snakemake-executor-plugin-sge 0.5.9__tar.gz

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  1. snakemake_executor_plugin_sge-0.5.9/PKG-INFO +117 -0
  2. snakemake_executor_plugin_sge-0.5.9/README.md +96 -0
  3. snakemake_executor_plugin_sge-0.5.9/pyproject.toml +29 -0
  4. snakemake_executor_plugin_sge-0.5.9/snakemake_executor_plugin_sge/__init__.py +1128 -0
  5. snakemake_executor_plugin_sge-0.5.9/snakemake_executor_plugin_sge/job_cancellation.py +34 -0
  6. snakemake_executor_plugin_sge-0.5.9/snakemake_executor_plugin_sge/job_status_query.py +226 -0
  7. snakemake_executor_plugin_sge-0.5.9/snakemake_executor_plugin_sge/submit_string.py +505 -0
snakemake_executor_plugin_sge-0.5.9/PKG-INFO ADDED
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+ Metadata-Version: 2.4
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+ Name: snakemake-executor-plugin-sge
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+ Version: 0.5.9
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+ Summary: A Snakemake executor plugin for submitting jobs to SGE/UGE/OGS clusters.
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+ License: MIT
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+ Keywords: snakemake,plugin,executor,cluster,sge,uge,gridengine
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+ Author: Stylianos Charalampous
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+ Author-email: stylianosc@github.com
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+ Requires-Python: >=3.11,<4.0
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+ Classifier: License :: OSI Approved :: MIT License
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+ Classifier: Programming Language :: Python :: 3
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+ Classifier: Programming Language :: Python :: 3.11
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+ Classifier: Programming Language :: Python :: 3.12
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+ Classifier: Programming Language :: Python :: 3.13
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+ Classifier: Programming Language :: Python :: 3.14
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+ Requires-Dist: snakemake-interface-common (>=1.21.0,<2.0.0)
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+ Requires-Dist: snakemake-interface-executor-plugins (>=9.3.9,<10.0.0)
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+ Project-URL: Repository, https://github.com/stylianosc/snakemake-executor-plugin-sge
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+ Description-Content-Type: text/markdown
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+
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+ # snakemake-executor-plugin-sge
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+
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+ A [Snakemake](https://snakemake.readthedocs.io) executor plugin for
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+ **Sun Grid Engine (SGE)**, **Univa Grid Engine (UGE)**, and
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+ **Open Grid Scheduler (OGS)** clusters.
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+
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+ ## Features
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+
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+ - **Every job is an array job** – singletons become `-t 1-1`, batches become
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+ `-t 1-N`. One submission path, one tracking path, no special cases.
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+ - **Group jobs as a single array job** – Snakemake group jobs (several rules
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+ bundled together) are submitted as one qsub call.
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+ - **Rich qsub flag coverage** – queue, project, parallel environment, wall
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+ time, memory (per-slot and total), priority, requeue, reservation, notify,
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+ mail, hold_jid, task concurrency, env-var export, join logs, and arbitrary
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+ extra flags.
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+ - **Per-rule resource overrides** – any global setting can be overridden via
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+ rule `resources:` (e.g. `sge_queue`, `sge_pe`, `sge_extra`, …).
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+ - **Two-stage status polling** – `qstat` for in-flight jobs, `qacct` for
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+ completed jobs; configurable retries and optional qacct disabling.
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+ - **Clean log management** – per-task stdout/stderr, optional auto-delete on
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+ success, age-based rotation.
