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How to use install_path method in molecule
Best Python code snippet using molecule_python
pvw-setup
Source:pvw-setup 
1#!/usr/bin/python2import urllib2, sys, os, zipfile, subprocess, json, shutil3# ===================================================================4# ParaView files / URLs5# ===================================================================6url = "http://paraview.org/files/v4.1/"7application = {8 'osx' : "ParaView-4.1.0-Darwin-64bit-Lion-Python27.dmg",9 'linux32': "ParaView-4.1.0-Linux-32bit-glibc-2.3.6.tar.gz",10 'linux64': "ParaView-4.1.0-Linux-64bit-glibc-2.3.6.tar.gz",11 'win32' : "ParaView-4.1.0-Windows-32bit.zip",12 'win64' : "ParaView-4.1.0-Windows-64bit.zip"13 }14data = "ParaViewData-v4.1.zip"15documentation = "ParaView-API-docs-v4.1.zip"16# ===================================================================17# Download helper18# ===================================================================19def download(url, file_name):20 u = urllib2.urlopen(url)21 f = open(file_name, 'wb')22 meta = u.info()23 file_size = int(meta.getheaders("Content-Length")[0])24 print "\nDownloading: %s Bytes: %s" % (file_name, file_size)25 file_size_dl = 026 block_sz = 819227 while True:28 buffer = u.read(block_sz)29 if not buffer:30 break31 file_size_dl += len(buffer)32 f.write(buffer)33 status = r"%10d [%3.2f%%]" % (file_size_dl, file_size_dl * 100. / file_size)34 status = status + chr(8)*(len(status)+1)35 print status,36 f.close()37# ===================================================================38def unzip(file, destination):39 zfile = zipfile.ZipFile(file)40 for name in zfile.namelist():41 fullPath = os.path.join(destination, name)42 if name.endswith('/'):43 os.makedirs(fullPath)44 else:45 if not os.path.exists(os.path.dirname(fullPath)):46 os.makedirs(os.path.dirname(fullPath))47 fd = open(fullPath,"w")48 fd.write(zfile.read(name))49 fd.close()50 status = r" Unzip "51 if len(name) > 70:52 status += "[..]" + name[-70:]53 else:54 status += name55 status += " "*(80-len(status))56 status = status + chr(8)*(len(status)+1)57 print status,58 print59# ===================================================================60# Get data locally61# ===================================================================62print63install_path = os.getcwd()64q = ''65while q != 'y' and q != 'yes':66 if q == 'n' or q == 'no':67 install_path = raw_input("Enter ParaViewWeb install path: ")68 if q == 'q' or q == 'quit':69 sys.exit("We did nothing")70 q = raw_input("Is ParaViewWeb install path correct? (%s) yes/no/quit: " % install_path)71print "\nInstalling ParaViewWeb inside:", install_path72if not os.path.exists(install_path):73 os.makedirs(install_path)74download_path = os.path.join(install_path, "download")75if not os.path.exists(download_path):76 os.makedirs(download_path)77# Download data + doc78data_file = os.path.join(download_path, data)79documentation_file = os.path.join(download_path, documentation)80if not os.path.exists(data_file):81 download(url + data, data_file)82if not os.path.exists(documentation_file):83 download(url + documentation, documentation_file)84# Download only for all OS for future setup85app_type = raw_input("\nWhich system? [osx, linux32, linux64, win32, win64, all]: ")86if app_type == 'all':87 print "\nThis will only download all OS files for future install."88 for app_type in application:89 app_file = os.path.join(download_path, application[app_type])90 if not os.path.exists(app_file):91 download(url + application[app_type], app_file)92 sys.exit("Downloading done")93else:94 # Check files and download them if needed95 app_file = os.path.join(download_path, application[app_type])96 if not os.path.exists(app_file):97 download(url + application[app_type], app_file)98print99# ===================================================================100# Unpack data101# ===================================================================102if app_type == 'osx':103 if not os.path.exists(os.path.join(install_path, 'paraview.app')):104 print " => Unpack ParaView"105 # Mount DMG106 retvalue = subprocess.check_output(['hdiutil', 'attach', app_file])107 list = retvalue.split()108 dir_path = list[-1]109 dmg_mount = list[-3]110 # Copy application111 os.system("cp -r %s/paraview.app %s/paraview.app" % (dir_path, install_path))112 # Unmount dmg113 subprocess.check_output(["hdiutil", "detach", dmg_mount])114elif not os.path.exists(os.path.join(install_path, 'paraview')):115 print " => Unpack ParaView"116 if app_type == 'linux32':117 os.system("cd %s;tar xvzf %s" % (install_path, app_file))118 os.rename(os.path.join(install_path, "ParaView-4.1.0-Linux-32bit"), os.path.join(install_path, "paraview"))119 elif app_type == 'linux64':120 os.system("cd %s;tar xvzf %s" % (install_path, app_file))121 os.rename(os.path.join(install_path, "ParaView-4.1.0-Linux-64bit"), os.path.join(install_path, "paraview"))122 else:123 # Unzip app124 unzip(app_file, install_path)125 if app_type == 'win64':126 os.rename(os.path.join(install_path, "ParaView-4.1.0-Windows-64bit"), os.path.join(install_path, "paraview"))127 if app_type == 'win32':128 os.rename(os.path.join(install_path, "ParaView-4.1.0-Windows-32bit"), os.path.join(install_path, "paraview"))129# ===================================================================130# Structure directories131# ===================================================================132# /data133if not os.path.exists(os.path.join(install_path, 'data')):134 print " => Unpack data"135 unzip(data_file, install_path)136 src = os.path.join(install_path, data[:-4], "Data")137 dst = os.path.join(install_path, 'data')138 os.rename(src, dst)139 shutil.rmtree(os.path.join(install_path, data[:-4]))140# /www141if not os.path.exists(os.path.join(install_path, 'www')):142 print " => Unpack Web"143 unzip(documentation_file, install_path)144 src = os.path.join(install_path, documentation[:-4], 'js-doc')145 dst = os.path.join(install_path, 'www')146 os.rename(src, dst)147 src = os.path.join(install_path, documentation[:-4], 'lib')148 dst = os.path.join(install_path, 'www/lib')149 os.rename(src, dst)150 src = os.path.join(install_path, documentation[:-4], 'ext')151 dst = os.path.join(install_path, 'www/ext')152 os.rename(src, dst)153 src = os.path.join(install_path, documentation[:-4], 'apps')154 dst = os.path.join(install_path, 'www/apps')155 os.rename(src, dst)156 print " => Clean web directory"157 shutil.rmtree(os.path.join(install_path, documentation[:-4]))158# /bin159if not os.path.exists(os.path.join(install_path, 'bin')):160 os.makedirs(os.path.join(install_path, 'bin'))161# /conf162if not os.path.exists(os.path.join(install_path, 'conf')):163 os.makedirs(os.path.join(install_path, 'conf'))164# /logs165if not os.path.exists(os.path.join(install_path, 'logs')):166 os.makedirs(os.path.join(install_path, 'logs'))167# ===================================================================168# Configure169# ===================================================================170print " => Configure local instance"171python_exec = ''172base_python_path = ''173if app_type == 'osx':174 python_exec = os.path.join(install_path, 'paraview.app/Contents/bin/pvpython')175 base_python_path = os.path.join(install_path, 'paraview.app/Contents/Python/')176elif app_type == 'linux32' or app_type == 'linux64':177 python_exec = os.path.join(install_path, 'paraview/bin/pvpython')178 base_python_path = os.path.join(install_path, 'paraview/lib/paraview-4.1/site-packages/')179elif app_type == 'win32' or app_type == 