Updating anvil-edge README for edge-24-09-04-18-15-1

anvilproject · Sep 4, 2024 · 73d533f · 73d533f
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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
@@ -28,11 +28,11 @@
         "date2": "Wed Aug 21 06:25:47 2024"
     },
     "5": {
-        "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-21-18-16-1/results.html",
-        "date1": "Wed Aug 21 18:31:30 2024",
-        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-21-18-16-1/tools.yml",
-        "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-14-18-15-1/results.html",
-        "date2": "Wed Aug 14 18:31:52 2024"
+        "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",
+        "date1": "Wed Sep 04 18:30:27 2024",
+        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/tools.yml",
+        "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-21-18-16-1/results.html",
+        "date2": "Wed Aug 21 18:31:30 2024"
     },
     "6": {
         "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-29-06-11-1/results.html",

diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/chunk.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/chunk.json
@@ -0,0 +1,7 @@
+{
+    "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",
+        "date1": "Wed Sep 04 18:30:27 2024",
+        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/tools.yml"
+    }
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/chunk.txt b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/chunk.txt
@@ -0,0 +1,25 @@
+-t collapse_collections --tool-version 90981f86000f
+-t deeptools_multi_bam_summary --tool-version 78f405266706
+-t fastq_paired_end_deinterlacer --tool-version f3936d0632cb
+-t circos --tool-version df7356989ac1
+-t mummer_mummer --tool-version 48823c9635a4
+-t porechop --tool-version 93d623d9979c
+-t limma_voom --tool-version 0921444c832d
+-t limma_voom --tool-version d6f5fa4ee473
+-t sam2interval --tool-version 75557c0908a9
+-t samtools_flagstat --tool-version 22970df7a40e
+-t music_construct_eset --tool-version 282819d09a4f
+-t music_construct_eset --tool-version 2cfd0db49bbc
+-t raceid_clustering --tool-version a4b734cd253b
+-t raceid_clustering --tool-version f911a64454fb
+-t scanpy_filter --tool-version b409c2486353
+-t scanpy_normalise_data --tool-version 439f7f939d46
+-t scanpy_normalise_data --tool-version 463d4fa8f5ec
+-t annotatemyids --tool-version 44018dd6b447
+-t annotatemyids --tool-version fe3ca740a485
+-t diff --tool-version 156d0908e232
+-t bcftools_consensus --tool-version d6dc477167f8
+-t bcftools_plugin_impute_info --tool-version 776ad0b21536
+-t bcftools_query --tool-version c9c5718edc19
+-t vcfgeno2haplo --tool-version a3dea556218d
+-t ivar_trim --tool-version db536ad45f28
diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/041a65779e107113.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/041a65779e107113.json
@@ -0,0 +1,45 @@
+{
+    "model_class": "Job",
+    "id": "041a65779e107113",
+    "history_id": "3cbec5b19229f469",
+    "tool_id": "upload1",
+    "state": "error",
+    "exit_code": null,
+    "create_time": "2024-09-04T18:44:20.942480",
+    "update_time": "2024-09-04T18:44:32.249013",
+    "galaxy_version": "24.1",
+    "external_id": "gxy-qzjfw",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/43/registry.xml' '/galaxy/server/database/jobs_directory/000/43/upload_params.json' '63:/galaxy/server/database/objects/a/7/b/dataset_a7b30079-21c9-45a3-8c69-6c7fd289d76b_files:/galaxy/server/database/objects/a/7/b/dataset_a7b30079-21c9-45a3-8c69-6c7fd289d76b.dat'",
+    "user_email": "tests@fake.org",
+    "command_version": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_q3aevr1i\"",
+        "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"factorinfo.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_3u_pu91e\", \"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": {},
+    "outputs": {
+        "output0": {
+            "id": "4bad1a2b93025157",
+            "src": "hda",
+            "uuid": "a7b30079-21c9-45a3-8c69-6c7fd289d76b"
+        }
+    },
+    "copied_from_job_id": null,
+    "output_collections": {},
+    "tool_stdout": "",
+    "tool_stderr": "",
+    "job_stdout": null,
+    "job_stderr": null,
+    "stdout": "",
+    "stderr": "",
+    "job_messages": null,
