def main():
""" Creates NSIS installer for BLAST command line binaries """
global VERBOSE #IGNORE:W0603
parser = OptionParser("%prog <blast_version> <installation directory>")
parser.add_option("-v",
"--verbose",
action="store_true",
default=False,
help="Show verbose output",
dest="VERBOSE")
options, args = parser.parse_args()
if len(args) != 2:
parser.error("Incorrect number of arguments")
return 1
blast_version, installdir = args
VERBOSE = options.VERBOSE
apps = [
"magicblast.exe", "ncbi-vdb-md.dll", "makeblastdb.exe",
"libgcc_s_seh-1.dll", "libgmp-10.dll", "libgnutls-30.dll",
"libhogweed-4-2.dll", "libnettle-6-2.dll", "libp11-kit-0.dll",
"msvcp140.dll"
# "msvcr120.dll"
]
cwd = os.getcwd()
for app in apps:
app = os.path.join(installdir, "bin", app)
if VERBOSE:
print("Copying", app, "to", cwd)
shutil.copy(app, cwd)
update_blast_version(NSIS_CONFIG, blast_version)
# Copy necessary files to the current working directory
shutil.copy(NSIS_CONFIG, cwd)
license_file = os.path.join(SCRIPT_DIR, "..", "..", "LICENSE")
shutil.copy(license_file, cwd)
# Copy the README file from the parent directory
readme_file = os.path.join(SCRIPT_DIR, "..", "..", "README")
shutil.copy(readme_file, cwd)
for aux_file in ("EnvVarUpdate.nsh", "ncbilogo.ico", "unix2dos.nsh"):
src = os.path.join(SCRIPT_DIR, aux_file)
if VERBOSE:
print("Copying", src, "to", cwd)
shutil.copy(src, cwd)
# makensis is in the path of the script courtesy of the release framework
cmd = "makensis " + os.path.basename(NSIS_CONFIG)
safe_exec(cmd)
installer_dir = os.path.join(installdir, "installer")
if not os.path.exists(installer_dir):
os.makedirs(installer_dir)
installer = extract_installer()
shutil.copy(installer, installer_dir)
def main():
""" Creates NSIS installer for BLAST command line binaries """
global VERBOSE #IGNORE:W0603
parser = OptionParser("%prog <blast_version> <installation directory>")
parser.add_option("-v", "--verbose", action="store_true", default=False,
help="Show verbose output", dest="VERBOSE")
options, args = parser.parse_args()
if len(args) != 2:
parser.error("Incorrect number of arguments")
return 1
blast_version, installdir = args
VERBOSE = options.VERBOSE
apps = [ "cobalt.exe",
"libgcc_s_seh-1.dll",
"libgmp-10.dll",
"libgnutls-30.dll",
"libhogweed-4-2.dll",
"libnettle-6-2.dll",
"libp11-kit-0.dll",
"msvcp120.dll",
"msvcr120.dll"
]
cwd = os.getcwd()
for app in apps:
app = os.path.join(installdir, "bin", app)
if VERBOSE:
print("Copying", app, "to", cwd)
shutil.copy(app, cwd)
update_blast_version(NSIS_CONFIG, blast_version)
# Copy necessary files to the current working directory
shutil.copy(NSIS_CONFIG, cwd)
license_file = os.path.join(SCRIPT_DIR, "..", "..", "LICENSE")
shutil.copy(license_file, cwd)
# Copy the README file from the parent directory
readme_file = os.path.join(SCRIPT_DIR, "..", "..", "README")
shutil.copy(readme_file, cwd)
for aux_file in ("EnvVarUpdate.nsh", "ncbilogo.ico", "unix2dos.nsh"):
src = os.path.join(SCRIPT_DIR, aux_file)
if VERBOSE:
print("Copying", src, "to", cwd)
shutil.copy(src, cwd)
# makensis is in the path of the script courtesy of the release framework
cmd = "makensis " + os.path.basename(NSIS_CONFIG)
safe_exec(cmd)
installer_dir = os.path.join(installdir, "installer")
if not os.path.exists(installer_dir):
os.makedirs(installer_dir)