'win64':180 python_exec = os.path.join(install_path, 'paraview/bin/pvpython.exe')181 base_python_path = os.path.join(install_path, 'paraview/lib/paraview-4.1/site-packages/')182default_launcher_config = {183 "sessionData" : {184 "updir": "/Home"185 },186 "resources" : [ { "host" : "localhost", "port_range" : [9001, 9003] } ],187 "properties" : {188 "python_exec": python_exec,189 "python_path": base_python_path,190 "data": os.path.join(install_path, 'data'),191 },192 "configuration": {193 "host": "localhost",194 "port": 8080,195 "endpoint": "paraview",196 "content": os.path.join(install_path, 'www'),197 "proxy_file": os.path.join(install_path, 'conf/proxy.conf'),198 "sessionURL" : "ws://${host}:${port}/ws",199 "timeout" : 5,200 "log_dir" : os.path.join(install_path, 'logs'),201 "upload_dir" : os.path.join(install_path, 'data'),202 "fields" : ["file", "host", "port", "updir"]203 },204 "apps": {205 "pipeline": {206 "cmd": ["${python_exec}", "${python_path}/paraview/web/pv_web_visualizer.py", "--port", "${port}", "--data-dir", "${data}" ]207 },208 "loader": {209 "cmd": ["${python_exec}", "${python_path}/paraview/web/pv_web_file_loader.py", "--port", "${port}", "--data-dir", "${data}"]210 },211 "data_prober": {212 "cmd": ["${python_exec}", "${python_path}/paraview/web/pv_web_data_prober.py", "--port", "${port}", "--data-dir", "${data}"]213 }214 }215}216with open(os.path.join(install_path, 'conf/launch.json'), "w") as config_file:217 config_file.write(json.dumps(default_launcher_config))218web_exec = ''219if app_type.startswith('win'):220 web_exec = os.path.join(install_path, 'bin/start.bat')221 with open(web_exec, "w") as run_file:222 run_file.write("%s %s %s" % (python_exec, os.path.join(base_python_path, 'vtk/web/launcher.py'), os.path.join(install_path, 'conf/launch.json')))223else:224 web_exec = os.path.join(install_path, 'bin/start.sh')225 with open(web_exec, "w") as run_file:226 run_file.write("%s %s %s" % (python_exec, os.path.join(base_python_path, 'vtk/web/launcher.py'), os.path.join(install_path, 'conf/launch.json')))227 os.chmod(web_exec, 0750)228# ===================================================================229# Enable ParaViewWeb application inside index.html230# ===================================================================231index_html = os.path.join(install_path,"www/index.html")232index_origin = os.path.join(install_path,"www/index.origin")233os.rename(index_html, index_origin)234with open(index_origin, "r") as fr:235 with open(index_html, "w") as fw:236 for line in fr:237 if not "DEMO-APPS" in line:238 fw.write(line)239# ===================================================================240# Print help241# ===================================================================242print243print "To start ParaViewWeb web server just run:"244print " "*5, web_exec245print246print "And go in your Web browser (Safari, Chrome, Firefox) to:"247print " "*5, "http://localhost:8080/"248print...
get_auto_backup.py
Source:get_auto_backup.py
1# linux: curl https://raw.githubusercontent.com/CrazyVideoGamer/auto-backup/main/get_auto_backup.py | python3 <-- not yet tested2# windows cmd: curl https://raw.githubusercontent.com/CrazyVideoGamer/auto-backup/main/get_auto_backup.py | python <-- not yet tested 3from pathlib import Path4import argparse5import sys, platform, subprocess6def does_git_exist():7 system = platform.system()8 if system == "Linux":9 log = subprocess.run("command -v git >/dev/null 2>&1 || { echo 'error: git not found' >&2;}", shell=True)10 if log.stdout == b'error: git not found':11 return False12 return True13 elif system == "Windows":14 log = subprocess.run("where git >nul 2>&1 || ( echo error: git not found )", shell=True)15 if log.stdout == b'error: git not found':16 return False17 return True18def