comparison jbrowse2.py @ 122:ae07c55ab96b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a9124072bc71dd670ee58ff8e4846e14d6d603ec

121:478ee3e780de

from collections import defaultdict

logging.basicConfig(level=logging.DEBUG)
log = logging.getLogger("jbrowse")

JB2VER = "v2.12.3"
# version pinned if cloning - but not cloning now
logCommands = True
# useful for seeing what's being written but not for production setups
TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
SELF_LOCATION = os.path.dirname(os.path.realpath(__file__))

            To allow running on internet-less compute and for reproducibility
            use frozen code with `realclone=false

        """
        dest = self.outdir
        if realclone:
            self.subprocess_check_call(
                ["jbrowse", "create", dest, "-f", "--tag", f"{JB2VER}"]
            )
        else:
            shutil.copytree(self.jbrowse2path, dest, dirs_exist_ok=True)

122:ae07c55ab96b

from collections import defaultdict

logging.basicConfig(level=logging.DEBUG)
log = logging.getLogger("jbrowse")

JB2VER = "v2.15.4"
# version pinned if cloning - but not cloning now
logCommands = True
# useful for seeing what's being written but not for production setups
TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
SELF_LOCATION = os.path.dirname(os.path.realpath(__file__))

            To allow running on internet-less compute and for reproducibility
            use frozen code with `realclone=false

        """
        dest = self.outdir
        if (not os.path.exists(self.jbrowse2path)) or realclone:
            self.subprocess_check_call(
                ["jbrowse", "create", dest, "-f", "--tag", f"{JB2VER}"]
            )
        else:
            shutil.copytree(self.jbrowse2path, dest, dirs_exist_ok=True)