Implement conda_init command.

jmchilton · jmchilton · commit ad3b2f0c3cb5 · 2015-12-15T18:43:23.000Z
Building up conda options to match brew options already available.
diff --git a/planemo/commands/cmd_conda_init.py b/planemo/commands/cmd_conda_init.py
@@ -0,0 +1,22 @@
+import click
+
+from planemo.cli import pass_context
+from planemo.io import shell
+from planmo import options
+from galaxy.tools.deps import conda_util
+
+
+@click.command('conda_init')
+@options.conda_prefix_option()
+@pass_context
+def cli(ctx, conda_prefix=None):
+    """Download and install conda.
+
+    This will download conda for managing dependencies for your platform
+    using the appropriate Miniconda installer.
+
+    By running this command, you are agreeing to the terms of the conda
+    license a 3-clause BSD 3 license. Please review full license at
+    http://docs.continuum.io/anaconda/eula.
+    """
+    conda_util(conda_prefix, shell_exec=shell)
diff --git a/planemo/options.py b/planemo/options.py
@@ -188,6 +188,14 @@ def brew_option():
     )
 
 
+def conda_prefix_option():
+    return click.option(
+        "--conda_prefix",
+        type=click.Path(file_okay=False, dir_okay=True),
+        help="Conda prefix to use for conda dependency commands."
+    )
+
+
 def required_tool_arg():
     """ Decorate click method as requiring the path to a single tool.
     """
diff --git a/planemo_ext/galaxy/tools/deps/conda_util.py b/planemo_ext/galaxy/tools/deps/conda_util.py
@@ -0,0 +1,35 @@
+from ..deps import commands
+from sys import platform as _platform
+import os.path
+
+IS_OS_X = _platform == "darwin"
+
+# BSD 3-clause
+CONDA_LICENSE = "http://docs.continuum.io/anaconda/eula"
+
+
+def conda_link():
+    if IS_OS_X:
+        url = "https://repo.continuum.io/miniconda/Miniconda-latest-MacOSX-x86_64.sh"
+    else:
+        url = "https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh"
+    return url
+
+
+def find_conda_prefix(conda_prefix=None):
+    """ If supplied conda_prefix is not set, default to the default location
+    for Miniconda installs.
+    """
+    if conda_prefix is None:
+        return os.path.join(os.path.expanduser("~"), "miniconda2")
+    return conda_prefix
+
+
+def install_conda_command(prefix, shell_exec=None):
+    if shell_exec is None:
+        shell_exec = commands.shell
+    download_cmd = " ".join(commands.download_command(conda_link(), quote=True))
+    download_cmd = "%s > /tmp/conda.bash"
+    install_cmd = "bash /tmp/conda.bash -b -p '%s'" % prefix
+    full_command = "%s; %s" % (download_cmd, install_cmd)
+    return shell_exec(full_command)
