#122 Adding bootstrap.py and buildout with instructions in README

calchoo · calchoo · commit 3b3ab40bf3fb · 2018-05-23T16:02:08.000-07:00
diff --git a/README.md b/README.md
@@ -5,25 +5,23 @@
 </object>
 
 ![master branch build Status](https://www.bcgsc.ca/bamboo/plugins/servlet/wittified/build-status/MAV-TEST) 
-*(master)* 
-
+*(master)*
 
 ![develop branch build status](https://www.bcgsc.ca/bamboo/plugins/servlet/wittified/build-status/MAV-TEST0) 
-*(develop)* 
+*(develop)*
 
 # About
 
 [MAVIS](http://mavis.bcgsc.ca) is python command-line tool for the post-processing of structural variant calls. 
 The general [MAVIS](http://mavis.bcgsc.ca) pipeline consists of six main stages
- 
+
 - convert
 - [cluster](http://mavis.bcgsc.ca/docs/latest/mavis.cluster.html#mavis-cluster)
 - [validate](http://mavis.bcgsc.ca/docs/latest/mavis.validate.html#mavis-validate)
 - [annotate](http://mavis.bcgsc.ca/docs/latest/mavis.annotate.html#mavis-annotate)
 - [pairing](http://mavis.bcgsc.ca/docs/latest/mavis.pairing.html#mavis-pairing)
 - [summary](http://mavis.bcgsc.ca/docs/latest/mavis.summary.html#mavis-summary)
 
-
 ## Getting Help
 
 All steps in the MAVIS pipeline are called following the main mavis entry point. The usage menu can be viewed
@@ -39,74 +37,83 @@ Common problems and questions are addressed on the [wiki](https://github.com/bcg
 If you have a question or issue that is not answered there (or already a github issue) please submit
 a github issue to our [github page](https://github.com/bcgsc/mavis/issues) or contact us by email at [mavis@bcgsc.ca](mailto:mavis@bcgsc.ca)
 
-
 ## Install Instructions
 
-
 There are 3 major steps to setting up and installing [MAVIS](http://mavis.bcgsc.ca).
 
-
 ### 1. Install Aligner
 
 In addition to the python package dependencies, [MAVIS](http://mavis.bcgsc.ca) also requires an aligner to be installed. 
 Currently the only aligners supported are [blat](http://mavis.bcgsc.ca/docs/latest/glossary.html#term-blat) and [bwa mem](http://mavis.bcgsc.ca/docs/latest/glossary.html#term-bwa). 
 For MAVIS to run successfully the aligner must be installed and accessible on the path. 
 If you have a non-standard install you may find it useful to edit the PATH environment variable. For example
 
-```
+``` bash
 export PATH=/path/to/directory/containing/blat/binary:$PATH
 ```
 
 [blat](http://mavis.bcgsc.ca/docs/latest/glossary.html#term-blat) is the default aligner. To configure MAVIS to use [bwa mem](http://mavis.bcgsc.ca/docs/latest/glossary.html#term-bwa) as a default instead, use the
 [MAVIS environment variables](http://mavis.bcgsc.ca/configuration.html#environment-variables). Make sure to specify BOTH of the variables below to change the default aligner.
 
-
-```
+``` bash
 export MAVIS_ALIGNER='bwa mem'
 export MAVIS_ALIGNER_REFERENCE=/path/to/mem/fasta/ref/file
 ```
 
 After these have been installed MAVIS itself can be installed through pip
 
+#### 2. Install MAVIS
 
-### 2. Install MAVIS
+##### Install using pip
 
 The easiest way to install [MAVIS](http://mavis.bcgsc.ca) is through the python package manager, pip. If you do not have python3 installed it can be found [here](https://www.python.org/downloads)
 
 Ensuring you have a recent version of pip and setuptools will improve the install experience. Older versions of pip and setuptools may have issues with obtaining some of the mavis python dependencies
 
-```
+``` bash
 pip install --upgrade pip setuptools
 ```
 
 or (for Anaconda users)
 
-```
+``` bash
 conda update pip setuptools
 ```
 
 If this is not a clean/new python install it may be useful to set up mavis in a [virtual python environment](https://docs.python.org/3/tutorial/venv.html)
 
