From bbbfde85efe507d0348f24326337ce5672726b70 Mon Sep 17 00:00:00 2001 From: Dave B Date: Tue, 18 May 2021 15:42:22 -0400 Subject: [PATCH 1/4] Open input file in read mode --- tools/extract/liftOver_wrapper.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/extract/liftOver_wrapper.py b/tools/extract/liftOver_wrapper.py index 6a59ddc6822..3ceb1c7a0d2 100644 --- a/tools/extract/liftOver_wrapper.py +++ b/tools/extract/liftOver_wrapper.py @@ -25,7 +25,7 @@ def safe_bed_file(infile): https://lists.soe.ucsc.edu/pipermail/genome/2007-May/013561.html """ fix_pat = re.compile("^(track|browser)") - with tempfile.NamedTemporaryFile(mode='w', delete=False) as out_handle, open(infile, 'w') as in_handle: + with tempfile.NamedTemporaryFile(mode='w', delete=False) as out_handle, open(infile, 'r') as in_handle: for line in in_handle: if fix_pat.match(line): line = "#" + line From abd3b7a2935e454fd692e11be8d15c3614ece484 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Fri, 21 May 2021 14:51:24 -0400 Subject: [PATCH 2/4] Version 21.1.1 of tool-util (tag galaxy-tool-util-21.1.1). --- packages/tool_util/HISTORY.rst | 2 +- packages/tool_util/galaxy/project_galaxy_tool_util.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst index f6fce4fb098..ff5680758c9 100644 --- a/packages/tool_util/HISTORY.rst +++ b/packages/tool_util/HISTORY.rst @@ -6,7 +6,7 @@ History .. to_doc --------------------- -21.1.1.dev0 +21.1.1 (2021-05-21) --------------------- diff --git a/packages/tool_util/galaxy/project_galaxy_tool_util.py b/packages/tool_util/galaxy/project_galaxy_tool_util.py index a9cc5a8b7af..785f40a84a4 100644 --- a/packages/tool_util/galaxy/project_galaxy_tool_util.py +++ b/packages/tool_util/galaxy/project_galaxy_tool_util.py @@ -1,4 +1,4 @@ -__version__ = '21.1.1.dev0' +__version__ = '21.1.1' PROJECT_NAME = "galaxy-tool-util" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From 9a97d616f8d8c1eaf89de8d9a14397f8ddbf9bb1 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Fri, 21 May 2021 14:52:02 -0400 Subject: [PATCH 3/4] Starting work on tool-util 21.1.2 --- packages/tool_util/HISTORY.rst | 6 ++++++ packages/tool_util/galaxy/project_galaxy_tool_util.py | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst index ff5680758c9..053ba4ab90e 100644 --- a/packages/tool_util/HISTORY.rst +++ b/packages/tool_util/HISTORY.rst @@ -5,6 +5,12 @@ History .. to_doc +--------------------- +21.1.2.dev0 +--------------------- + + + --------------------- 21.1.1 (2021-05-21) --------------------- diff --git a/packages/tool_util/galaxy/project_galaxy_tool_util.py b/packages/tool_util/galaxy/project_galaxy_tool_util.py index 785f40a84a4..fb12eda4e1b 100644 --- a/packages/tool_util/galaxy/project_galaxy_tool_util.py +++ b/packages/tool_util/galaxy/project_galaxy_tool_util.py @@ -1,4 +1,4 @@ -__version__ = '21.1.1' +__version__ = '21.1.2.dev0' PROJECT_NAME = "galaxy-tool-util" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From 533f86287dd726e689f38634aa825946c213de09 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 23 May 2021 12:26:34 +0200 Subject: [PATCH 4/4] add GALAXY_MEMORY_MB* to passt hrough --- lib/galaxy/tool_util/deps/dependencies.py | 2 +- lib/galaxy/tool_util/parser/interface.py | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/tool_util/deps/dependencies.py b/lib/galaxy/tool_util/deps/dependencies.py index 2d362f8cbc1..760eac66239 100644 --- a/lib/galaxy/tool_util/deps/dependencies.py +++ b/lib/galaxy/tool_util/deps/dependencies.py @@ -42,7 +42,7 @@ class ToolInfo: def __init__(self, container_descriptions=None, requirements=None, requires_galaxy_python_environment=False, env_pass_through=None, guest_ports=None, tool_id=None, tool_version=None, profile=-1): if env_pass_through is None: - env_pass_through = ["GALAXY_SLOTS"] + env_pass_through = ["GALAXY_SLOTS", "GALAXY_MEMORY_MB", "GALAXY_MEMORY_MB_PER_SLOT"] if container_descriptions is None: container_descriptions = [] if requirements is None: diff --git a/lib/galaxy/tool_util/parser/interface.py b/lib/galaxy/tool_util/parser/interface.py index 8c549f3aa4a..96c974dd2d2 100644 --- a/lib/galaxy/tool_util/parser/interface.py +++ b/lib/galaxy/tool_util/parser/interface.py @@ -110,7 +110,8 @@ class ToolSource(metaclass=ABCMeta): return ["TMPDIR", "TMP", "TEMP"] def parse_docker_env_pass_through(self): - return ["GALAXY_SLOTS", "HOME", "_GALAXY_JOB_HOME_DIR", "_GALAXY_JOB_TMP_DIR"] + self.parse_tmp_directory_vars() + return ["GALAXY_SLOTS", "GALAXY_MEMORY_MB", "GALAXY_MEMORY_MB_PER_SLOT", "HOME", + "_GALAXY_JOB_HOME_DIR", "_GALAXY_JOB_TMP_DIR"] + self.parse_tmp_directory_vars() @abstractmethod def parse_interpreter(self):