installer = extract_installer()
shutil.copy(installer, installer_dir)
def main():
""" Creates NSIS installer for BLAST command line binaries """
global VERBOSE #IGNORE:W0603
parser = OptionParser("%prog <blast_version> <installation directory>")
parser.add_option("-v",
"--verbose",
action="store_true",
default=False,
help="Show verbose output",
dest="VERBOSE")
options, args = parser.parse_args()
if len(args) != 2:
parser.error("Incorrect number of arguments")
return 1
blast_version, installdir = args
VERBOSE = options.VERBOSE
apps = [
"blastn.exe", "blastp.exe", "blastx.exe", "tblastx.exe", "tblastn.exe",
"rpsblast.exe", "rpstblastn.exe", "psiblast.exe", "blastdbcmd.exe",
"makeblastdb.exe", "blastdb_aliastool.exe", "segmasker.exe",
"dustmasker.exe", "windowmasker.exe", "legacy_blast.pl"
]
cwd = os.getcwd()
for app in apps:
app = os.path.join(installdir, "bin", app)
if VERBOSE:
print "Copying", app, "to", cwd
copy(app, cwd)
update_blast_version(NSIS_CONFIG, blast_version)
# Copy necessary files to the current working directory
copy(NSIS_CONFIG, cwd)
license_file = os.path.join(SCRIPT_DIR, "..", "..", "LICENSE")
copy(license_file, cwd)
(manual_path, headers) = urlretrieve(MANUAL_URL, "user_manual.pdf")
for aux_file in ("EnvVarUpdate.nsh", "ncbilogo.ico"):
src = os.path.join(SCRIPT_DIR, aux_file)
if VERBOSE:
print "Copying", src, "to", cwd
copy(src, cwd)
# makensis is in the path of the script courtesy of the release framework
cmd = "makensis " + os.path.basename(NSIS_CONFIG)
safe_exec(cmd)
installer_dir = os.path.join(installdir, "installer")
if not os.path.exists(installer_dir):
os.makedirs(installer_dir)
installer = extract_installer()
copy(installer, installer_dir)
def main():
""" Creates NSIS installer for BLAST command line binaries """
global VERBOSE #IGNORE:W0603
parser = OptionParser("%prog <blast_version> <installation directory>")
parser.add_option("-v", "--verbose", action="store_true", default=False,
help="Show verbose output", dest="VERBOSE")
options, args = parser.parse_args()
if len(args) != 2:
parser.error("Incorrect number of arguments")
return 1
blast_version, installdir = args
VERBOSE = options.VERBOSE
apps = [ "blastn.exe",
"blastp.exe",
"blastx.exe",
"tblastx.exe",
"tblastn.exe",
"rpsblast.exe",
"rpstblastn.exe",
"psiblast.exe",
"blastdbcmd.exe",
"makeblastdb.exe",
"makembindex.exe",
"makeprofiledb.exe",
"blastdb_aliastool.exe",
"segmasker.exe",
"dustmasker.exe",
"windowmasker.exe",
"convert2blastmask.exe",
"blastdbcheck.exe",
"blast_formatter.exe",
"deltablast.exe",
"legacy_blast.pl",
"update_blastdb.pl" ]
cwd = os.getcwd()
for app in apps:
app = os.path.join(installdir, "bin", app)
if VERBOSE:
print "Copying", app, "to", cwd
shutil.copy(app, cwd)
update_blast_version(NSIS_CONFIG, blast_version)
# Copy necessary files to the current working directory
shutil.copy(NSIS_CONFIG, cwd)
license_file = os.path.join(SCRIPT_DIR, "..", "..", "LICENSE")
shutil.copy(license_file, cwd)
# User manual PDF is replaced by README.txt
f = open("README.txt", "w")
f.write("Documentation available in http://www.ncbi.nlm.nih.gov/books/NBK1762\n")
f.close()
for aux_file in ("EnvVarUpdate.nsh", "ncbilogo.ico"):
src = os.path.join(SCRIPT_DIR, aux_file)
if VERBOSE:
print "Copying", src, "to", cwd
shutil.copy(src, cwd)
