_up(self):
    method clean (line 79) | def clean(self):
    method compressed_basename (line 83) | def compressed_basename(self):
    method decompressed_basename (line 90) | def decompressed_basename(self):
    method compressed_file (line 98) | def compressed_file(self):
    method build_simple_chunk (line 102) | def build_simple_chunk(self):
  class TransferChunk (line 111) | class TransferChunk:
    method __init__ (line 113) | def __init__(self, chunk_path, transfer_target):
    method clean_up (line 117) | def clean_up(self):
  class FileTransferManager (line 124) | class FileTransferManager:
    method __init__ (line 126) | def __init__(self,
    method handle_chunk (line 152) | def handle_chunk(self, chunk, transfer_target):
    method transfer_files (line 155) | def transfer_files(self, files=[], compressed_files=[]):
    method _setup_workers (line 167) | def _setup_workers(self):
    method _setup_destination_directory (line 172) | def _setup_destination_directory(self):
    method _setup_compress_threads (line 176) | def _setup_compress_threads(self):
    method _setup_decompress_threads (line 180) | def _setup_decompress_threads(self):
    method _setup_transfer_threads (line 184) | def _setup_transfer_threads(self):
    method _launch_threads (line 188) | def _launch_threads(self, num_threads, func):
    method _enqueue_files (line 194) | def _enqueue_files(self, files, compressed_files):
    method _sort_transfer_targets (line 209) | def _sort_transfer_targets(self, transfer_targets):
    method _wait_for_completion (line 216) | def _wait_for_completion(self):
    method _compress_files (line 225) | def _compress_files(self):
    method _decompress_files (line 243) | def _decompress_files(self):
    method _put_files (line 274) | def _put_files(self):
    method _chown (line 291) | def _chown(self, destination):
    method _put_as_user (line 294) | def _put_as_user(self, source, destination):
    method _enqueue_chunk (line 314) | def _enqueue_chunk(self, transfer_chunk):

FILE: cloudbio/deploy/volume.py
  function attach_volumes (line 8) | def attach_volumes(vm_launcher, options, format=False):
  function _mount (line 53) | def _mount(device_id, path):
  function _format_device (line 57) | def _format_device(device_id):
  function detach_volumes (line 61) | def detach_volumes(vm_launcher, options):
  function make_snapshots (line 75) | def make_snapshots(vm_launcher, options):
  function _get_attached (line 88) | def _get_attached(conn, instance_id, device_id, valid_states=['attached']):
  function _make_snapshot (line 99) | def _make_snapshot(vm_launcher, fs_path, desc):
  function _find_mounted_device_id (line 143) | def _find_mounted_device_id(path):
  function _attach (line 149) | def _attach(ec2_conn, instance_id, volume_id, device):
  function _detach (line 175) | def _detach(ec2_conn, instance_id, volume_id):
  function _delete_volume (line 198) | def _delete_volume(ec2_conn, vol_id):
  function _create_snapshot (line 206) | def _create_snapshot(ec2_conn, volume_id, description=None):

FILE: cloudbio/distribution.py
  function _setup_distribution_environment (line 15) | def _setup_distribution_environment(ignore_distcheck=False):
  function _setup_fullpaths (line 66) | def _setup_fullpaths(env):
  function _cloudman_compatibility (line 76) | def _cloudman_compatibility(env):
  function _validate_target_distribution (line 82) | def _validate_target_distribution(dist, dist_name=None):
  function _setup_ubuntu (line 108) | def _setup_ubuntu():
  function _setup_debian (line 126) | def _setup_debian():
  function _setup_deb_general (line 139) | def _setup_deb_general():
  function _setup_centos (line 166) | def _setup_centos():
  function _setup_scientificlinux (line 179) | def _setup_scientificlinux():
  function _setup_macosx (line 187) | def _setup_macosx(env):
  function _setup_nixpkgs (line 195) | def _setup_nixpkgs():
  function _setup_local_environment (line 214) | def _setup_local_environment():
  function _setup_vagrant_environment (line 222) | def _setup_vagrant_environment():
  function _add_source_versions (line 239) | def _add_source_versions(version, sources):
  function _ubuntu_dist_name (line 252) | def _ubuntu_dist_name(env):
  function _debian_dist_name (line 259) | def _debian_dist_name(env):
  function _determine_distribution (line 266) | def _determine_distribution(env):