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+
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+ ## Installation
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+
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+ ```bash
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+ pip install snakemake-executor-plugin-sge
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+ ```
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+
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+ ## Quick start
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+
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+ ```bash
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+ snakemake --executor sge --jobs 100
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+ ```
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+
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+ ## Common options
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+
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+ | CLI flag | Default | Description |
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+ |---|---|---|
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+ | `--sge-queue` | — | Default queue (`-q`) |
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+ | `--sge-pe` | — | Parallel environment for multi-thread jobs |
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+ | `--sge-project` | — | Project (`-P`) |
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+ | `--sge-export-env` | `True` | Export environment (`-V`) |
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+ | `--sge-join-logs` | `False` | Merge stdout+stderr (`-j y`) |
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+ | `--sge-requeue` | — | Requeue on failure (`-r y/n`) |
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+ | `--sge-reservation` | — | Resource reservation (`-R y/n`) |
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+ | `--sge-notify` | `False` | Send notify signal |
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+ | `--sge-mail-on` | — | Mail events (`b`, `e`, `a`, `s`, `n`) |
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+ | `--sge-mail-address` | — | Mail address (`-M`) |
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+ | `--sge-hold-jid` | — | Hold until job(s) finish |
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+ | `--sge-array-limit` | `75000` | Max tasks per `qsub -t` call |
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+ | `--sge-task-concurrency` | — | Max concurrent array tasks (`-tc`) |
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+ | `--sge-logdir` | `.snakemake/sge_logs` | Log directory |
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+ | `--sge-keep-successful-logs` | `False` | Keep logs for successful jobs |
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+ | `--sge-use-qacct` | `True` | Use `qacct` for finished-job detection |
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+ | `--sge-extra` | — | Raw extra qsub flags (global) |
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+ | `--sge-jobname-prefix` | — | Prefix for SGE job names |
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+
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+ ## Per-rule resource overrides
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+
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+ ```python
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+ rule my_rule:
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+ resources:
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+ runtime = 120, # minutes → h_rt=02:00:00
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+ mem_mb = 8192, # total memory (divided by threads per slot)
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+ mem_mb_per_cpu = 2048, # per-slot memory (takes precedence)
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+ threads = 4,
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+ sge_queue = "highmem.q",
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+ sge_pe = "smp",
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+ sge_project = "myproject",
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+ sge_extra = "-l gpu=1", # arbitrary extra qsub flags
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+ sge_resources = {"h_cpu": "24:00:00", "arch": "lx-amd64"},
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+ sge_join_logs = True,
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+ sge_requeue = True,
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+ sge_priority = -100,
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+ sge_notify = True,
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+ sge_mail_on = "e",
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+ sge_mail_address = "me@example.com",
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+ sge_hold_jid = "12345",
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+ sge_task_concurrency = 8,
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+ sge_export_env = False,
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+ threads: 4
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+ shell: "..."
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+ ```
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+
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+ ## Array-job design
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+
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+ Every qsub submission uses `qsub -t start-end`. Execution commands are
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+ stored in a JSON file on the shared filesystem before `qsub` is called. The
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+ submission script reads `$SGE_TASK_ID`, looks up the compressed command, and
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+ evaluates it. This avoids command-line length limits and all heredoc/quoting
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+ problems.
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+
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+ ## License
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+
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+ MIT
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+
snakemake_executor_plugin_sge-0.5.9/README.md ADDED
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+ # snakemake-executor-plugin-sge
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+
3
+ A [Snakemake](https://snakemake.readthedocs.io) executor plugin for
4
+ **Sun Grid Engine (SGE)**, **Univa Grid Engine (UGE)**, and
5
+ **Open Grid Scheduler (OGS)** clusters.
6
+
7
+ ## Features
8
+
9
+ - **Every job is an array job** – singletons become `-t 1-1`, batches become
10
+ `-t 1-N`. One submission path, one tracking path, no special cases.
11
+ - **Group jobs as a single array job** – Snakemake group jobs (several rules
12
+ bundled together) are submitted as one qsub call.
13
+ - **Rich qsub flag coverage** – queue, project, parallel environment, wall
14
+ time, memory (per-slot and total), priority, requeue, reservation, notify,
15
+ mail, hold_jid, task concurrency, env-var export, join logs, and arbitrary
16
+ extra flags.
17
+ - **Per-rule resource overrides** – any global setting can be overridden via
18
+ rule `resources:` (e.g. `sge_queue`, `sge_pe`, `sge_extra`, …).
19
+ - **Two-stage status polling** – `qstat` for in-flight jobs, `qacct` for
20
+ completed jobs; configurable retries and optional qacct disabling.
21
+ - **Clean log management** – per-task stdout/stderr, optional auto-delete on
22
+ success, age-based rotation.