# makensis is in the path of the script courtesy of the release framework
cmd = "makensis " + os.path.basename(NSIS_CONFIG)
safe_exec(cmd)
installer_dir = os.path.join(installdir, "installer")
if not os.path.exists(installer_dir):
os.makedirs(installer_dir)
installer = extract_installer()
shutil.copy(installer, installer_dir)
def main():
""" Creates NSIS installer for BLAST command line binaries """
global VERBOSE #IGNORE:W0603
parser = OptionParser("%prog <blast_version> <installation directory>")
parser.add_option("-v", "--verbose", action="store_true", default=False,
help="Show verbose output", dest="VERBOSE")
options, args = parser.parse_args()
if len(args) != 2:
parser.error("Incorrect number of arguments")
return 1
blast_version, installdir = args
VERBOSE = options.VERBOSE
apps = [ "igblastn.exe", "igblastp.exe" ]
cwd = os.getcwd()
for app in apps:
app = os.path.join(installdir, "bin", app)
if VERBOSE:
print("Copying", app, "to", cwd)
shutil.copy(app, cwd)
update_blast_version(NSIS_CONFIG, blast_version)
# Copy necessary files to the current working directory
shutil.copy(NSIS_CONFIG, cwd)
license_file = os.path.join(SCRIPT_DIR, "..", "..", "LICENSE")
shutil.copy(license_file, cwd)
# Copy the README file from the parent directory
readme_file = os.path.join(SCRIPT_DIR, "..", "..", "README")
shutil.copy(readme_file, cwd)
# Copy the data directories, make sure there are no .svn directories
for directory in ("internal_data", "optional_file"):
newdir = os.path.join(SCRIPT_DIR, "..", "..", "..", "..", "..",
"src", "app", "igblast")
os.chdir(newdir)
dest = os.path.join(cwd, directory)
if VERBOSE:
print("Copying", directory, "to", dest)
shutil.copytree(directory, dest)
os.chdir(cwd)
for root, dirs, files in os.walk(cwd):
for subdir in dirs:
path = os.path.join(root, subdir)
if subdir == ".svn":
if VERBOSE:
print("Removing", path)
shutil.rmtree(path)
for aux_file in ("EnvVarUpdate.nsh", "unix2dos.nsh", "ncbilogo.ico"):
src = os.path.join(SCRIPT_DIR, aux_file)
if VERBOSE:
print("Copying", src, "to", cwd)
shutil.copy(src, cwd)
# makensis is in the path of the script courtesy of the release framework
cmd = "makensis " + os.path.basename(NSIS_CONFIG)
safe_exec(cmd)
installer_dir = os.path.join(installdir, "installer")
if not os.path.exists(installer_dir):
os.makedirs(installer_dir)
installer = extract_installer()
shutil.copy(installer, installer_dir)
def main():
""" Creates NSIS installer for BLAST command line binaries """
global VERBOSE #IGNORE:W0603
parser = OptionParser("%prog <blast_version> <installation directory>")
parser.add_option("-v",
"--verbose",
action="store_true",
default=False,
help="Show verbose output",
dest="VERBOSE")
options, args = parser.parse_args()
if len(args) != 2:
parser.error("Incorrect number of arguments")
return 1
blast_version, installdir = args
VERBOSE = options.VERBOSE
apps = [
"igblastn.exe", "igblastp.exe", "edit_imgt_file.pl", "ncbi-vdb-md.dll",
"makeblastdb.exe"
]
cwd = os.getcwd()
for app in apps:
app = os.path.join(installdir, "bin", app)
if VERBOSE:
print("Copying", app, "to", cwd)
shutil.copy(app, cwd)
dll = os.path.join('\\\\', 'snowman', 'win-coremake', 'Lib', 'ThirdParty',
'nghttp2', 'vs2017.64', '1.33.0', 'bin', 'ReleaseDLL',
'nghttp2.dll')
shutil.copy(dll, cwd)
update_blast_version(NSIS_CONFIG, blast_version)
