Merge remote-tracking branch 'upstream/release_20.09' into release_21.01

2026-09-24 16:30:27 +08:00 · 2021-03-01 16:47:23 -05:00
parent 064a54fa3e 373489e8f4
commit 7ed0f5337f
11 changed files with 22 additions and 12 deletions
@@ -83,9 +83,9 @@ class CondorJobRunner(AsynchronousJobRunner):

        galaxy_slots = query_params.get('request_cpus', None)
        if galaxy_slots:
-            galaxy_slots_statement = 'GALAXY_SLOTS="%s"; export GALAXY_SLOTS_CONFIGURED="1"' % galaxy_slots
+            galaxy_slots_statement = 'GALAXY_SLOTS="%s"; export GALAXY_SLOTS; GALAXY_SLOTS_CONFIGURED="1"; export GALAXY_SLOTS_CONFIGURED;' % galaxy_slots
        else:
-            galaxy_slots_statement = 'GALAXY_SLOTS="1"'
+            galaxy_slots_statement = 'GALAXY_SLOTS="1"; export GALAXY_SLOTS;'

        # define job attributes
        cjs = CondorJobState(
@@ -30,3 +30,4 @@ else
    GALAXY_SLOTS="1"
    unset GALAXY_SLOTS_CONFIGURED
 fi
+export GALAXY_SLOTS
@@ -27,13 +27,14 @@ _galaxy_setup_environment() {

 $integrity_injection
 $slots_statement
-export GALAXY_SLOTS
 export PYTHONWARNINGS="ignore"
 GALAXY_VIRTUAL_ENV="$galaxy_virtual_env"
 _GALAXY_VIRTUAL_ENV="$galaxy_virtual_env"
 PRESERVE_GALAXY_ENVIRONMENT="$preserve_python_environment"
 GALAXY_LIB="$galaxy_lib"
 _galaxy_setup_environment "$PRESERVE_GALAXY_ENVIRONMENT"
+export _GALAXY_JOB_HOME_DIR
+export _GALAXY_JOB_TMP_DIR
 GALAXY_PYTHON=`command -v python`
 cd $working_directory
 $memory_statement
@@ -80,7 +80,7 @@ def job_script(template=DEFAULT_JOB_FILE_TEMPLATE, **kwds):
    >>> script.startswith('#!/bin/bash\\n\\n#PBS -test\\n')
    True
    >>> script = job_script(working_directory='wd', command='uptime', exit_code_path='ec', slots_statement='GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"')
-    >>> script.find('GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"\\nexport GALAXY_SLOTS\\n') > 0
+    >>> script.find('GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"\\n') > 0
    True
    >>> script = job_script(working_directory='wd', command='uptime', exit_code_path='ec', memory_statement='GALAXY_MEMORY_MB="32768"')
    >>> script.find('GALAXY_MEMORY_MB="32768"\\n') > 0
@@ -200,7 +200,6 @@ class HasDockerLikeVolumes:
        add_var("library_import_dir", self.app_info.library_import_dir)
        add_var('tool_data_path', self.app_info.tool_data_path)
        add_var('shed_tool_data_path', self.app_info.shed_tool_data_path)
-
        if self.job_info.job_directory and self.job_info.job_directory_type == "pulsar":
            # We have a Pulsar job directory, so everything needed (excluding index
            # files) should be available in job_directory...
@@ -248,7 +247,6 @@ class HasDockerLikeVolumes:
            if end_index < 0:
                end_index = len(volumes_str)
            volumes_str = volumes_str[0:tool_directory_index] + volumes_str[end_index:len(volumes_str)]
-
        return volumes_str


@@ -299,8 +297,9 @@ class DockerContainer(Container, HasDockerLikeVolumes):
        # and Galaxy.
        if self.job_info.tmp_directory is not None:
            volumes.append(DockerVolume.from_str("%s:/tmp:rw" % self.job_info.tmp_directory))
+        else:
+            volumes.append(DockerVolume.from_str("$_GALAXY_JOB_TMP_DIR:$_GALAXY_JOB_TMP_DIR:rw"))
        volumes_from = self.destination_info.get("docker_volumes_from", docker_util.DEFAULT_VOLUMES_FROM)
-
        docker_host_props = self.docker_host_props

        cached_image_file = self.__get_cached_image_file()
@@ -3162,6 +3162,7 @@ Name | Description
 ``\${GALAXY_SLOTS:-4}`` | Number of cores/threads allocated by the job runner or resource manager to the tool for the given job (here 4 is the default number of threads to use if running via custom runner that does not configure GALAXY_SLOTS or in an older Galaxy runtime).
 ``\$GALAXY_MEMORY_MB`` | Total amount of memory in megabytes (1024^2 bytes) allocated by the administrator (via the resource manager) to the tool for the given job. If unset, tools should not attempt to limit memory usage.
 ``\$GALAXY_MEMORY_MB_PER_SLOT`` | Amount of memory per slot in megabytes (1024^2 bytes) allocated by the administrator (via the resource manager) to the tool for the given job. If unset, tools should not attempt to limit memory usage.
+``\$_GALAXY_JOB_TMP_DIR`` | Path to an empty directory in the job's working directory that can be used as a temporary directory.

 See the [Planemo docs](https://planemo.readthedocs.io/en/latest/writing_advanced.html#cluster-usage)
 on the topic of ``GALAXY_SLOTS`` for more information and examples.
@@ -6,7 +6,13 @@ History
 .. to_doc

 ---------------------
-20.9.1.dev0
+20.9.2.dev0
+---------------------
+
+
+
+---------------------
+20.9.1 (2021-03-01)
 ---------------------


@@ -1,4 +1,4 @@
-__version__ = '20.9.1.dev0'
+__version__ = '20.9.2.dev0'

 PROJECT_NAME = "galaxy-objectstore"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
@@ -10,7 +10,9 @@ echo \$(id -g) > '$group_id' &&
 echo \$(pwd) > '$pwd' &&
 echo "\$HOME" > '$home' &&
 echo "\$TMP"  > '$tmp' &&
-echo "\$SOME_ENV_VAR" > '$some_env_var'
+echo "\$SOME_ENV_VAR" > '$some_env_var' &&
+touch "\$_GALAXY_JOB_TMP_DIR/tmp_test" &&
+touch "\$HOME/home_test"
    ]]></command>
    <inputs>
    </inputs>
@@ -14,6 +14,6 @@ def dyndest_chain_2():


 def dyndest_chain_3(tmp_dir_prefix_two):
-    tmp_dir = '$(mktemp %sand3XXXXXXXXXXXX)' % tmp_dir_prefix_two
+    tmp_dir = '$(mktemp -d -p $(pwd) %sand3XXXXXXXXXXXX)' % tmp_dir_prefix_two
    return JobDestination(runner="local",
                          params={'tmp_dir': tmp_dir})
@@ -6,7 +6,7 @@

    <destinations>
        <destination id="local_dest" runner="local">
-            <param id="tmp_dir">$(mktemp cooltmpXXXXXXXXXXXX)</param>
+            <param id="tmp_dir">$(mktemp -d -p $(pwd) cooltmpXXXXXXXXXXXX)</param>
        </destination>
    </destinations>