FILE: cloudbio/fabutils.py
  function local_exists (line 30) | def local_exists(path, use_sudo=False):
  function run_local (line 39) | def run_local(use_sudo=False, capture=False):
  function local_put (line 53) | def local_put(orig_file, new_file):
  function local_sed (line 56) | def local_sed(filename, before, after, limit='', use_sudo=False, backup=...
  function local_comment (line 99) | def local_comment(filename, regex, use_sudo=False, char='#', backup='.ba...
  function _escape_for_regex (line 117) | def _escape_for_regex(text):
  function _expand_path (line 128) | def _expand_path(path):
  function local_contains (line 131) | def local_contains(filename, text, exact=False, use_sudo=False, escape=T...
  function local_append (line 142) | def local_append(filename, text, use_sudo=False, partial=False, escape=T...
  function run_output (line 156) | def run_output(*args, **kwargs):
  function configure_runsudo (line 161) | def configure_runsudo(env):
  function find_cmd (line 198) | def find_cmd(env, cmd, args):
  function quiet (line 212) | def quiet():
  function warn_only (line 218) | def warn_only():

FILE: cloudbio/flavor/__init__.py
  class Flavor (line 11) | class Flavor:
    method __init__ (line 14) | def __init__(self, env):
    method rewrite_config_items (line 20) | def rewrite_config_items(self, name, items):
    method check_distribution (line 28) | def check_distribution(self):
    method check_packages_source (line 35) | def check_packages_source(self):
    method rewrite_apt_sources_list (line 40) | def rewrite_apt_sources_list(self, sources):
    method rewrite_apt_preferences (line 45) | def rewrite_apt_preferences(self, preferences):
    method rewrite_apt_automation (line 50) | def rewrite_apt_automation(self, package_info):
    method rewrite_apt_keys (line 55) | def rewrite_apt_keys(self, standalone, keyserver):
    method apt_upgrade_system (line 59) | def apt_upgrade_system(self, env=None):
    method post_install (line 64) | def post_install(self):
  class Minimal (line 69) | class Minimal(Flavor):
    method __init__ (line 71) | def __init__(self, env):
    method rewrite_config_items (line 76) | def rewrite_config_items(self, name, items):
    method post_install (line 84) | def post_install(self, pkg_install=None):

FILE: cloudbio/flavor/config.py
  function _find_fname (line 7) | def _find_fname(env, fname):
  function get_config_file (line 15) | def get_config_file(env, fname):

FILE: cloudbio/galaxy/__init__.py
  function _setup_users (line 25) | def _setup_users(env):
  function _setup_galaxy_env_defaults (line 39) | def _setup_galaxy_env_defaults(env):
  function _install_galaxy (line 67) | def _install_galaxy(env):
  function _clone_galaxy_repo (line 94) | def _clone_galaxy_repo(env):
  function _setup_galaxy_db (line 128) | def _setup_galaxy_db(env):
  function _get_galaxy_db_configs (line 138) | def _get_galaxy_db_configs(env):
  function _galaxy_db_exists (line 161) | def _galaxy_db_exists(env):
  function _create_galaxy_db (line 194) | def _create_galaxy_db(env):
  function _init_galaxy_db (line 234) | def _init_galaxy_db(env):
  function _configure_galaxy_options (line 255) | def _configure_galaxy_options(env, option_dict=None, prefix="galaxy_univ...
  function _setup_shed_tools_dir (line 281) | def _setup_shed_tools_dir(env):
  function _setup_trackster (line 288) | def _setup_trackster(env):
  function _configure_galaxy_repository (line 305) | def _configure_galaxy_repository(env):
  function _setup_service (line 347) | def _setup_service(env):
  function _setup_xvfb (line 353) | def _setup_xvfb(env):
  function _setup_nginx_service (line 362) | def _setup_nginx_service(env):
  function _install_nginx_standalone (line 369) | def _install_nginx_standalone(env):
  function _install_nginx_package (line 374) | def _install_nginx_package(env):
  function _install_nginx (line 394) | def _install_nginx(env):
  function _get_nginx_modules (line 452) | def _get_nginx_modules(env):
  function _get_nginx_module_upload (line 471) | def _get_nginx_module_upload(env):
  function _get_nginx_module_chunk (line 481) | def _get_nginx_module_chunk(env):
  function _get_nginx_module_ldap (line 492) | def _get_nginx_module_ldap(env):
  function _setup_postgresql (line 498) | def _setup_postgresql(env):
  function _configure_postgresql (line 505) | def _configure_postgresql(env, delete_main_dbcluster=False):
  function _init_postgresql_data (line 532) | def _init_postgresql_data(env):
  function _postgres_running (line 538) | def _postgres_running(env):
  function _make_dir_for_galaxy (line 548) | def _make_dir_for_galaxy(env, path):

