def __init__(self, install_methods=None):
if install_methods is None:
install_methods = []
mafft_os = get_mafft_os()
mafft_bitdepth = get_mafft_bitdepth()
mafft_archive_extension = get_mafft_archive_extension(mafft_os)
binaryPath = get_mafft_binary_path(mafft_os, mafft_bitdepth)
binaryDir = get_mafft_binary_path(mafft_os,
mafft_bitdepth,
full=False)
target_rel_path = '{binPath}'.format(binPath=binaryPath)
verify_command = 'cd {dir}/mafft-{ver}/{bin_dir} && {dir}/mafft-{ver}/{binPath} --version > /dev/null 2>&1'.format(
dir=util.file.get_build_path(),
ver=TOOL_VERSION,
binPath=binaryPath,
bin_dir=binaryDir)
destination_dir = '{dir}/mafft-{ver}'.format(
dir=util.file.get_build_path(), ver=TOOL_VERSION)
install_methods.append(
tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION))
install_methods.append(
tools.DownloadPackage(
TOOL_URL.format(ver=TOOL_VERSION,
os=mafft_os,
ext=mafft_archive_extension),
target_rel_path=target_rel_path,
destination_dir=destination_dir,
verifycmd=verify_command))
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None):
self.subtool_name = self.subtool_name if hasattr(self, "subtool_name") else "bmtagger.sh"
if install_methods is None:
install_methods = []
install_methods.append(tools.CondaPackage(TOOL_NAME, executable=self.subtool_name, version=TOOL_VERSION))
install_methods.append(DownloadBmtagger(self.subtool_name))
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None):
if install_methods is None:
path = _get_vphaser2_path()
install_methods = []
install_methods.append(tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION))
install_methods.append(tools.PrexistingUnixCommand(path))
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None):
unwanted = [
'blast_formatter', 'blastdb_aliastool', 'blastdbcheck',
'blastdbcmd', 'convert2blastmask', 'deltablast', 'legacy_blast.pl',
'makembindex', 'makeprofiledb', 'psiblast', 'rpsblast',
'rpstblastn', 'segmasker', 'tblastn', 'tblastx',
'update_blastdb.pl', 'windowmasker'
]
self.subtool_name = self.subtool_name if hasattr(
self, "subtool_name") else "blastn"
if install_methods is None:
target_rel_path = 'ncbi-blast-2.2.29+/bin/' + self.subtool_name
install_methods = []
install_methods.append(
tools.CondaPackage(TOOL_NAME,
executable=self.subtool_name,
version=TOOL_VERSION))
install_methods.append(
tools.DownloadPackage(
get_url(),
target_rel_path,
post_download_command=' '.join(
['rm'] +
['ncbi-blast-2.2.29+/bin/' + f for f in unwanted]),
post_download_ret=None))
#tools.Tool.__init__(self, install_methods=install_methods)
super(BlastTools, self).__init__(install_methods=install_methods)
def __init__(self, install_methods=None):
if install_methods is None:
install_methods = []
install_methods.append(
tools.CondaPackage(TOOL_NAME, version=CONDA_TOOL_VERSION))
muscle_os = get_muscle_os()
if muscle_os != 'src':
install_methods.append(
tools.DownloadPackage(
TOOL_URL.format(ver=TOOL_VERSION, os=muscle_os),
'muscle{}_{}'.format(TOOL_VERSION, muscle_os),
verifycmd='{}/muscle{}_{} -version > /dev/null 2>&1'.
format(util.file.get_build_path(), TOOL_VERSION,
muscle_os)))
# install_methods.append(
# tools.DownloadPackage(TOOL_URL.format(ver=TOOL_VERSION,
# os=muscle_os),
# 'muscle{}/src/muscle'.format(TOOL_VERSION),
# post_download_command='cd muscle{}/src; make -s'.format(TOOL_VERSION),
# verifycmd='{}/muscle{}/src/muscle -version > /dev/null 2>&1'.format(
# util.file.get_build_path(), TOOL_VERSION)))
install_methods.append(
tools.DownloadPackage(
UNRELEASED_URL,
'muscle{}/src/muscle'.format(TOOL_VERSION),
post_download_command='cd muscle{}/src; make -s'.format(
TOOL_VERSION),
verifycmd='{}/muscle{}/src/muscle -version > /dev/null 2>&1'
.format(util.file.get_build_path(), TOOL_VERSION)))
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None):
self.subtool_name = self.subtool_name if hasattr(self, "subtool_name") else None
self.subtool_name_on_broad = self.subtool_name_on_broad if hasattr(self, "subtool_name_on_broad") else None
if install_methods is None:
install_methods = []
install_methods.append(tools.CondaPackage(TOOL_NAME, executable=self.subtool_name, version=TOOL_VERSION))
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, path=None, license_path=None):
self.tool_version = None
install_methods = []
for novopath in [path, os.environ.get('NOVOALIGN_PATH'), '']:
if novopath is not None:
install_methods.append(
tools.PrexistingUnixCommand(
os.path.join(novopath, 'novoalign'),
require_executability=True
)
)
post_verify_command = None
for novo_license_path in [license_path, os.environ.get("NOVOALIGN_LICENSE_PATH"), '']:
if novo_license_path is not None and os.path.isfile(novo_license_path):
# called relative to the conda bin/ directory
uname = os.uname()
