natefoo

nate@weyerbacher% python
Python 2.7.6 (default, Mar 22 2014, 22:59:56) 
[GCC 4.8.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import os, tempfile
>>> f = tempfile.NamedTemporaryFile()
>>> f.name
'/tmp/tmptZ3yCX'
>>> os.rename(f.name, '/tmp/foo')
>>> f.write('foo\n')

natefoo

nate@weyerbacher% python ./scripts/galaxy -h
usage: galaxy [-h] [-c INI_PATH] [-d] [-k] [-p PYTHON_EXE] operation

Control Galaxy server process(es)

positional arguments:
  operation             Operation to perform (start, stop, status,
                        supervisorctl

optional arguments:

natefoo

e69de29bb2d1d6434b8b29ae775ad8c2e48c5391,DELETE,regular-file,lib/galaxy/actions/__init__.py,0,
e69de29bb2d1d6434b8b29ae775ad8c2e48c5391,DELETE,regular-file,lib/galaxy/dataset_collections/__init__.py,0,
e69de29bb2d1d6434b8b29ae775ad8c2e48c5391,DELETE,regular-file,lib/galaxy/datatypes/__init__.py,0,
e69de29bb2d1d6434b8b29ae775ad8c2e48c5391,DELETE,regular-file,lib/galaxy/datatypes/converters/__init__.py,0,
44caf2e67482788e5f1f3893eadf43fe4b58c2d5,DELETE,regular-file,lib/galaxy/datatypes/test/2.fastqsanger,303,
356bb1aefb39e9a16844abf4cb63a7788a40e3c0,DELETE,regular-file,lib/galaxy/datatypes/test/megablast_xml_parser_test1.blastxml,176755,
6e2081304e9f81eaabbc4bbe7122e6ed587837c3,DELETE,regular-file,lib/galaxy/datatypes/test/test.gtf,103056,
e69de29bb2d1d6434b8b29ae775ad8c2e48c5391,DELETE,regular-file,lib/galaxy/forms/__init__.py,0,
e69de29bb2d1d6434b8b29ae775ad8c2e48c5391,DELETE,regular-file,lib/galaxy/jobs/rules/__init__.py,0,
e69de29bb2d1d6434b8b29ae775ad8c2e48c5391,DELETE,regular-file,lib/galaxy/jobs/runners/

natefoo

nate@weyerbacher% git branch
* master
nate@weyerbacher% git log
commit 1572db612b5f7149ceb8001b74f67d662048af00
Merge: db2c863 899330c
Author: Nate Coraor <nate@bx.psu.edu>
Date:   Wed Feb 25 18:13:57 2015 -0500

    Merge branch 'feature'

natefoo

#!/bin/sh
arch=x86_64
pkg=ucsc
version=312
build_deps="libc6-dev zlib1g-dev libncurses5-dev libmysqlclient-dev unzip libpng-dev libssl-dev"
urls="
http://hgdownload.soe.ucsc.edu/admin/jksrc.v${version}.zip
"

build=/build

natefoo

diff --git a/lib/galaxy/metadata/set_metadata.py b/lib/galaxy/metadata/set_metadata.py
index 0ffcb35..2e705d8 100644
--- a/lib/galaxy/metadata/set_metadata.py
+++ b/lib/galaxy/metadata/set_metadata.py
@@ -50,7 +50,7 @@ def set_meta_with_tool_provided( dataset_instance, file_dict, set_meta_kwds ):
 def set_metadata():
     # locate galaxy_root for loading datatypes
     galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir))
-    tool_job_working_directory = os.path.abspath(os.getcwd())
+    galaxy.datatypes.metadata.MetadataTempFile.tmp_dir = tool_job_working_directory = os.path.abspath(os.getcwd())

natefoo

---

- name: ro-user setup
  hosts: all
  remote_user: rouser
  vars_files:
    - vars.yml
  roles:
    - role: galaxy
      galaxy_manage_mutable_setup: no

natefoo

(gravitydev)nate@weyerbacher% gravity create foo
Created instance: foo
(gravitydev)nate@weyerbacher% gravity create foo/gxgx ~/galaxy/galaxy/config/galaxy.ini
Registered galaxy config: /home/nate/galaxy/galaxy/config/galaxy.ini as gxgx
(gravitydev)nate@weyerbacher% gravity create foo/gxreports ~/galaxy/galaxy/config/reports_wsgi.ini.sample
Registered reports config: /home/nate/galaxy/galaxy/config/reports_wsgi.ini.sample as gxreports
(gravitydev)nate@weyerbacher% gravity create foo/gxpulsar ~/pulsar/pulsar/server.ini.sample
Registered pulsar config: /home/nate/pulsar/pulsar/server.ini.sample as gxpulsar
(gravitydev)nate@weyerbacher% gravity list
NAME                      TYPE     DETAILS                                                             

natefoo

PLAY [localhost] ************************************************************** 

GATHERING FACTS *************************************************************** 
ok: [localhost]

TASK: [debug var=hash] ******************************************************** 
ok: [localhost] => {
    "var": {
        "hash": {
            "bar": "bar", 

natefoo

        SELECT ctimes[1] - ctimes[2]
        FROM (SELECT jsh.job_id,
                     array_agg(jsh.create_time ORDER BY jsh.create_time DESC) AS ctimes
              FROM job_state_history jsh
              JOIN job j ON jsh.job_id = j.id
              WHERE jsh.state IN ('running','ok')
                    AND j.tool_id LIKE '%/bwa_wrapper/%'
              GROUP BY jsh.job_id) AS t_arrs