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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