FILE: cloudbio/galaxy/applications.py
  function install_fastx_toolkit (line 26) | def install_fastx_toolkit(env):
  function install_maq (line 53) | def install_maq(env):
  function install_macs (line 61) | def install_macs(env):
  function install_megablast (line 71) | def install_megablast(env):
  function install_blast (line 87) | def install_blast(env):
  function install_sputnik (line 104) | def install_sputnik(env):
  function install_taxonomy (line 118) | def install_taxonomy(env):
  function install_add_scores (line 134) | def install_add_scores(env):
  function install_hyphy (line 148) | def install_hyphy(env):
  function install_gatk (line 176) | def install_gatk(env):
  function install_srma (line 207) | def install_srma(env):
  function install_beam (line 226) | def install_beam(env):
  function install_pass (line 242) | def install_pass(env):
  function install_lps_tool (line 258) | def install_lps_tool(env):
  function install_plink (line 277) | def install_plink(env):
  function install_fbat (line 294) | def install_fbat(env):
  function install_haploview (line 311) | def install_haploview(env):
  function install_eigenstrat (line 326) | def install_eigenstrat(env):
  function install_augustus (line 343) | def install_augustus(env):
  function install_picard (line 356) | def install_picard(env):
  function install_fastqc (line 381) | def install_fastqc(env):
  function _update_default (line 399) | def _update_default(env, install_dir):

FILE: cloudbio/galaxy/r.py
  function _install_r_packages (line 18) | def _install_r_packages(tools_conf):
  function _concat_strings (line 34) | def _concat_strings(strings):

FILE: cloudbio/galaxy/tools.py
  function _install_tools (line 19) | def _install_tools(env, tools_conf=None):
  function _tools_conf_path (line 39) | def _tools_conf_path(env):
  function _load_tools_conf (line 51) | def _load_tools_conf(env):
  function _setup_install_dir (line 57) | def _setup_install_dir(env):
  function _install_configured_applications (line 75) | def _install_configured_applications(env, tools_conf):
  function _install_application (line 106) | def _install_application(name, versions, tool_install_dir=None):
  function _install_tool (line 151) | def _install_tool(env, name, version, requirement_name, bin_dirs=["bin"]...
  function _build_tool_env (line 159) | def _build_tool_env(env, name, version, tool_install_dir):
  function __check_conditional (line 173) | def __check_conditional(conf_dict):
  class AttributeDict (line 188) | class AttributeDict(dict):
  function _install_galaxy_config (line 201) | def _install_galaxy_config(tool_env, bin_dirs, env_vars):

FILE: cloudbio/galaxy/utils.py
  function _read_boolean (line 5) | def _read_boolean(env, name, default):
  function _chown_galaxy (line 11) | def _chown_galaxy(env, path):
  function _dir_is_empty (line 21) | def _dir_is_empty(path):

FILE: cloudbio/libraries.py
  function r_library_installer (line 9) | def r_library_installer(config):
  function _make_install_script (line 36) | def _make_install_script(out_file, config):

FILE: cloudbio/manifest.py
  function create (line 24) | def create(out_dir, tooldir="/usr/local", fetch_remote=False):
  function _get_custom_pkg_info (line 37) | def _get_custom_pkg_info(name, fn):
  function write_custom_pkg_info (line 64) | def write_custom_pkg_info(out_dir, tooldir):
  function write_brew_pkg_info (line 93) | def write_brew_pkg_info(out_dir, tooldir):
  function get_r_pkg_info (line 120) | def get_r_pkg_info():
  function write_r_pkg_info (line 136) | def write_r_pkg_info(out_dir):
  function _get_conda_envs (line 148) | def _get_conda_envs(conda_bin):
  function get_python_pkg_info (line 153) | def get_python_pkg_info():
  function _resolve_latest_pkg (line 180) | def _resolve_latest_pkg(pkgs):
  function write_python_pkg_info (line 187) | def write_python_pkg_info(out_dir):
  function _get_pkg_popcon (line 202) | def _get_pkg_popcon():
  function get_debian_pkg_info (line 212) | def get_debian_pkg_info(fetch_remote=False):
  function write_debian_pkg_info (line 227) | def write_debian_pkg_info(out_dir, fetch_remote=False):

FILE: cloudbio/package/__init__.py
  function _configure_and_install_native_packages (line 7) | def _configure_and_install_native_packages(env, pkg_install):
  function _connect_native_packages (line 40) | def _connect_native_packages(env, pkg_install, lib_install):
  function _get_shell_exports (line 59) | def _get_shell_exports(env):
  function _print_shell_exports (line 63) | def _print_shell_exports(env):
  function _create_local_virtualenv (line 71) | def _create_local_virtualenv(target_dir):

