jmchilton

library(mzR)
library(msdata)
library(jsonlite)
library("RSQLite")
z <- openMSfile("iTRAQ_Erwinia.mzML")
x <- openIDfile("iTRAQ_Erwinia.mzid")
p <- psms(x)
m <- modifications(x)
s <- score(x)
## add a column for the scanNum by parsing

jmchilton

#!/bin/sh
 
tags="
latest_2013.06.03:/tmp/old.patch
latest_2013.08.12:/tmp/old.patch
latest_2013.11.04:/tmp/old.patch
latest_2014.02.10:/tmp/new.patch
latest_2014.04.14:/tmp/new.patch
latest_2014.06.02:/tmp/new.patch
latest_2014.08.11:/tmp/new.patch

jmchilton

    # Is dataset an image?
    image = check_image( dataset.path )
    if image:
        if not PIL:
            image = None
        # get_image_ext() returns None if nor a supported Image type
        ext = get_image_ext( dataset.path, image )
        data_type = ext
    # Is dataset content multi-byte?
    elif dataset.is_multi_byte:

jmchilton

from bioblend import toolshed
ts = toolshed.ToolShedInstance(url='http://localhost:9009/', key="3eb77b8c27ae339e1d8056473ce1d6c2")
print ts.key
rl = ts.repositories.update_repository('adb5f5c93f827949', 'test_repo.tar.gz')
print rl

jmchilton

diff --git a/lib/galaxy/tools/deps/resolvers/tool_shed_packages.py b/lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
index d72b4d6..c54885f 100644
--- a/lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
+++ b/lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
@@ -3,6 +3,9 @@ from os.path import abspath, join, exists
 from .galaxy_packages import GalaxyPackageDependencyResolver, GalaxyPackageDependency
 from ..resolvers import INDETERMINATE_DEPENDENCY
 
+import logging
+log = logging.getLogger( __name__ )

jmchilton

Summary of new options added to universe_wsgi.ini:

display_chunk_size - Size of chunks to use when incrementally loading tabular data in the web browser.

citation_cache_type, citation_cache_data_dir, citation_cache_lock_dir - Tool citation (add this release) information maybe fetched from external sources such as http://dx.doi.org/ by Galaxy - these parameters can be used to control the caching used to store this information.

job_resource_params_file - An experimental feature allowing deployers to inject extra parameters into the tool form that can be parsed and used when allocating resources via dynamic job destinations. This option describes the tool form elements.

Options that have been removed: rsync_url, genome_data_path.

jmchilton

PR #        Open Date    Merge/Decline Date
-------------------------------------------
PR 1:       2011-07-03 - 2011-08-03
PR 4:       2011-07-25 - 2011-09-01
PR 5:       2011-08-18 - 2011-10-10
PR 8:       2011-10-05 - 2013-01-17
PR 13:      2011-10-16 - 2013-09-11
PR 177/241: 2013-06-06 - 2014-07-09
PR 419:     2014-06-13 - 2014-07-30

jmchilton

diff --git a/lib/galaxy/util/topsort.py b/lib/galaxy/util/topsort.py
index 80c6bd3..84cedae 100644
--- a/lib/galaxy/util/topsort.py
+++ b/lib/galaxy/util/topsort.py
@@ -31,9 +31,10 @@ then CycleError is raised, and the exception object supports
 many methods to help analyze and break the cycles.  This requires
 a good deal more code than topsort itself!
 """
-
+from collections import OrderedDict

jmchilton

from galaxy.util import topsort


def test_topsort_level_stability():
    data = [
        (0, 2),
        (1, 2),
        (2, 3),
        (2, 4),
        (3, 4),

jmchilton

# Setup Galaxy instance and dataset for testing...
from bioblend import galaxy
gi = galaxy.GalaxyInstance("localhost:8080", "1957431058be3aa3c57ca312f4a05521")
history = gi.histories.create_history(name="TestRandomLines")
dataset_id = gi.tools.paste_content("1\n2\n3", history["id"])['outputs'][0]["id"]

# Prepare tool inputs.
from bioblend.galaxy.tools.inputs import inputs, dataset
random_lines_inputs = inputs().set("num_lines", 1).set("input", dataset(dataset_id))