def sample1_se_tiny_fq(tmpdir_factory):
"""
Single-end FASTQ file with 1010 reads
"""
d = tmpdir_for_func(tmpdir_factory)
fn = 'rnaseq_samples/sample1/sample1.tiny_R1.fastq.gz'
return _download_file(fn, d)
def sample1_pe_tiny_fq(tmpdir_factory):
pair = []
d = tmpdir_for_func(tmpdir_factory)
for fn in [
'rnaseq_samples/sample1/sample1.tiny_R1.fastq.gz',
'rnaseq_samples/sample1/sample1.tiny_R2.fastq.gz'
]:
pair.append(_download_file(fn, d))
return pair
def sample1_se_tiny_bam(tmpdir_factory):
d = tmpdir_for_func(tmpdir_factory)
fn = 'rnaseq_samples/sample1/sample1.tiny.single.sorted.bam'
return _download_file(fn, d)
def sample1_pe_bam(tmpdir_factory):
d = tmpdir_for_func(tmpdir_factory)
fn = 'rnaseq_samples/sample1/sample1.small.paired.sorted.bam'
return _download_file(fn, d)
def annotation_refflat(tmpdir_factory):
fn = 'annotation/dm6.small.refflat'
d = tmpdir_for_func(tmpdir_factory)
return _download_file(fn, d)
def annotation(tmpdir_factory):
fn = 'annotation/dm6.small.gtf'
d = tmpdir_for_func(tmpdir_factory)
return _download_file(fn, d)
def dm6_fa(tmpdir_factory):
fn = 'seq/dm6.small.fa'
d = tmpdir_for_func(tmpdir_factory)
return _download_file(fn, d)
def transcriptome(tmpdir_factory):
d = tmpdir_for_func(tmpdir_factory)
fn = 'seq/dm6.small.transcriptome.fa'
return _download_file(fn, d)
def sample1_se_fq(tmpdir_factory):
d = tmpdir_for_func(tmpdir_factory)
fn = 'rnaseq_samples/sample1/sample1.small_R1.fastq.gz'
return _download_file(fn, d)
def install_cntk(target_dir):
logger.info("Begin to install CNTK(BrainScript) ...")
if SysInfo.os != TOOLSFORAI_OS_WIN and SysInfo.os != TOOLSFORAI_OS_LINUX:
logger.warning(
"CNTK(BrainScript) is not supported on your OS, we recommend 64-bit Windows-10 OS or 64-bit Linux OS."
)
# fail_install.append("CNTK(BrainScript)")
return False
if SysInfo.cuda == "8.0":
ver = "2.3.1"
else:
ver = "2.5.1"
target_version = 'CNTK-{0}'.format(ver.replace('.', '-'))
logger.debug(
"In install_cntk(), target_version: {0}".format(target_version))
version = utils._get_cntk_version(target_dir)
if target_version == version:
logger.info('CNTK(BrainScript)-{0} is already installed.'.format(ver))
return True
logger.debug('In install_cntk(), target_dir: {0}'.format(target_dir))
cntk_root = os.path.join(target_dir, 'cntk')
if os.path.isdir(cntk_root):
try:
shutil.rmtree(cntk_root)
except:
logger.error(
'Fail to install CNTK(BrainScript), the error message: can not remove old version in directory {0}.'
'Please manually remove old version, and run the installer script again.'
.format(cntk_root))
# fail_install.append("CNTK(BrainScript)")
return False
if not os.path.isdir(target_dir):
try:
os.makedirs(target_dir)
except:
logger.error(
'Fail to install CNTK(BrainScript), the error message: can not create directory {0}.'
'Please check if there is permission for creating directory.'.
format(target_dir))
# fail_install.append("CNTK(BrainScript)")
return False
cntk_file_name = "{}-{}-64bit-{}.{}".format(
target_version,
"Windows" if SysInfo.os == TOOLSFORAI_OS_WIN else "Linux",
"GPU" if SysInfo.gpu else "CPU-Only",
"zip" if SysInfo.os == TOOLSFORAI_OS_WIN else "tar.gz")
logger.debug(
"In install_cntk(), cntk_file_name: {0}".format(cntk_file_name))
cntk_url = "https://cntk.ai/BinaryDrop/{0}".format(cntk_file_name)
logger.debug("In install_cntk(), cntk_url: {0}".format(cntk_url))
cntk_file_path = os.path.join(target_dir, cntk_file_name)
logger.debug(
"In install_cntk(), cntk_file_path: {0}".format(cntk_file_path))
if SysInfo.os == TOOLSFORAI_OS_WIN:
download_dir = cntk_file_path
elif SysInfo.os == TOOLSFORAI_OS_LINUX:
download_dir = os.path.join(r"/tmp", cntk_file_name)
skip_downloading = False
if not skip_downloading:
if not utils._download_file(cntk_url, download_dir):
logger.error(
'Fail to install CNTK(BrainScript), the error message: cannot download {0}.'
'Please check your network.'.format(cntk_url))
# fail_install.append("CNTK(BrainScript)")
return False
if (not (utils._unzip_file(download_dir, target_dir)
if SysInfo.os == TOOLSFORAI_OS_WIN else utils._extract_tar(
download_dir, target_dir))):
logger.error(
'Fail to install CNTK(BrainScript), the error message: cannot decompress the downloaded package.'
)
# fail_install.append("CNTK(BrainScript)")
return False
if not skip_downloading:
if os.path.isfile(download_dir):
os.remove(download_dir)
if (SysInfo.os == TOOLSFORAI_OS_WIN):
suc = install_cntk_win(cntk_root)
else:
suc = install_cntk_linux(cntk_root)
version = utils._get_cntk_version(target_dir)
if (suc and (target_version == version)):
logger.info("Install CNTK(BrainScript) successfully!")
logger.warning(
"Please open a new terminal to make the updated Path environment variable effective."
)
return True
else:
logger.error("Fail to install CNTK(BrainScript).")
logger.warning(
"Please manually install {0} and update PATH environment.".format(
target_version))
logger.warning(
"You can reference this link based on your OS: https://docs.microsoft.com/en-us/cognitive-toolkit/Setup-CNTK-on-your-machine"
)
# fail_install.append("CNTK(BrainScript)")
return False
return True