 Then install mavis itself
-```
+
+``` bash
 pip install mavis
 ```
 
 This will install mavis and its python dependencies.
 
-### 3. Build or Download Reference Files
+##### Install using Buildout
 
-After [MAVIS](http://mavis.bcgsc.ca) is installed the [reference files](http://mavis.bcgsc.ca/docs/latest/mavis_input.html#reference-input-files) must be generated (or downloaded) before it can be run. A simple bash script to download the hg19 reference files and generate a MAVIS environment file is provided under mavis/tools for convenience. 
+Alternatively you can use the [bootstrap/buildout](http://www.buildout.org/en/latest/) to install mavis into bin/mavis
 
+``` bash
+git clone https://github.com/bcgsc/mavis.git
+cd mavis
+pip install zc.buildout
+python bootstrap.py
+bin/buildout
 ```
+
+This will install mavis and its python dependencies into eggs inside the cloned mavis directory which can be used by simply running bin/mavis
+
+### 3. Build or Download Reference Files
+
+After [MAVIS](http://mavis.bcgsc.ca) is installed the [reference files](http://mavis.bcgsc.ca/docs/latest/mavis_input.html#reference-input-files) must be generated (or downloaded) before it can be run. A simple bash script to download the hg19 reference files and generate a MAVIS environment file is provided under mavis/tools for convenience.
+
+``` bash
 cd /path/to/where/you/want/to/put/the/files
 wget https://raw.githubusercontent.com/bcgsc/mavis/master/tools/get_hg19_reference_files.sh
 bash get_hg19_reference_files.sh
 source reference_inputs/hg19_env.sh
 ```
 
-Once the above 3 steps are complete [MAVIS](http://mavis.bcgsc.ca) is ready to be run. 
+Once the above 3 steps are complete [MAVIS](http://mavis.bcgsc.ca) is ready to be run.
 See the MAVIS [tutorial](http://mavis.bcgsc.ca/docs/latest/pipeline.html#mavis-tutorial) to learn about running MAVIS.
-
-
-
diff --git a/bootstrap.py b/bootstrap.py
@@ -0,0 +1,212 @@
+##############################################################################
+#
+# Copyright (c) 2006 Zope Foundation and Contributors.
+# All Rights Reserved.
+#
+# This software is subject to the provisions of the Zope Public License,
+# Version 2.1 (ZPL).  A copy of the ZPL should accompany this distribution.
+# THIS SOFTWARE IS PROVIDED "AS IS" AND ANY AND ALL EXPRESS OR IMPLIED
+# WARRANTIES ARE DISCLAIMED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF TITLE, MERCHANTABILITY, AGAINST INFRINGEMENT, AND FITNESS
+# FOR A PARTICULAR PURPOSE.
+#
+##############################################################################
+"""Bootstrap a buildout-based project
+
+Simply run this script in a directory containing a buildout.cfg.
+The script accepts buildout command-line options, so you can
+use the -c option to specify an alternate configuration file.
+"""
+
+from optparse import OptionParser
+import os
+import shutil
+import subprocess
+import sys
+import tempfile
+
+import pkg_resources
+import setuptools
+
+import zc.buildout.buildout
+
+
+__version__ = '2015-07-01'
+# See zc.buildout's changelog if this version is up to date.
+
+tmpeggs = tempfile.mkdtemp(prefix='bootstrap-')
+
+usage = '''\
+[DESIRED PYTHON FOR BUILDOUT] bootstrap.py [options]
+
+Bootstraps a buildout-based project.
+
+Simply run this script in a directory containing a buildout.cfg, using the
+Python that you want bin/buildout to use.
+
+Note that by using --find-links to point to local resources, you can keep
+this script from going over the network.
+'''
+
+parser = OptionParser(usage=usage)
+parser.add_option("--version",
+                  action="store_true", default=False,
+                  help=("Return bootstrap.py version."))
+parser.add_option("-t", "--accept-buildout-test-releases",
+                  dest='accept_buildout_test_releases',
+                  action="store_true", default=False,
+                  help=("Normally, if you do not specify a --buildout-version, "
+                        "the bootstrap script and buildout gets the newest "
+                        "*final* versions of zc.buildout and its recipes and "
+                        "extensions for you.  If you use this flag, "
+                        "bootstrap and buildout will get the newest releases "
+                        "even if they are alphas or betas."))
+parser.add_option("-c", "--config-file",
+                  help=("Specify the path to the buildout configuration "
+                        "file to be used."))
+parser.add_option("-f", "--find-links",
+                  help=("Specify a URL to search for buildout releases"))
+parser.add_option("--allow-site-packages",
+                  action="store_true", default=False,
+                  help=("Let bootstrap.py use existing site packages"))
+parser.add_option("--buildout-version",
+                  help="Use a specific zc.buildout version")
+parser.add_option("--setuptools-version",
