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Improving docker_shell #334

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Merged
jmchilton merged 2 commits into from
Oct 20, 2015
Merged

Improving docker_shell #334

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96c0b5e
Adding the '-t' flag to the docker shell command (add psuedo terminal…
kellrott Oct 19, 2015
9311e36
Fixing whitespace to pass lint
kellrott Oct 20, 2015
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21 changes: 20 additions & 1 deletion planemo/commands/cmd_docker_shell.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
"""
from __future__ import print_function
import click

import os
from planemo.cli import pass_context
from planemo import options

Expand Down Expand Up @@ -59,10 +59,29 @@ def cli(ctx, path, **kwds):
if kwds["from_tag"]:
identifier = "-t %s" % identifier

tool_dir = os.path.dirname(os.path.abspath(path))
working_dir = os.path.abspath(os.getcwd())
if tool_dir.startswith(working_dir):
volumes = [
"%s:%s" % (working_dir, working_dir)
]
elif working_dir.startswith(tool_dir):
volumes = [
"%s:%s" % (tool_dir, tool_dir)
]
else:
volumes = [
"%s:%s" % (working_dir, working_dir),
"%s:%s" % (tool_dir, tool_dir)
]

script = docker_util.build_docker_run_command(
"/bin/bash",
identifier,
interactive=True,
terminal=True,
working_directory=working_dir,
volumes=volumes,
**dockerfiles.docker_host_args(**kwds)
)
print(script)
3 changes: 3 additions & 0 deletions planemo_ext/galaxy/tools/deps/docker_util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -109,6 +109,7 @@ def build_docker_run_command(
container_command,
image,
interactive=False,
terminal=False,
tag=None,
volumes=[],
volumes_from=DEFAULT_VOLUMES_FROM,
Expand All @@ -134,6 +135,8 @@ def build_docker_run_command(
command_parts.append("run")
if interactive:
command_parts.append("-i")
if terminal:
command_parts.append("-t")
for env_directive in env_directives:
command_parts.extend(["-e", env_directive])
for volume in volumes:
Expand Down
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