Enable custom installs of brew bottles for difficult to build Linux p…

…ackages. Add cmake to avoid Python dependency with Sphinx

cloudbio/custom/shared.py

@@ -172,7 +172,11 @@ def _remote_fetch(env, url, out_file=None, allow_fail=False, fix_fn=None, samedi
  if out_file is None:
  out_file = os.path.basename(url)
  if not env.safe_exists(out_file):
- orig_dir = env.safe_run_output("pwd").strip()
+ if samedir and os.path.isabs(out_file):
+ orig_dir = os.path.dirname(out_file)
+ out_file = os.path.basename(out_file)
+ else:
+ orig_dir = env.safe_run_output("pwd").strip()
  temp_ext = "/%s" % uuid.uuid3(uuid.NAMESPACE_URL,
  str("file://%s/%s/%s" %
  (env.host, socket.gethostname(), out_file)))
@@ -188,6 +192,8 @@ def _remote_fetch(env, url, out_file=None, allow_fail=False, fix_fn=None, samedi
  out_file = None
  else:
  raise IOError("Failure to retrieve remote file")
+ if samedir:
+ out_file = os.path.join(orig_dir, out_file)
  return out_file
 
 def _fetch_and_unpack(url, need_dir=True, dir_name=None, revision=None,

cloudbio/package/brew.py

@@ -6,13 +6,15 @@
 from distutils.version import LooseVersion
 import os
 
-from cloudbio.custom import system
+from cloudbio.custom import system, shared
 from cloudbio.flavor.config import get_config_file
 from cloudbio.fabutils import quiet, find_cmd
 from cloudbio.package.shared import _yaml_to_packages
 
 from fabric.api import cd, settings
 
+BOTTLE_URL = "https://s3.amazonaws.com/cloudbiolinux/brew_bottles/{pkg}-{version}.x86_64-linux.bottle.tar.gz"
+
 def install_packages(env, to_install=None, packages=None):
  """Install packages using the home brew package manager.
 
@@ -194,13 +196,34 @@ def _get_pkg_version_args(pkg_str):
  name, version = parts
  return name, version, args
 
+def _install_bottle(env, brew_cmd, pkg, ipkgs):
+ """Install Linux bottles for brew packages that can be tricky to build.
+ """
+ if env.distribution == "macosx": # Only Linux bottles, build away on Mac
+ return
+ pkg_version = _latest_pkg_version(env, brew_cmd, pkg)
+ install_version = ipkgs["current"].get(pkg)
+ if pkg_version == install_version: # Up to date
+ return
+ url = BOTTLE_URL.format(pkg=pkg, version=pkg_version)
+ brew_cachedir = env.safe_run_output("%s --cache" % brew_cmd)
+ brew_cellar = os.path.join(env.safe_run_output("%s --prefix" % brew_cmd), "Cellar")
+ bottle_file = shared._remote_fetch(env, url, out_file=os.path.join(brew_cachedir, os.path.basename(url)),
+ allow_fail=True, samedir=True)
+ if bottle_file:
+ with cd(brew_cellar):
+ env.safe_run("tar -xf %s" % bottle_file)
+ env.safe_run("%s link --overwrite %s" % (brew_cmd, pkg))
+
 def _install_brew_baseline(env, brew_cmd, ipkgs, packages):
  """Install baseline brew components not handled by dependency system.
 
  - Installation of required Perl libraries.
  - Ensures installed samtools does not overlap with bcftools
  - Upgrades any package dependencies
  """
+ for dep in ["cmake"]:
+ _install_bottle(env, brew_cmd, dep, ipkgs)
  for dep in ["expat"]:
  _install_pkg_latest(env, dep, [], brew_cmd, ipkgs)
  # if installing samtools, avoid bcftools conflicts