FILE: cloudbio/package/brew.py
  function install_packages (line 24) | def install_packages(env, to_install=None, packages=None):
  function _remove_old (line 64) | def _remove_old(env, config_file):
  function _safe_update (line 75) | def _safe_update(env, brew_cmd, formula_repos, cur_taps):
  function _git_stash (line 94) | def _git_stash(env, brew_cmd):
  function _get_current_pkgs (line 122) | def _get_current_pkgs(env, brew_cmd):
  function _safe_unlink_pkg (line 136) | def _safe_unlink_pkg(env, pkg_str, brew_cmd):
  function _safe_link_pkg (line 143) | def _safe_link_pkg(env, pkg_str, brew_cmd):
  function _safe_uninstall_pkg (line 150) | def _safe_uninstall_pkg(env, pkg_str, brew_cmd):
  function _install_pkg (line 157) | def _install_pkg(env, pkg_str, brew_cmd, ipkgs):
  function _install_pkg_version (line 170) | def _install_pkg_version(env, pkg, args, version, brew_cmd, ipkgs):
  function _git_pkg_version (line 200) | def _git_pkg_version(env, brew_cmd, pkg, version):
  function _git_cmd_for_pkg_version (line 222) | def _git_cmd_for_pkg_version(env, brew_cmd, pkg, version):
  function _latest_pkg_version (line 234) | def _latest_pkg_version(env, brew_cmd, pkg, devel=False):
  function _get_brew_install_cmd (line 255) | def _get_brew_install_cmd(brew_cmd, env, pkg):
  function _install_pkg_latest (line 267) | def _install_pkg_latest(env, pkg, args, brew_cmd, ipkgs):
  function _custom_unlink (line 302) | def _custom_unlink(env, brew_cmd, pkg):
  function _get_pkg_version_args (line 318) | def _get_pkg_version_args(pkg_str):
  function _install_bottle (line 335) | def _install_bottle(env, brew_cmd, pkg, ipkgs):
  function _install_brew_baseline (line 366) | def _install_brew_baseline(env, brew_cmd, ipkgs, packages):
  function _brew_cmd (line 404) | def _brew_cmd(env):

FILE: cloudbio/package/conda.py
  function install_packages (line 29) | def install_packages(env, to_install=None, packages=None):
  function _install_env_pkgs (line 44) | def _install_env_pkgs(env_name, env_packages, conda_bin, conda_envs, cha...
  function install_in (line 83) | def install_in(conda_bin, system_installdir, config_file=None, packages=...
  function _initial_base_install (line 148) | def _initial_base_install(conda_bin, env_packages, check_channels):
  function _link_bin (line 186) | def _link_bin(package, system_installdir, conda_info, conda_bin, conda_p...
  function _do_link (line 224) | def _do_link(orig_file, final_file):
  function _split_by_condaenv (line 244) | def _split_by_condaenv(packages):
  function _get_conda_envs (line 262) | def _get_conda_envs(conda_bin):
  function _create_environments (line 266) | def _create_environments(conda_bin, packages):
  function _clean_environment (line 300) | def _clean_environment(env_dir):

FILE: cloudbio/package/cpan.py
  function install_packages (line 12) | def install_packages(env):
  function _install_from_cpan (line 22) | def _install_from_cpan(env, cpanm_cmd, package):
  function _install_from_url (line 48) | def _install_from_url(env, cpanm_cmd, package):

FILE: cloudbio/package/deb.py
  function _apt_packages (line 11) | def _apt_packages(to_install=None, pkg_list=None):
  function _add_apt_gpg_keys (line 51) | def _add_apt_gpg_keys():
  function _setup_apt_automation (line 77) | def _setup_apt_automation():
  function _setup_apt_sources (line 125) | def _setup_apt_sources():

FILE: cloudbio/package/nix.py
  function _setup_nix_sources (line 9) | def _setup_nix_sources():
  function _nix_packages (line 40) | def _nix_packages(to_install):

FILE: cloudbio/package/rpm.py
  function _yum_packages (line 10) | def _yum_packages(to_install):
  function _partition_all (line 30) | def _partition_all(n, iterable):
  function _setup_yum_bashrc (line 40) | def _setup_yum_bashrc():
  function _setup_yum_sources (line 52) | def _setup_yum_sources():