23
+
24
+ ## Installation
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+
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+ ```bash
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+ pip install snakemake-executor-plugin-sge
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+ ```
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+
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+ ## Quick start
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+
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+ ```bash
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+ snakemake --executor sge --jobs 100
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+ ```
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+
36
+ ## Common options
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+
38
+ | CLI flag | Default | Description |
39
+ |---|---|---|
40
+ | `--sge-queue` | — | Default queue (`-q`) |
41
+ | `--sge-pe` | — | Parallel environment for multi-thread jobs |
42
+ | `--sge-project` | — | Project (`-P`) |
43
+ | `--sge-export-env` | `True` | Export environment (`-V`) |
44
+ | `--sge-join-logs` | `False` | Merge stdout+stderr (`-j y`) |
45
+ | `--sge-requeue` | — | Requeue on failure (`-r y/n`) |
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+ | `--sge-reservation` | — | Resource reservation (`-R y/n`) |
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+ | `--sge-notify` | `False` | Send notify signal |
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+ | `--sge-mail-on` | — | Mail events (`b`, `e`, `a`, `s`, `n`) |
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+ | `--sge-mail-address` | — | Mail address (`-M`) |
50
+ | `--sge-hold-jid` | — | Hold until job(s) finish |
51
+ | `--sge-array-limit` | `75000` | Max tasks per `qsub -t` call |
52
+ | `--sge-task-concurrency` | — | Max concurrent array tasks (`-tc`) |
53
+ | `--sge-logdir` | `.snakemake/sge_logs` | Log directory |
54
+ | `--sge-keep-successful-logs` | `False` | Keep logs for successful jobs |
55
+ | `--sge-use-qacct` | `True` | Use `qacct` for finished-job detection |
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+ | `--sge-extra` | — | Raw extra qsub flags (global) |
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+ | `--sge-jobname-prefix` | — | Prefix for SGE job names |
58
+
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+ ## Per-rule resource overrides
60
+
61
+ ```python
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+ rule my_rule:
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+ resources:
64
+ runtime = 120, # minutes → h_rt=02:00:00
65
+ mem_mb = 8192, # total memory (divided by threads per slot)
66
+ mem_mb_per_cpu = 2048, # per-slot memory (takes precedence)
67
+ threads = 4,
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+ sge_queue = "highmem.q",
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+ sge_pe = "smp",
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+ sge_project = "myproject",
71
+ sge_extra = "-l gpu=1", # arbitrary extra qsub flags
72
+ sge_resources = {"h_cpu": "24:00:00", "arch": "lx-amd64"},
73
+ sge_join_logs = True,
74
+ sge_requeue = True,
75
+ sge_priority = -100,
76
+ sge_notify = True,
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+ sge_mail_on = "e",
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+ sge_mail_address = "me@example.com",
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+ sge_hold_jid = "12345",
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+ sge_task_concurrency = 8,
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+ sge_export_env = False,
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+ threads: 4
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+ shell: "..."
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+ ```
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+
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+ ## Array-job design
87
+
88
+ Every qsub submission uses `qsub -t start-end`. Execution commands are
89
+ stored in a JSON file on the shared filesystem before `qsub` is called. The
90
+ submission script reads `$SGE_TASK_ID`, looks up the compressed command, and
91
+ evaluates it. This avoids command-line length limits and all heredoc/quoting
92
+ problems.
93
+
94
+ ## License
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+
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+ MIT
snakemake_executor_plugin_sge-0.5.9/pyproject.toml ADDED
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+ [tool.poetry]
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+ name = "snakemake-executor-plugin-sge"
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+ version = "0.5.9"
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+ description = "A Snakemake executor plugin for submitting jobs to SGE/UGE/OGS clusters."
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+ authors = ["Stylianos Charalampous <stylianosc@github.com>"]
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+ readme = "README.md"
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+ license = "MIT"
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+ repository = "https://github.com/stylianosc/snakemake-executor-plugin-sge"
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+ keywords = ["snakemake", "plugin", "executor", "cluster", "sge", "uge", "gridengine"]
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+
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+ [tool.poetry.dependencies]
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+ python = "^3.11"
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+ snakemake-interface-common = "^1.21.0"
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+ snakemake-interface-executor-plugins = "^9.3.9"
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+
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+ [tool.poetry.group.dev.dependencies]
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+ black = "^23.7.0"
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+ flake8 = "^6.1.0"
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+ pytest = "^8.3.5"
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+
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+ [tool.black]
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+ line-length = 88
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+
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+ [tool.pytest.ini_options]
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+ python_files = ["test_*.py"]
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+
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+ [build-system]
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+ requires = ["poetry-core"]
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+ build-backend = "poetry.core.masonry.api"