Skip to main content
  • Home
  • Development
  • Documentation
  • Donate
  • Operational login
  • Browse the archive

swh logo
SoftwareHeritage
Software
Heritage
Archive
Features
  • Search

  • Downloads

  • Save code now

  • Add forge now

  • Help

https://github.com/fenderglass/Ragout
22 June 2021, 01:27:41 UTC
  • Code
  • Branches (21)
  • Releases (0)
  • Visits
    • Branches
    • Releases
    • HEAD
    • refs/heads/chr_map
    • refs/heads/devel
    • refs/heads/gh-pages
    • refs/heads/ismb_2014
    • refs/heads/master
    • refs/heads/path_cover
    • refs/heads/py3
    • refs/heads/rr_devel
    • refs/heads/tree_infer
    • refs/remotes/origin/devel
    • refs/tags/1.0
    • refs/tags/1.1
    • refs/tags/2.0
    • refs/tags/2.1
    • refs/tags/2.1.1
    • refs/tags/2.2
    • refs/tags/2.3
    • refs/tags/v0.1b
    • refs/tags/v0.2b
    • refs/tags/v0.3b
    • refs/tags/v1.2
    No releases to show
  • 20036ba
  • /
  • scripts
  • /
  • install-sibelia.py
Raw File Download
Take a new snapshot of a software origin

If the archived software origin currently browsed is not synchronized with its upstream version (for instance when new commits have been issued), you can explicitly request Software Heritage to take a new snapshot of it.

Use the form below to proceed. Once a request has been submitted and accepted, it will be processed as soon as possible. You can then check its processing state by visiting this dedicated page.
swh spinner

Processing "take a new snapshot" request ...

Permalinks

To reference or cite the objects present in the Software Heritage archive, permalinks based on SoftWare Hash IDentifiers (SWHIDs) must be used.
Select below a type of object currently browsed in order to display its associated SWHID and permalink.

  • content
  • directory
  • revision
  • snapshot
origin badgecontent badge Iframe embedding
swh:1:cnt:7182424c3bc444c69e9118719dc3e6474878fa9d
origin badgedirectory badge Iframe embedding
swh:1:dir:cebde40034378667d1ccf9347e427744435f8e8a
origin badgerevision badge
swh:1:rev:a68b9dba9aa7570c0a8e3f579b662524ee919e2b
origin badgesnapshot badge
swh:1:snp:049c406b15a9a28e76d942bfc1fe2a04f4142f61
Citations

This interface enables to generate software citations, provided that the root directory of browsed objects contains a citation.cff or codemeta.json file.
Select below a type of object currently browsed in order to generate citations for them.

  • content
  • directory
  • revision
  • snapshot
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Tip revision: a68b9dba9aa7570c0a8e3f579b662524ee919e2b authored by Mikhail Kolmogorov on 27 July 2018, 01:48:58 UTC
bioconda badge
Tip revision: a68b9db
install-sibelia.py
#!/usr/bin/env python

#(c) 2013-2014 by Authors
#This file is a part of Ragout program.
#Released under the BSD license (see LICENSE file)

"""
A script which installs Sibelia
"""

from __future__ import print_function
import sys, os
import subprocess
import shutil
import argparse
try:
    from urllib import urlretrieve
except ImportError:
    from urllib.request import urlretrieve

SIBELIA_LINK = "https://github.com/bioinf/Sibelia/archive/master.tar.gz"
DEFAULT_PREFIX = "lib"

def install_deps(prefix):
    if which("Sibelia"):
        print("Sibelia is already installed", file=sys.stderr)
        return True
    else:
        print("Installing Sibelia", file=sys.stderr)
        try:
            return install_sibelia(prefix)
        except OSError as e:
            print("Error while installing - exiting", file=sys.stderr)
            print(e, file=sys.stderr)
            return False


def install_sibelia(prefix):
    if not test_tools():
        return False

    initial_dir = os.getcwd()

    tmp_dir = os.path.join(initial_dir, "sibelia-build")
    if os.path.isdir(tmp_dir):
        shutil.rmtree(tmp_dir)
    os.mkdir(tmp_dir)
    os.chdir(tmp_dir)

    print("Downloading source...", file=sys.stderr)
    urlretrieve(SIBELIA_LINK, "master.tar.gz")
    subprocess.check_call(["tar", "-xf", "master.tar.gz"])

    os.chdir("Sibelia-master/build")

    srcdir = os.path.join("..", "src")
    subprocess.check_call(["cmake", srcdir, "-DONLY_SIBELIA=1",
                            "-DCMAKE_INSTALL_PREFIX=" + tmp_dir])
    subprocess.check_call(["make"])
    subprocess.check_call(["make", "install"])

    sibelia_bin_src = os.path.join(tmp_dir, "bin", "Sibelia")
    sibelia_bin_dst = os.path.join(initial_dir, prefix, "Sibelia")
    shutil.copy(sibelia_bin_src, sibelia_bin_dst)

    os.chdir(initial_dir)
    shutil.rmtree(tmp_dir)

    return True


#Mimics UNIX "which" command
def which(program):
    def is_exe(fpath):
        return os.path.isfile(fpath) and os.access(fpath, os.X_OK)

    fpath, fname = os.path.split(program)
    if fpath:
        if is_exe(program):
            return program
    else:
        for path in os.environ["PATH"].split(os.pathsep):
            path = path.strip('"')
            exe_file = os.path.join(path, program)
            if is_exe(exe_file):
                return exe_file

    return None


def test_tools():
    for tool in ["cmake", "make", "tar"]:
        if not which(tool):
            print("ERROR: building Sibelia requires " + tool, file=sys.stderr)
            return False
    return True


def main():
    parser = argparse.ArgumentParser(description="A helper script for "
                                                 "Sibelia installation")
    parser.add_argument("--prefix", dest="prefix",
                        help="installation prefix (default = \"{0}\")"
                        .format(DEFAULT_PREFIX),
                        default=DEFAULT_PREFIX)
    args = parser.parse_args()
    return int(not install_deps(args.prefix))


if __name__ == "__main__":
    sys.exit(main())

Software Heritage — Copyright (C) 2015–2025, The Software Heritage developers. License: GNU AGPLv3+.
The source code of Software Heritage itself is available on our development forge.
The source code files archived by Software Heritage are available under their own copyright and licenses.
Terms of use: Archive access, API— Contact— JavaScript license information— Web API

back to top