Updating anvil-edge README for edge-24-09-11-06-11-1

anvilproject · Sep 11, 2024 · 8f7f84c · 8f7f84c
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diff --git a/reports/anvil-edge/README.md b/reports/anvil-edge/README.md
diff --git a/reports/anvil-edge/tool-tests/chunks.json b/reports/anvil-edge/tool-tests/chunks.json
@@ -21,11 +21,11 @@
         "date2": "Tue Sep 03 18:31:25 2024"
     },
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-        "date1": "Wed Aug 28 06:26:28 2024",
-        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-28-06-10-1/tools.yml",
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-        "date2": "Wed Aug 21 06:25:47 2024"
+        "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-11-06-11-1/results.html",
+        "date1": "Wed Sep 11 06:26:47 2024",
+        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-11-06-11-1/tools.yml",
+        "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-28-06-10-1/results.html",
+        "date2": "Wed Aug 28 06:26:28 2024"
     },
     "5": {
         "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/results.html",

diff --git a/reports/anvil-edge/tool-tests/edge-24-09-11-06-11-1/chunk.json b/reports/anvil-edge/tool-tests/edge-24-09-11-06-11-1/chunk.json
@@ -0,0 +1,7 @@
+{
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+        "date1": "Wed Sep 11 06:26:47 2024",
+        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-11-06-11-1/tools.yml"
+    }
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-09-11-06-11-1/chunk.txt b/reports/anvil-edge/tool-tests/edge-24-09-11-06-11-1/chunk.txt
@@ -0,0 +1,23 @@
+-t bedtools --tool-version ce3c7f062223
+-t bedtools --tool-version 07e8b80f278c
+-t deeptools_correct_gc_bias --tool-version 2c37ce318bc3
+-t fasta_compute_length --tool-version 7d37cfda8e00
+-t pygenometracks --tool-version 2824d77cd8f8
+-t mummer_dnadiff --tool-version 60698466facd
+-t poretools_yield_plot --tool-version ca22d8497db5
+-t deseq2 --tool-version 6a3a025714d3
+-t bamtools_split --tool-version 9676127a1ed2
+-t samtool_filter2 --tool-version 649a225999a5
+-t music_deconvolution --tool-version 2ba99a52bd44
+-t raceid_filtnormconf --tool-version c891d8b33ede
+-t raceid_filtnormconf --tool-version 43c146e25a43
+-t scanpy_cluster_reduce_dimension --tool-version aaa5da8e73a9
+-t scanpy_filter_genes --tool-version 7857ea93a011
+-t scanpy_filter_genes --tool-version a1698b43abeb
+-t sqlite_to_tabular --tool-version bce29ec10b78
+-t replace_column_by_key_value_file --tool-version d533e4b75800
+-t jasminesv --tool-version 2b62154e39c8
+-t bcftools_convert_from_vcf --tool-version b8e9da766b0f
+-t bcftools_plugin_dosage --tool-version 5c232a738c74
+-t vcfflatten --tool-version f285aa6bdcfb
+-t vcftools_slice --tool-version 1363e5d4a8b8
diff --git a/reports/anvil-edge/tool-tests/edge-24-09-11-06-11-1/errors/2f09a516f940d5e9.json b/reports/anvil-edge/tool-tests/edge-24-09-11-06-11-1/errors/2f09a516f940d5e9.json
@@ -0,0 +1,45 @@
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+        "file_count": "\"auto\"",
+        "file_type": "\"auto\""
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+            "id": "d65c0261000acf84",
+            "src": "hda",
+            "uuid": "6ea2e8c5-8ea9-483f-8522-2901b4351723"
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+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-09-11-06-11-1/errors/4784dddddc8e7937.json b/reports/anvil-edge/tool-tests/edge-24-09-11-06-11-1/errors/4784dddddc8e7937.json
@@ -0,0 +1,45 @@
+{
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+    "external_id": "gxy-rvkld",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/156/registry.xml' '/galaxy/server/database/jobs_directory/000/156/upload_params.json' '225:/galaxy/server/database/objects/8/2/b/dataset_82b68007-ac66-4964-9ba7-1ea7beefec27_files:/galaxy/server/database/objects/8/2/b/dataset_82b68007-ac66-4964-9ba7-1ea7beefec27.dat'",
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+            "src": "hda",
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+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-09-11-06-11-1/errors/4801aeef02223711.json b/reports/anvil-edge/tool-tests/edge-24-09-11-06-11-1/errors/4801aeef02223711.json
@@ -0,0 +1,45 @@
+{
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+    "id": "4801aeef02223711",
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+    "external_id": "gxy-wm6mv",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/66/registry.xml' '/galaxy/server/database/jobs_directory/000/66/upload_params.json' '69:/galaxy/server/database/objects/d/b/3/dataset_db31ee7c-71fa-4df0-a21b-62e3583cfeb5_files:/galaxy/server/database/objects/d/b/3/dataset_db31ee7c-71fa-4df0-a21b-62e3583cfeb5.dat'",
+    "user_email": "tests@fake.org",
+    "command_version": null,
+    "params": {
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+        "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+        "dbkey": "\"?\"",
