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)