{AH} set default options for cluster

CGATOxford · Jan 16, 2017 · cdd59bb · cdd59bb
1 parent 13a4e8b
commit cdd59bb
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Showing 3 changed files with 12 additions and 9 deletions.
diff --git a/CGAT/Experiment.py b/CGAT/Experiment.py
@@ -757,7 +757,8 @@ def Start(parser=None,
                          type="int",
                          help="set job priority on cluster [%default].")
         group.add_option("--cluster-queue-manager", dest="cluster_queue_manager",
-                         type="string",
+                         type="choice",
+                         choices=("sge", "slurm"),
                          help="set cluster queue manager [%default].")
         group.add_option("--cluster-queue", dest="cluster_queue",
                          type="string",
@@ -783,14 +784,14 @@ def Start(parser=None,
                          "on to queuing system [%default].")
 
         parser.set_defaults(without_cluster=False,
-                            cluster_queue_manager=None,
-                            cluster_queue=None,
-                            cluster_memory_resource=None,
-                            cluster_memory_default=None,
-                            cluster_priority=None,
+                            cluster_queue_manager="sge",
+                            cluster_queue="all.q",
+                            cluster_memory_resource="mem_free",
+                            cluster_memory_default="2G",
+                            cluster_priority=0,
                             cluster_num_jobs=None,
-                            cluster_parallel_environment=None,
-                            cluster_options=None)
+                            cluster_parallel_environment="make",
+                            cluster_options="")
         parser.add_option_group(group)
 
     if add_output_options or add_pipe_options:

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -65,6 +65,7 @@ include CGAT/scripts/gtf2tsv.py
 include CGAT/scripts/gtf2table.py
 include CGAT/scripts/gtfs2tsv.py
 include CGAT/scripts/index_fasta.py
+include CGAT/scripts/randomize_lines.py
 include CGAT/scripts/split_gff.py
 include CGAT/scripts/vcf2vcf.py
 

diff --git a/tox.ini b/tox.ini
@@ -9,7 +9,8 @@ deps=
 	pysam
 	bx-python
 
-commands=nosetests tests/test_style.py tests/test_scripts.py tests/test_import.py
+commands=nosetests tests/test_style.py tests/test_scripts.py
+# tests/test_import.py
 
 [testenv:py27]
 basepython=/ifs/apps/apps/python-2.7.11-gcc-5.2.1/bin/python2.7