# we ideally want the "update" copy operation
# but only GNU cp has it. On OSX, the license will be copied each time.
if uname[0] == 'Darwin':
copy_operation = ''
else:
copy_operation = '-u'
post_verify_command = "cp {copy_operation} {lic_path} ./".format(copy_operation=copy_operation, lic_path=novo_license_path)
break # if we've found a license file, stop looking
install_methods.append(tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION, post_verify_command=post_verify_command))
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None):
if install_methods is None:
install_methods = [
tools.CondaPackage(TOOL_NAME,
executable="mummer",
version=tool_version)
]
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None):
if not install_methods:
install_methods = []
install_methods.append(
tools.CondaPackage(TOOL_NAME,
version=CONDA_TOOL_VERSION,
executable='ktImportTaxonomy'))
super(Krona, self).__init__(install_methods=install_methods)
def __init__(self, install_methods=None):
if install_methods is None:
install_methods = []
install_methods.append(
tools.CondaPackage(TOOL_NAME,
executable="Trinity",
version=CONDA_TOOL_VERSION))
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None):
if install_methods is None:
install_methods = [
tools.CondaPackage(TOOL_NAME,
version=TOOL_VERSION,
executable='Gap2Seq')
]
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None):
if install_methods is None:
install_methods = []
install_methods.append(
tools.CondaPackage(TOOL_NAME, version=CONDA_TOOL_VERSION))
install_methods.append(
DownloadAndBuildMuscleUnreleased(ver=TOOL_VERSION))
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None):
if install_methods is None:
install_methods = [
tools.CondaPackage(TOOL_NAME,
version=TOOL_VERSION,
executable='spades.py',
verifycmd='spades.py --version')
]
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None, extra_genomes=None):
extra_genomes = extra_genomes or ['KJ660346.2']
if not install_methods:
install_methods = []
install_methods.append(tools.CondaPackage(TOOL_NAME, executable="snpEff", version=TOOL_VERSION))
install_methods.append(DownloadAndTweakSnpEff(URL, extra_genomes))
self.known_dbs = set()
self.installed_dbs = set()
super(SnpEff, self).__init__(install_methods=install_methods)
def __init__(self, install_methods=None):
if install_methods is None:
install_methods = []
install_methods.append(
tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION))
install_methods.append(
DownloadGzipBinary(TOOL_URL.format(os=get_bintype()),
'tbl2asn'))
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None):
self.subtool_name = self.subtool_name if hasattr(self, "subtool_name") else None
if install_methods is None:
install_methods = []
install_methods.append(tools.CondaPackage(TOOL_NAME, executable=self.subtool_name, version=TOOL_VERSION))
target_rel_path = 'picard-tools-{}/picard.jar'.format(TOOL_VERSION)
install_methods.append(tools.DownloadPackage(TOOL_URL, target_rel_path, require_executability=False))
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None):
if install_methods is None:
install_methods = []
install_methods.append(
tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION))
install_methods.append(
tools.DownloadPackage(TOOL_URL,
'Trimmomatic-0.32/trimmomatic-0.32.jar',
require_executability=False))
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None):
if not install_methods:
install_methods = []
install_methods.append(tools.CondaPackage("jellyfish1", version=JELLYFISH_VERSION))
install_methods.append(
DownloadAndInstallJellyfish(
JELLYFISH_URL, os.path.join(JELLYFISH_DIR, 'bin', 'jellyfish')
)
)
super().__init__(install_methods=install_methods)
def __init__(self, install_methods=None):
self.subtool_name = self.subtool_name if hasattr(
self, "subtool_name") else "kraken"
if not install_methods:
install_methods = []
install_methods.append(
tools.CondaPackage(TOOL_NAME,
executable=self.subtool_name,
version=TOOL_VERSION))
super(Kraken, self).__init__(install_methods=install_methods)
def __init__(self, install_methods=None):
if install_methods is None:
install_methods = []
install_methods.append(
tools.CondaPackage(TOOL_NAME,
executable="Trinity",
version=CONDA_TOOL_VERSION))
install_methods.append(
DownloadAndBuildTrinity(url, TRINITY_VERSION + '/Trinity.pl'))
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None):
if not install_methods:
install_methods = []
install_methods.append(
tools.CondaPackage(TOOL_NAME,
version=CONDA_TOOL_VERSION,
executable='ktImportTaxonomy',