FILE: cloudbio/package/shared.py
  function _yaml_to_packages (line 6) | def _yaml_to_packages(yaml_file, to_install=None, subs_yaml_file=None, n...
  function _filter_subs_packages (line 47) | def _filter_subs_packages(initial, subs, namesort=True):

FILE: cloudbio/utils.py
  class ColorFormatter (line 17) | class ColorFormatter(logging.Formatter):
    method __init__ (line 27) | def __init__(self, fmt="%(name)s %(levelname)s: %(msg)s"):
    method format (line 30) | def format(self, record):
  function _setup_logging (line 49) | def _setup_logging(env):
  function _update_biolinux_log (line 59) | def _update_biolinux_log(env, target, flavor):
  function _configure_fabric_environment (line 85) | def _configure_fabric_environment(env, flavor=None, fabricrc_loader=None,
  function _setup_flavor (line 96) | def _setup_flavor(env, flavor):
  function _parse_fabricrc (line 132) | def _parse_fabricrc(env):
  function _create_local_paths (line 147) | def _create_local_paths(env):

FILE: contrib/flavor/boinc/boincflavor.py
  class BoincFlavor (line 8) | class BoincFlavor(Flavor):
    method __init__ (line 11) | def __init__(self, env):
    method rewrite_config_items (line 15) | def rewrite_config_items(self, name, packages):
    method post_install (line 22) | def post_install(self):

FILE: contrib/flavor/millstone/installer.py
  function install_millstone (line 274) | def install_millstone(env):

FILE: contrib/flavor/millstone/millstoneflavor.py
  class MillstoneFlavor (line 14) | class MillstoneFlavor(Flavor):
    method __init__ (line 15) | def __init__(self, env):
    method rewrite_config_items (line 19) | def rewrite_config_items(self, name, packages):
    method post_install (line 22) | def post_install(self):

FILE: contrib/flavor/neuro/neuro.py
  class NeuroFlavor (line 12) | class NeuroFlavor(Flavor):
    method __init__ (line 17) | def __init__(self, env):
    method rewrite_config_items (line 20) | def rewrite_config_items(self, name, packages):
    method rewrite_apt_sources_list (line 28) | def rewrite_apt_sources_list(self, name, sources):

FILE: contrib/flavor/phylogeny/phylogenyflavor.py
  class PhylogenyFlavor (line 9) | class PhylogenyFlavor(Flavor):
    method __init__ (line 12) | def __init__(self, env):
    method rewrite_config_items (line 16) | def rewrite_config_items(self, name, packages):
    method post_install (line 28) | def post_install(self):

FILE: contrib/flavor/pjotrp/biotest/biotestflavor.py
  class BioTestFlavor (line 8) | class BioTestFlavor(Flavor):
    method __init__ (line 11) | def __init__(self, env):
    method rewrite_config_items (line 15) | def rewrite_config_items(self, name, items):
    method post_install (line 31) | def post_install(self):

FILE: contrib/flavor/seal/sealflavor.py
  class SealFlavor (line 44) | class SealFlavor(Flavor):
    method __init__ (line 47) | def __init__(self, env):
    method rewrite_config_items (line 51) | def rewrite_config_items(self, name, packages):
    method post_install (line 63) | def post_install(self):

FILE: data_fabfile.py
  function setup_environment (line 35) | def setup_environment():
  function _add_defaults (line 42) | def _add_defaults():
  function install_data (line 56) | def install_data(config_source=CONFIG_FILE):
  function install_data_raw (line 62) | def install_data_raw(config_source=CONFIG_FILE):
  function install_data_s3 (line 68) | def install_data_s3(config_source=CONFIG_FILE, do_setup_environment=True):
  function install_data_rsync (line 74) | def install_data_rsync(config_source=CONFIG_FILE):
  function install_data_ggd (line 80) | def install_data_ggd(recipe, organism):
  function upload_s3 (line 89) | def upload_s3(config_source=CONFIG_FILE):

FILE: deploy/test_install_galaxy_tool.py
  function __clone_cloudbiolinux (line 28) | def __clone_cloudbiolinux(cbl_config):
  function install_cbl_tool (line 44) | def install_cbl_tool(tool_name, tool_version, install_dir, cbl_config={}):