error_message(message: str) -> None:19 # \u001b[31m makes it red, \u001b[0m makes the color reset20 system = platform.system()21 if system == "Windows":22 subprocess.run("color", shell=True) 23 print("\u001b[31;1m" + message + "\u001b[0m", file=sys.stderr)24 sys.exit(0)25def create_parser() -> argparse.ArgumentParser:26 parser = argparse.ArgumentParser(description="Install or uninstall auto-backup")27 parser.add_argument("--uninstall", action='store_true')28 return parser29args = create_parser().parse_args()30system = platform.system()31if system == "Linux":32 install_path = Path.home() / ".auto-backup"33 34 if not args.uninstall:35 if (install_path.exists() and (install_path / '.is-auto-backup').exists()):36 error_message("Already installed auto-backup")37 elif (install_path.exists() and not (install_path / '.is-auto-backup').exists()):38 error_message("Could not create the ~/.auto-backup directory: directory already exists")39 else: # this else statement only runs if ~/.auto-backup doesn't exist40 install_path.mkdir(exist_ok=True)41 (install_path / ".is-auto-backup").touch()42 # add this git repository (and also leave out the .git directory and name it `backup`)43 if does_git_exist():44 if not (install_path / "backup").exists():45 print("Installing auto-backup...")46 subprocess.run("git clone --quiet --depth=1 --branch=main https://github.com/CrazyVideoGamer/auto-backup.git backup", cwd=install_path, shell=True)47 subprocess.run("rm -rf ./backup/.git", cwd=install_path, shell=True)48 subprocess.run("pip install -r requirements.txt -t lib2 > /dev/null 2>&1", cwd=(install_path / "backup"), shell=True)49 print("Done!\n")50 else:51 error_message("Please install git using `sudo apt install git`")52 print(f"add `export PATH={str(install_path / 'auto-backup' / 'backup' / 'bin')}:$PATH` to ~/.bashrc to complete the installation")53 else:54 if (not install_path.exists() or (install_path.exists() and not (install_path / '.is-auto-backup').exists())):55 error_message("auto-backup is not installed")56 print("Uninstalling auto-backup...")57 subprocess.run(f"rm -r {str(install_path)}", shell=True)58 print("Done!")59elif system == "Windows":60 install_path = Path.home() / "auto-backup"61 if not args.uninstall:62 if (install_path.exists() and (install_path / 'is-auto-backup').exists()):63 error_message("Already installed auto-backup")64 elif (install_path.exists() and not (install_path / 'is-auto-backup').exists()):65 error_message(f"Could not create the {str(install_path)} directory: directory already exists")66 else:67 install_path.mkdir(exist_ok=True)68 (install_path / "is-auto-backup").touch() # note that it is "is-auto-backup", not ".is-auto-backup"69 # add this git repository (and also leave out the .git directory and name it `backup`)70 if does_git_exist():71 if not (install_path / "backup").exists():72 print("Installing auto-backup...")73 subprocess.run("git clone --quiet --depth=1 --branch=main https://github.com/CrazyVideoGamer/auto-backup.git backup", cwd=install_path, shell=True)74 subprocess.run("rd /s /q \"backup/.git\"", cwd=install_path, shell=True)75 subprocess.run("pip install -r requirements.txt -t lib > nul 2>&1", cwd=(install_path / "backup"), shell=True)76 77 print("Done!\n")78 else:79 error_message("Please install git first (go to https://git-scm.com/) ")80 print(f"add {str(install_path / 'auto-backup' / 'backup' / 'bin')} to PATH to complete the installation")81 else:82 if (not install_path.exists() or (install_path.exists() and not (install_path / 'is-auto-backup').exists())):83 error_message("auto-backup is not installed")84 print("Uninstalling auto-backup...")85 subprocess.run(f"rd /s /q {str(install_path)}", shell=True)86 print("Done!")87else:...
installation.smk
Source:installation.smk