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+        "files": "[{\"NAME\": \"sailfish_quant.sf4.tab\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_1sgi_xd7\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+        "file_count": "\"auto\"",
+        "file_type": "\"auto\""
+    },
+    "inputs": {},
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+        "output0": {
+            "id": "3345412decec5cf3",
+            "src": "hda",
+            "uuid": "db31ee7c-71fa-4df0-a21b-62e3583cfeb5"
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+    "stdout": "",
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+    "dependencies": [],
+    "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-09-11-06-11-1/errors/490c12acf889139f.json b/reports/anvil-edge/tool-tests/edge-24-09-11-06-11-1/errors/490c12acf889139f.json
@@ -0,0 +1,45 @@
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+    "galaxy_version": "24.1",
+    "external_id": "gxy-n8rgg",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/182/registry.xml' '/galaxy/server/database/jobs_directory/000/182/upload_params.json' '258:/galaxy/server/database/objects/9/f/3/dataset_9f30f320-85f5-488c-849c-cd0257483c79_files:/galaxy/server/database/objects/9/f/3/dataset_9f30f320-85f5-488c-849c-cd0257483c79.dat'",
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+    "command_version": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_fc6zewmf\"",
+        "files_metadata": "{\"__current_case__\": 342, \"file_type\": \"vcf\"}",
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+        "file_count": "\"auto\"",
+        "file_type": "\"vcf\""
+    },
+    "inputs": {},
+    "outputs": {
+        "output0": {
+            "id": "cc00da642815bf69",
+            "src": "hda",
+            "uuid": "9f30f320-85f5-488c-849c-cd0257483c79"
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+    "copied_from_job_id": null,
+    "output_collections": {},
+    "tool_stdout": "",
+    "tool_stderr": "",
+    "job_stdout": null,
+    "job_stderr": null,
+    "stdout": "",
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+    "job_messages": null,
+    "dependencies": [],
+    "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-09-11-06-11-1/errors/5e0f1f0e43b29f03.json b/reports/anvil-edge/tool-tests/edge-24-09-11-06-11-1/errors/5e0f1f0e43b29f03.json
@@ -0,0 +1,56 @@
+{
+    "model_class": "Job",
+    "id": "5e0f1f0e43b29f03",
+    "history_id": "966387fad1972f6d",
+    "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1",
+    "state": "error",
+    "exit_code": null,
+    "create_time": "2024-09-11T06:47:37.033614",
+    "update_time": "2024-09-11T06:47:41.982935",
+    "galaxy_version": "24.1",
+    "external_id": "gxy-x6dtv",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "ln -s '/galaxy/server/database/objects/1/9/d/dataset_19d10d81-7fc6-4ce6-8d6a-7b914e121937.dat' input.sam && samtools view -o '/galaxy/server/database/objects/9/2/a/dataset_92aacc2d-66f7-4208-a395-0f4cf863ea71.dat'   -S   -r 'rg1' input.sam",
+    "user_email": "tests@fake.org",
+    "command_version": null,
+    "params": {
+        "__input_ext": "\"sam\"",
+        "dbkey": "\"?\"",
+        "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+        "outputtype": "\"sam\"",
+        "regions": "\"\"",
+        "possibly_select_inverse": "false",
+        "bed_file": null,
+        "read_group": "\"rg1\"",
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+        "flag": "{\"__current_case__\": 0, \"filter\": \"no\"}",
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+        "header": "\"\""
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+            "src": "hda",
+            "uuid": "19d10d81-7fc6-4ce6-8d6a-7b914e121937"
+        }
+    },
+    "outputs": {
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+            "id": "64b5e97886eb0aae",
+            "src": "hda",
+            "uuid": "92aacc2d-66f7-4208-a395-0f4cf863ea71"
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+    "stdout": "",
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+    "job_messages": null,
+    "dependencies": [],
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+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-09-11-06-11-1/errors/6ee1da2681bf950e.json b/reports/anvil-edge/tool-tests/edge-24-09-11-06-11-1/errors/6ee1da2681bf950e.json
@@ -0,0 +1,45 @@
+{
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+        "dbkey": "\"?\"",
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+        "file_count": "\"auto\"",
+        "file_type": "\"auto\""
+    },
+    "inputs": {},
+    "outputs": {
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+            "id": "921e95927684a600",
+            "src": "hda",
+            "uuid": "7d3bc67f-3c95-432b-96a7-0f11b7caadf9"
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+    "job_stderr": null,
+    "stdout": "",
+    "stderr": "",
+    "job_messages": null,
+    "dependencies": [],
+    "job_metrics": []
+}