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):
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 = []
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 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):
_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, 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, install_methods=None):
if install_methods is None:
install_methods = []
install_methods.append(tools.CondaPackage(TOOL_NAME, executable="prinseq-lite.pl", version=TOOL_VERSION))
target_rel_path = 'prinseq-lite-{ver}/prinseq-lite.pl'.format(ver=TOOL_VERSION)
install_methods.append(
tools.DownloadPackage(
TOOL_URL,
target_rel_path,
post_download_command='chmod +x {}'.format(target_rel_path),
require_executability=True
)
)
tools.Tool.__init__(self, install_methods=install_methods)