1rule install_augustus:2 output:3 os.path.join(INSTALL_PATH, 'augustus/bin/augustus'),4 directory(os.path.join(INSTALL_PATH, 'augustus/config')),5 params:6 git_commit= 'd1fd097',7 INSTALL_PATH= INSTALL_PATH,8 shell:9 r"""10 rm -rf Augustus11 git clone https://github.com/Gaius-Augustus/Augustus.git12 cd Augustus13 git checkout {params.git_commit}14 git checkout common.mk # Reset to original before editing it15 > common.tmp16 echo "17 INCLUDE_PATH_ZLIB := -I{params.INSTALL_PATH}/include18 INCLUDE_PATH_BOOST := -I{params.INSTALL_PATH}/include19 INCLUDE_PATH_LPSOLVE := -I{params.INSTALL_PATH}/include/lpsolve20 INCLUDE_PATH_SUITESPARSE := -I{params.INSTALL_PATH}/include/suitesparse/21 INCLUDE_PATH_GSL := -I{params.INSTALL_PATH}/include22 INCLUDE_PATH_SQLITE := -I{params.INSTALL_PATH}/include23 INCLUDE_PATH_BAMTOOLS := -I{params.INSTALL_PATH}/include/bamtools24 INCLUDE_PATH_HTSLIB := -I{params.INSTALL_PATH}/include/htslib25 INCLUDE_PATH_SEQLIB := -I {params.INSTALL_PATH}/include/SeqLib -I{params.INSTALL_PATH}/include/htslib -I{params.INSTALL_PATH}/include/jsoncpp26 LIBRARY_PATH_LPSOLVE := -L{params.INSTALL_PATH}/lib/lp_solve/ -Wl,-rpath,{params.INSTALL_PATH}/lib/lp_solve/27 LIBRARY_PATH_ZLIB := -L{params.INSTALL_PATH}/lib -Wl,-rpath,{params.INSTALL_PATH}/lib28 LIBRARY_PATH_BOOST := -L{params.INSTALL_PATH}/lib -Wl,-rpath,{params.INSTALL_PATH}/lib29 LIBRARY_PATH_SUITESPARSE := -L{params.INSTALL_PATH}/lib -Wl,-rpath,{params.INSTALL_PATH}/lib30 LIBRARY_PATH_GSL := -L{params.INSTALL_PATH}/lib -Wl,-rpath,{params.INSTALL_PATH}/lib31 LIBRARY_PATH_SQLITE := -L{params.INSTALL_PATH}/lib -Wl,-rpath,{params.INSTALL_PATH}/lib32 LIBRARY_PATH_BAMTOOLS := -L{params.INSTALL_PATH}/lib -Wl,-rpath,{params.INSTALL_PATH}/lib33 LIBRARY_PATH_HTSLIB := -L{params.INSTALL_PATH}/lib -Wl,-rpath,{params.INSTALL_PATH}/lib34 LIBRARY_PATH_SEQLIB := -L{params.INSTALL_PATH}/lib -Wl,-rpath,{params.INSTALL_PATH}/lib35 " >> common.tmp36 cat common.mk >> common.tmp37 mv common.tmp common.mk38 make -j 8 MYSQL=false augustus auxprogs39 mkdir -p {params.INSTALL_PATH}/augustus/bin40 mv bin/* {params.INSTALL_PATH}/augustus/bin/41 cp -r scripts/* {params.INSTALL_PATH}/augustus/bin/42 cp -r config {params.INSTALL_PATH}/augustus/43 # Some basic tests:44 {params.INSTALL_PATH}/augustus/bin/augustus --version45 {params.INSTALL_PATH}/augustus/bin/autoAug.pl --help46 """47rule install_braker:48 # Braker is on bioconda but it may be outdated so we install it ourselves49 output:50 os.path.join(INSTALL_PATH, 'bin/braker.pl'),51 params:52 git_commit= '1af9bdc',53 INSTALL_PATH= INSTALL_PATH,54 shell:55 r"""56 rm -rf BRAKER57 git clone https://github.com/Gaius-Augustus/BRAKER58 cd BRAKER59 git checkout {params.git_commit}60 chmod +x scripts/*.pl scripts/*.py61 cp scripts/*.pl {params.INSTALL_PATH}/bin/62 cp scripts/*.pm {params.INSTALL_PATH}/bin/63 cp scripts/*.py {params.INSTALL_PATH}/bin/64 cp -r scripts/cfg/ {params.INSTALL_PATH}/bin/65 rm -rf BRAKER66 braker.pl --help > /dev/null67 """68rule install_genemark:69 input:70 gm= config['genemark_tar_gz'],71 output:72 touch('genemark_installation.done'),73 params:74 gmpath= GENEMARK_PATH,75 shell:76 r"""77 gm=`basename {input.gm} .tar.gz`78 rm -rf {params.gmpath}79 cp {input.gm} ${{gm}}.tar.gz80 tar zxf ${{gm}}.tar.gz81 mv ${{gm}} {params.gmpath} 82 rm -rf ${{gm}}.tar.gz83 cd {params.gmpath}84 # Copy key if necessary. We assume the key in the tar archive is valid 85 if [ -f ~/.gm_key ]86 then87 my5=`md5sum ~/.gm_key | cut -d ' ' -f 1`88 else89 my5='notfound'90 fi91 this5=`md5sum gm_key | cut -d ' ' -f 1`92 if [ "$my5" != "$this5" ]93 then94 cp gm_key ~/.gm_key95 fi96 # Use perl on PATH97 perl change_path_in_perl_scripts.pl '/usr/bin/env perl'98 99 # Test installation100 ./check_install.bash...
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