patches=[('opt/krona/updateTaxonomy.sh',
'krona_updateTaxonomy.sh.patch')
]))
super().__init__(install_methods=install_methods)
def __init__(self, install_methods=None):
self.subtool_name = self.subtool_name if hasattr(
self, "subtool_name") else "kraken"
if not install_methods:
install_methods = []
install_methods.append(
tools.CondaPackage('kraken',
executable=self.subtool_name,
version=KRAKEN_VERSION,
channel='broad-viral'))
super(Kraken, self).__init__(install_methods=install_methods)
def __init__(self, install_methods=None):
unwanted = [
'blast_formatter', 'blastdb_aliastool', 'blastdbcheck', 'blastdbcmd', 'convert2blastmask', 'deltablast',
'legacy_blast.pl', 'makembindex', 'makeprofiledb', 'psiblast', 'rpsblast', 'rpstblastn', 'segmasker',
'tblastn', 'tblastx', 'update_blastdb.pl', 'windowmasker'
]
self.subtool_name = self.subtool_name if hasattr(self, "subtool_name") else "blastn"
if install_methods is None:
install_methods = []
install_methods.append(tools.CondaPackage(TOOL_NAME, executable=self.subtool_name, version=TOOL_VERSION))
super(BlastTools, self).__init__(install_methods=install_methods)
def __init__(self, install_methods=None):
_log.debug("BWA_DIR: %s", BWA_DIR)
if install_methods is None:
install_methods = []
install_methods.append(
tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION))
install_methods.append(
tools.DownloadPackage(
URL,
os.path.join(BWA_DIR, 'bwa'),
post_download_command="cd {}; make -s".format(BWA_DIR)))
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, path=None):
self.tool_version = None
install_methods = []
for novopath in [path, os.environ.get('NOVOALIGN_PATH'), '']:
if novopath is not None:
install_methods.append(
tools.PrexistingUnixCommand(os.path.join(
novopath, 'novoalign'),
require_executability=True))
install_methods.append(
tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION))
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods = None):
if install_methods is None:
install_methods = []
os_type = self.get_os_type()
binaryPath = self.get_selscan_binary_path( os_type )
target_rel_path = 'selscan-{ver}/{binPath}'.format(ver=TOOL_VERSION, binPath=binaryPath)
verify_command = '{dir}/selscan-{ver}/{binPath} --help > /dev/null 2>&1'.format(dir=util.file.get_build_path(),
ver=TOOL_VERSION, binPath=binaryPath)
install_methods.append(tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION))
super(SelscanBaseTool, self).__init__(install_methods=install_methods)
def __init__(self, install_methods=None):
if install_methods is None:
install_methods = [
tools.CondaPackage(TOOL_NAME, version=tool_version),
tools.DownloadPackage(
url.format(ver=tool_version),
'MUMmer{}'.format(tool_version),
post_download_command='cd MUMmer{}; make -s'.format(
tool_version),
verifycmd='{}/MUMmer{}/mummer -h > /dev/null 2>&1'.format(
util.file.get_build_path(), tool_version))
]
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None):
if install_methods is None:
install_methods = []
install_methods.append(tools.CondaPackage(TOOL_NAME, version=CONDA_TOOL_VERSION))
install_methods.append(
tools.DownloadPackage(
TOOL_URL,
'samtools-{}/samtools'.format(TOOL_VERSION),
post_download_command='cd samtools-{}; make -s'.format(
TOOL_VERSION
)
)
)
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, path=None):
self.tool_version = None
install_methods = []
for jarpath in [path, os.environ.get('GATK_PATH')]:
if jarpath:
if not jarpath.endswith('.jar'):
jarpath = os.path.join(jarpath, 'GenomeAnalysisTK.jar')
install_methods.append(
tools.PrexistingUnixCommand(
jarpath,
verifycmd='java -jar %s --version &> /dev/null' %
jarpath,
verifycode=0,
require_executability=False))
install_methods.append(
tools.CondaPackage(TOOL_NAME,
version=TOOL_VERSION,
executable="gatk3"))
install_methods.append(
tools.CondaPackage(TOOL_NAME,
version=TOOL_VERSION,
executable="gatk"))
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods = None):
super(SelscanNormTool, self).__init__()
if install_methods is None:
install_methods = []
os_type = self.get_os_type()
normBinaryPath = self.get_selscan_binary_path( os_type, binaryName="norm" )
target_norm_rel_path = 'selscan-{ver}/{binPath}'.format(ver=TOOL_VERSION, binPath=normBinaryPath)
verify_norm_command = '{dir}/selscan-{ver}/{binPath} --help > /dev/null 2>&1'.format(dir=util.file.get_build_path(),
ver=TOOL_VERSION, binPath=normBinaryPath)
install_methods.append(tools.CondaPackage(TOOL_NAME, executable="norm", version=TOOL_VERSION))
tools.Tool.__init__(self, install_methods = install_methods)