# Copy necessary files to the current working directory
shutil.copy(NSIS_CONFIG, cwd)
license_file = os.path.join(SCRIPT_DIR, "..", "..", "LICENSE")
shutil.copy(license_file, cwd)
# Copy the README file from the parent directory
readme_file = os.path.join(SCRIPT_DIR, "..", "..", "README")
shutil.copy(readme_file, cwd)
# Copy the data directories, make sure there are no .svn directories
for directory in ("internal_data", "optional_file"):
newdir = os.path.join(SCRIPT_DIR, "..", "..", "..", "..", "..", "src",
"app", "igblast")
os.chdir(newdir)
dest = os.path.join(cwd, directory)
if VERBOSE:
print("Copying", directory, "to", dest)
shutil.copytree(directory, dest)
os.chdir(cwd)
for root, dirs, files in os.walk(cwd):
for subdir in dirs:
path = os.path.join(root, subdir)
if subdir == ".svn":
if VERBOSE:
print("Removing", path)
shutil.rmtree(path)
for aux_file in ("EnvVarUpdate.nsh", "unix2dos.nsh", "ncbilogo.ico"):
src = os.path.join(SCRIPT_DIR, aux_file)
if VERBOSE:
print("Copying", src, "to", cwd)
shutil.copy(src, cwd)
# makensis is in the path of the script courtesy of the release framework
cmd = "makensis " + os.path.basename(NSIS_CONFIG)
safe_exec(cmd)
installer_dir = os.path.join(installdir, "installer")
if not os.path.exists(installer_dir):
os.makedirs(installer_dir)
installer = extract_installer()
shutil.copy(installer, installer_dir)
def main():
""" Creates NSIS installer for BLAST command line binaries """
global VERBOSE #IGNORE:W0603
parser = OptionParser("%prog <blast_version> <installation directory>")
parser.add_option("-v",
"--verbose",
action="store_true",
default=False,
help="Show verbose output",
dest="VERBOSE")
options, args = parser.parse_args()
if len(args) != 2:
parser.error("Incorrect number of arguments")
return 1
blast_version, installdir = args
VERBOSE = options.VERBOSE
apps = [
"blastn.exe", "blastp.exe", "blastx.exe", "tblastx.exe", "tblastn.exe",
"rpsblast.exe", "rpstblastn.exe", "psiblast.exe", "blastdbcmd.exe",
"makeblastdb.exe", "makembindex.exe", "makeprofiledb.exe",
"blastdb_aliastool.exe", "segmasker.exe", "dustmasker.exe",
"windowmasker.exe", "convert2blastmask.exe", "blastdbcheck.exe",
"blast_formatter.exe", "deltablast.exe", "legacy_blast.pl",
"update_blastdb.pl"
]
cwd = os.getcwd()
for app in apps:
app = os.path.join(installdir, "bin", app)
if VERBOSE:
print "Copying", app, "to", cwd
shutil.copy(app, cwd)
update_blast_version(NSIS_CONFIG, blast_version)
# Copy necessary files to the current working directory
shutil.copy(NSIS_CONFIG, cwd)
license_file = os.path.join(SCRIPT_DIR, "..", "..", "LICENSE")
shutil.copy(license_file, cwd)
# User manual PDF is replaced by README.txt
f = open("README.txt", "w")
f.write(
"Documentation available in http://www.ncbi.nlm.nih.gov/books/NBK1762\n"
)
f.close()
for aux_file in ("EnvVarUpdate.nsh", "ncbilogo.ico"):
src = os.path.join(SCRIPT_DIR, aux_file)
if VERBOSE:
print "Copying", src, "to", cwd
shutil.copy(src, cwd)
# makensis is in the path of the script courtesy of the release framework
cmd = "makensis " + os.path.basename(NSIS_CONFIG)
safe_exec(cmd)
installer_dir = os.path.join(installdir, "installer")
if not os.path.exists(installer_dir):
os.makedirs(installer_dir)
installer = extract_installer()
shutil.copy(installer, installer_dir)