+                  help="Use a specific setuptools version")
+parser.add_option("--setuptools-to-dir",
+                  help=("Allow for re-use of existing directory of "
+                        "setuptools versions"))
+
+options, args = parser.parse_args()
+if options.version:
+    print("bootstrap.py version %s" % __version__)
+    sys.exit(0)
+
+
+######################################################################
+# load/install setuptools
+
+try:
+    from urllib.request import urlopen
+except ImportError:
+    from urllib2 import urlopen
+
+ez = {}
+if os.path.exists('ez_setup.py'):
+    exec(open('ez_setup.py').read(), ez)
+else:
+    exec(urlopen('https://bootstrap.pypa.io/ez_setup.py').read(), ez)
+
+if not options.allow_site_packages:
+    # ez_setup imports site, which adds site packages
+    # this will remove them from the path to ensure that incompatible versions
+    # of setuptools are not in the path
+    import site
+    # inside a virtualenv, there is no 'getsitepackages'.
+    # We can't remove these reliably
+    if hasattr(site, 'getsitepackages'):
+        for sitepackage_path in site.getsitepackages():
+            # Strip all site-packages directories from sys.path that
+            # are not sys.prefix; this is because on Windows
+            # sys.prefix is a site-package directory.
+            if sitepackage_path != sys.prefix:
+                sys.path[:] = [x for x in sys.path
+                               if sitepackage_path not in x]
+
+setup_args = dict(to_dir=tmpeggs, download_delay=0)
+
+if options.setuptools_version is not None:
+    setup_args['version'] = options.setuptools_version
+if options.setuptools_to_dir is not None:
+    setup_args['to_dir'] = options.setuptools_to_dir
+
+ez['use_setuptools'](**setup_args)
+
+# This does not (always?) update the default working set.  We will
+# do it.
+for path in sys.path:
+    if path not in pkg_resources.working_set.entries:
+        pkg_resources.working_set.add_entry(path)
+
+######################################################################
+# Install buildout
+
+ws = pkg_resources.working_set
+
+setuptools_path = ws.find(
+    pkg_resources.Requirement.parse('setuptools')).location
+
+# Fix sys.path here as easy_install.pth added before PYTHONPATH
+cmd = [sys.executable, '-c',
+       'import sys; sys.path[0:0] = [%r]; ' % setuptools_path +
+       'from setuptools.command.easy_install import main; main()',
+       '-mZqNxd', tmpeggs]
+
+find_links = os.environ.get(
+    'bootstrap-testing-find-links',
+    options.find_links or
+    ('http://downloads.buildout.org/'
+     if options.accept_buildout_test_releases else None)
+    )
+if find_links:
+    cmd.extend(['-f', find_links])
+
+requirement = 'zc.buildout'
+version = options.buildout_version
+if version is None and not options.accept_buildout_test_releases:
+    # Figure out the most recent final version of zc.buildout.
+    import setuptools.package_index
+    _final_parts = '*final-', '*final'
+
+    def _final_version(parsed_version):
+        try:
+            return not parsed_version.is_prerelease
+        except AttributeError:
+            # Older setuptools
+            for part in parsed_version:
+                if (part[:1] == '*') and (part not in _final_parts):
+                    return False
+            return True
+
+    index = setuptools.package_index.PackageIndex(
+        search_path=[setuptools_path])
+    if find_links:
+        index.add_find_links((find_links,))
+    req = pkg_resources.Requirement.parse(requirement)
+    if index.obtain(req) is not None:
+        best = []
+        bestv = None
+        for dist in index[req.project_name]:
+            distv = dist.parsed_version
+            if _final_version(distv):
+                if bestv is None or distv > bestv:
+                    best = [dist]
+                    bestv = distv
+                elif distv == bestv:
+                    best.append(dist)
+        if best:
+            best.sort()
+            version = best[-1].version
+if version:
+    requirement = '=='.join((requirement, version))
+cmd.append(requirement)
+
+if subprocess.call(cmd) != 0:
+    raise Exception(
+        "Failed to execute command:\n%s" % repr(cmd)[1:-1])
+
+######################################################################
+# Import and run buildout
+
+ws.add_entry(tmpeggs)
+ws.require(requirement)
+
+if not [a for a in args if '=' not in a]:
+    args.append('bootstrap')
+
+# if -c was provided, we push it back into args for buildout' main function
+if options.config_file is not None:
+    args[0:0] = ['-c', options.config_file]
+
+zc.buildout.buildout.main(args)
+shutil.rmtree(tmpeggs)
diff --git a/buildout.cfg b/buildout.cfg
@@ -0,0 +1,7 @@
+[buildout]
+develop = .
+parts = mavis
+
+[mavis]
+recipe = zc.recipe.egg:scripts
+eggs = mavis