FILE: fabfile.py
  function install_biolinux (line 48) | def install_biolinux(target=None, flavor=None):
  function _perform_install (line 82) | def _perform_install(target=None, flavor=None, more_custom_add=None):
  function _print_time_stats (line 135) | def _print_time_stats(action, event, prev_time=None):
  function _check_fabric_version (line 158) | def _check_fabric_version():
  function _custom_installs (line 165) | def _custom_installs(to_install, ignore=None, add=None):
  function _provision_chef_recipes (line 180) | def _provision_chef_recipes(to_install, ignore=None):
  function _provision_puppet_classes (line 193) | def _provision_puppet_classes(to_install, ignore=None):
  function install_chef_recipe (line 206) | def install_chef_recipe(recipe, automated=False, flavor=None):
  function install_puppet_class (line 230) | def install_puppet_class(classes, automated=False, flavor=None):
  function install_custom (line 251) | def install_custom(p, automated=False, pkg_to_group=None, flavor=None):
  function _install_custom (line 291) | def _install_custom(p, pkg_to_group=None):
  function install_brew (line 298) | def install_brew(p=None, version=None, flavor=None, automated=False):
  function install_conda (line 313) | def install_conda(p=None, flavor=None, automated=False):
  function _custom_install_function (line 323) | def _custom_install_function(env, p, pkg_to_group):
  function _read_main_config (line 352) | def _read_main_config():
  function _python_library_installer (line 374) | def _python_library_installer(config):
  function _ruby_library_installer (line 395) | def _ruby_library_installer(config):
  function _perl_library_installer (line 414) | def _perl_library_installer(config):
  function _haskell_library_installer (line 430) | def _haskell_library_installer(config):
  function install_libraries (line 446) | def install_libraries(language):
  function _do_library_installs (line 454) | def _do_library_installs(to_install):

FILE: installed_files/ec2autorun.py
  function _setup_logging (line 41) | def _setup_logging():
  function _get_user_data (line 56) | def _get_user_data():
  function _get_bucket_name (line 83) | def _get_bucket_name(cluster_name, access_key):
  function _isurl (line 89) | def _isurl(path):
  function _get_s3_conn (line 98) | def _get_s3_conn(ud):
  function _bucket_exists (line 125) | def _bucket_exists(s3_conn, bucket_name):
  function _remote_file_exists (line 143) | def _remote_file_exists(s3_conn, bucket_name, remote_filename):
  function _save_file_to_bucket (line 159) | def _save_file_to_bucket(s3_conn, bucket_name, remote_filename, local_fi...
  function _get_file_from_bucket (line 190) | def _get_file_from_bucket(s3_conn, bucket_name, remote_filename, local_f...
  function _get_file_from_url (line 212) | def _get_file_from_url(url):
  function _get_boot_script (line 228) | def _get_boot_script(ud):
  function _run_boot_script (line 282) | def _run_boot_script(boot_script_name):
  function _create_basic_user_data_file (line 295) | def _create_basic_user_data_file():
  function _get_default_bucket_url (line 310) | def _get_default_bucket_url(ud=None):
  function _user_exists (line 326) | def _user_exists(username):
  function _allow_password_logins (line 333) | def _allow_password_logins(passwd):
  function _handle_freenx (line 347) | def _handle_freenx(passwd):
  function _handle_empty (line 367) | def _handle_empty():
  function _handle_url (line 376) | def _handle_url(url):
  function _merge (line 384) | def _merge(specific, default):
  function _load_user_data (line 398) | def _load_user_data(user_data):
  function _handle_yaml (line 417) | def _handle_yaml(user_data):
  function _parse_user_data (line 501) | def _parse_user_data(ud):
  function main (line 509) | def main():

FILE: test/testlib/test_biolinux.rb
  function test_for_completed_install (line 3) | def test_for_completed_install(ssh, hostname, box_name)
  function test_for_match (line 13) | def test_for_match(ssh, cmd, regex)
  function test_in_path (line 20) | def test_in_path(ssh, program)
  function test_phylogeny_flavor (line 24) | def test_phylogeny_flavor(vagrant)

FILE: test/testlib/test_support.rb
  function run (line 2) | def run cmd
  function error (line 12) | def error msg

FILE: utils/cbl_exome_setup.py
  function main (line 22) | def main():
  function setup_custom_galaxy (line 37) | def setup_custom_galaxy():
  function install_latest_pipeline (line 50) | def install_latest_pipeline():
  function run_nextgen_analysis_server (line 73) | def run_nextgen_analysis_server(pp_config, work_dir, work_user):
  function setup_rabbitmq (line 83) | def setup_rabbitmq(vhost, user, passwd):
  function read_pp_config (line 92) | def read_pp_config(fname):
  function read_ampq_config (line 99) | def read_ampq_config(fname):
  function update_amqp_config (line 107) | def update_amqp_config(fname, hostname):
  function wait_until_mounted (line 128) | def wait_until_mounted(fname):
  function chdir (line 144) | def chdir(new_dir):

FILE: utils/cbl_installed_software.py
  function main (line 11) | def main():

FILE: utils/convert_to_xz.py
  function main (line 17) | def main(bucket_name):
  function download_parallel (line 33) | def download_parallel(url):
  function swap_s3_item (line 43) | def swap_s3_item(xz_file, bucket, orig_s3_item):
  function gzip_to_xz (line 52) | def gzip_to_xz(local_file):

FILE: utils/get_biolinux_packages.py
  function main (line 16) | def main():
  function get_package (line 37) | def get_package(pname):

FILE: utils/get_yum_packages.py
  function main (line 14) | def main(orig_file):
  function get_yum_package (line 27) | def get_yum_package(pname):

FILE: utils/images_and_snapshots.py
  function images_and_snapshots (line 6) | def images_and_snapshots(owner):
  function _data_libraries (line 18) | def _data_libraries(conn, owner):
  function _sorted_images (line 33) | def _sorted_images(images, start_name):

FILE: utils/prep_esp_hg38.py
  function main (line 16) | def main():
  function _add_contigs (line 49) | def _add_contigs(out_handle, ref_file):

FILE: utils/prepare_cosmic.py
  function main (line 37) | def main(cosmic_version, bcbio_genome_dir, overwrite=False, clean=False):
  function remove_installed (line 99) | def remove_installed(installed_file, installed_link):
  function make_links (line 116) | def make_links(installed_file, installed_link):
  function map_coords_to_ucsc (line 124) | def map_coords_to_ucsc(grc_cosmic, ref_file, out_file):
  function _rename_to_ucsc (line 138) | def _rename_to_ucsc(line):
  function combine_cosmic (line 147) | def combine_cosmic(fnames, ref_file, out_file):
  function sort_to_ref (line 157) | def sort_to_ref(fname, ref_file, add_chr):
  function get_cosmic_vcf_files (line 178) | def get_cosmic_vcf_files(genome_build, cosmic_version, clean):
  function remove_cosmic_directory (line 213) | def remove_cosmic_directory(installed_directory):
  function update_version_file (line 217) | def update_version_file(bcbio_base, version):

FILE: utils/prepare_dbsnp.py
  function main (line 17) | def main(org):
  function fix_info (line 48) | def fix_info(parts):
  function fix_chrom (line 54) | def fix_chrom(parts):
  function get_file (line 65) | def get_file(x, ftp_dir, conn):
  function karyotype_sort (line 74) | def karyotype_sort(xs):

FILE: utils/prepare_tx_gff.py
  function which (line 55) | def which(program):
  function manual_ucsc_ensembl_map (line 71) | def manual_ucsc_ensembl_map(org_build):
  function ucsc_ensembl_map_via_download (line 84) | def ucsc_ensembl_map_via_download(org_build):
  function ensembl_to_ucsc (line 93) | def ensembl_to_ucsc(ensembl_dict, ucsc_dict, org_build):
  function ucsc_ensembl_map_via_query (line 108) | def ucsc_ensembl_map_via_query(org_build):
  function parse_sequence_dict (line 190) | def parse_sequence_dict(fasta_dict):
  class SequenceDictParser (line 202) | class SequenceDictParser(object):
    method __init__ (line 204) | def __init__(self, fname):
    method _get_sequences_in_genome_dict (line 207) | def _get_sequences_in_genome_dict(self):
    method _sequence_from_line (line 212) | def _sequence_from_line(self, line):
  function get_ensembl_dict (line 217) | def get_ensembl_dict(org_build):
  function get_ucsc_dict (line 227) | def get_ucsc_dict(org_build):
  function make_fasta_dict (line 234) | def make_fasta_dict(fasta_file):
  function _download_ensembl_genome (line 241) | def _download_ensembl_genome(org_build):
  function write_version (line 254) | def write_version(build=None, gtf_file=None, build_version=None):
  function main (line 265) | def main(org_build, gtf_file, genome_fasta, genome_dir, cores, args):
  function make_hisat2_splicesites (line 326) | def make_hisat2_splicesites(gtf_file):
  function make_transcriptome_fasta (line 340) | def make_transcriptome_fasta(gtf_file, genome_fasta):
  function clean_gtf (line 346) | def clean_gtf(gtf_file, genome_fasta):
  function get_genome_fasta (line 372) | def get_genome_fasta(org_build):
  function get_fasta_names (line 377) | def get_fasta_names(genome_fasta):
  function cleanup (line 384) | def cleanup(work_dir, out_dir, org_build):
  function create_tarball (line 395) | def create_tarball(tar_dirs, org_build):
  function upload_to_s3 (line 403) | def upload_to_s3(tarball):
  function genepred_to_UCSC_table (line 409) | def genepred_to_UCSC_table(genepred):
  function gtf_to_genepred (line 430) | def gtf_to_genepred(gtf):
  function gtf_to_refflat (line 438) | def gtf_to_refflat(gtf):
  function gtf_to_bed (line 451) | def gtf_to_bed(gtf):
  function _is_selenocysteine (line 469) | def _is_selenocysteine(feature):
  function db_to_gtf (line 474) | def db_to_gtf(db, out_file):
  function make_miso_events (line 485) | def make_miso_events(gtf, org_build):
  function prepare_bowtie_index (line 503) | def prepare_bowtie_index(genome_fasta, bowtie_dir):
  function prepare_tophat_index (line 511) | def prepare_tophat_index(gtf, org_build, genome_fasta):
  function prepare_kallisto_index (line 526) | def prepare_kallisto_index(transcriptome_fasta, org_build):
  function prepare_sailfish_index (line 539) | def prepare_sailfish_index(transcriptome_fasta, org_build):
  function _create_dummy_fastq (line 551) | def _create_dummy_fastq():
  function gtf_to_interval (line 561) | def gtf_to_interval(gtf, genome_fasta):
  function prepare_mask_gtf (line 580) | def prepare_mask_gtf(gtf):
  function prepare_rrna_gtf (line 603) | def prepare_rrna_gtf(gtf):
  function prepare_tx2gene (line 625) | def prepare_tx2gene(gtf):
  function _biotype_lookup_fn (line 640) | def _biotype_lookup_fn(gtf):
  function prepare_tx_gff (line 661) | def prepare_tx_gff(build, org_name):
  function _remap_gff (line 675) | def _remap_gff(base_gff, name_map):
  function _download_ensembl_gff (line 693) | def _download_ensembl_gff(build, org_name):
  function _create_tiny_gffutils_db (line 705) | def _create_tiny_gffutils_db(gtf_file):
  function subfeature_handler (line 725) | def subfeature_handler(f):
  function guess_disable_infer_extent (line 743) | def guess_disable_infer_extent(gtf_file):
  function guess_id_spec (line 755) | def guess_id_spec(gtf_file):
  function _get_gtf_db (line 773) | def _get_gtf_db(gtf):
  function _dexseq_preparation_path (line 791) | def _dexseq_preparation_path():
  function prepare_dexseq (line 806) | def prepare_dexseq(gtf):

FILE: utils/prioritize/az300_to_bed.py
  function read_targets (line 20) | def read_targets(in_file):
  function get_gene_info (line 28) | def get_gene_info(cur_symbol):
  function find_missing_targets (line 44) | def find_missing_targets(missing, in_file, genome):
  function write_from_transcript_file (line 61) | def write_from_transcript_file(targets, ref_dir, genome, out_handle):
  function write_from_remap_names (line 72) | def write_from_remap_names(targets, ref_dir, genome, out_handle, in_file):
  function write_from_gene_info (line 84) | def write_from_gene_info(targets, genome, out_handle):

FILE: utils/prioritize/prep_ccds_genes.py
  function main (line 12) | def main(in_file, out_name, fai_file):
  function get_chrom (line 24) | def get_chrom(chrom):
  function split_coords (line 28) | def split_coords(coords):

FILE: utils/query_conda_deps.py
  function main (line 11) | def main(config_file):
  function get_dependencies (line 28) | def get_dependencies(channel, package):

FILE: utils/s3_multipart_upload.py
  function main (line 40) | def main(transfer_file, bucket_name, s3_key_name=None, use_rr=True,
  function s3_has_uptodate_file (line 65) | def s3_has_uptodate_file(bucket, transfer_file, s3_key_name):
  function upload_cb (line 77) | def upload_cb(complete, total):
  function _standard_transfer (line 81) | def _standard_transfer(bucket, s3_key_name, transfer_file, use_rr):
  function map_wrap (line 88) | def map_wrap(f):
  function mp_from_ids (line 94) | def mp_from_ids(mp_id, mp_keyname, mp_bucketname, profile=None):
  function transfer_part (line 111) | def transfer_part(mp_id, mp_keyname, mp_bucketname, i, part, profile):
  function _multipart_upload (line 120) | def _multipart_upload(bucket, s3_key_name, tarball, mb_size, use_rr=True,
  function multimap (line 143) | def multimap(cores=None):