+    "dependencies": [],
+    "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/09976a7dbbbe05e4.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/09976a7dbbbe05e4.json
@@ -0,0 +1,45 @@
+{
+    "model_class": "Job",
+    "id": "09976a7dbbbe05e4",
+    "history_id": "3cbec5b19229f469",
+    "tool_id": "upload1",
+    "state": "error",
+    "exit_code": null,
+    "create_time": "2024-09-04T19:23:53.373692",
+    "update_time": "2024-09-04T19:24:03.542977",
+    "galaxy_version": "24.1",
+    "external_id": "gxy-5f2lr",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/163/registry.xml' '/galaxy/server/database/jobs_directory/000/163/upload_params.json' '245:/galaxy/server/database/objects/d/f/7/dataset_df78a9b9-6910-4c9e-839d-ff43b481a802_files:/galaxy/server/database/objects/d/f/7/dataset_df78a9b9-6910-4c9e-839d-ff43b481a802.dat'",
+    "user_email": "tests@fake.org",
+    "command_version": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_osxn731w\"",
+        "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"file1.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_o3j_y0qq\", \"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": {},
+    "outputs": {
+        "output0": {
+            "id": "061a6db00a48f33c",
+            "src": "hda",
+            "uuid": "df78a9b9-6910-4c9e-839d-ff43b481a802"
+        }
+    },
+    "copied_from_job_id": null,
+    "output_collections": {},
+    "tool_stdout": "",
+    "tool_stderr": "",
+    "job_stdout": null,
+    "job_stderr": null,
+    "stdout": "",
+    "stderr": "",
+    "job_messages": null,
+    "dependencies": [],
+    "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/0a3d65af2197e1a0.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/0a3d65af2197e1a0.json
@@ -0,0 +1,45 @@
+{
+    "model_class": "Job",
+    "id": "0a3d65af2197e1a0",
+    "history_id": "3cbec5b19229f469",
+    "tool_id": "upload1",
+    "state": "error",
+    "exit_code": null,
+    "create_time": "2024-09-04T19:24:41.130085",
+    "update_time": "2024-09-04T19:24:50.813497",
+    "galaxy_version": "24.1",
+    "external_id": "gxy-zc5zr",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/167/registry.xml' '/galaxy/server/database/jobs_directory/000/167/upload_params.json' '249:/galaxy/server/database/objects/a/2/a/dataset_a2a9b0f2-5655-4eb9-a9b4-56d732807c61_files:/galaxy/server/database/objects/a/2/a/dataset_a2a9b0f2-5655-4eb9-a9b4-56d732807c61.dat'",
+    "user_email": "tests@fake.org",
+    "command_version": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_pq6mum_m\"",
+        "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"file1.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_b39zz2e0\", \"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": {},
+    "outputs": {
+        "output0": {
+            "id": "8b09306c242ed41b",
+            "src": "hda",
+            "uuid": "a2a9b0f2-5655-4eb9-a9b4-56d732807c61"
+        }
+    },
+    "copied_from_job_id": null,
+    "output_collections": {},
+    "tool_stdout": "",
+    "tool_stderr": "",
+    "job_stdout": null,
+    "job_stderr": null,
+    "stdout": "",
+    "stderr": "",
+    "job_messages": null,
+    "dependencies": [],
+    "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/0a3ea1b885987c08.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/0a3ea1b885987c08.json
@@ -0,0 +1,54 @@
+{
+    "model_class": "Job",
+    "id": "0a3ea1b885987c08",
+    "history_id": "3cbec5b19229f469",
+    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0",
+    "state": "error",
+    "exit_code": null,
+    "create_time": "2024-09-04T19:14:01.874664",
+    "update_time": "2024-09-04T19:14:10.613857",
+    "galaxy_version": "24.1",
+    "external_id": "gxy-cm9w5",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "cp '/galaxy/server/database/objects/3/1/5/dataset_31560881-ef28-4f42-9279-93241afca87a.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/137/configs/tmpu5om38ov' > '/galaxy/server/database/objects/9/8/7/dataset_9871714f-f2ce-4a0f-bd7c-dba53bbd7541.dat' && python '/galaxy/server/database/jobs_directory/000/137/configs/tmpu5om38ov' >> '/galaxy/server/database/objects/9/8/7/dataset_9871714f-f2ce-4a0f-bd7c-dba53bbd7541.dat' && ls . >> '/galaxy/server/database/objects/9/8/7/dataset_9871714f-f2ce-4a0f-bd7c-dba53bbd7541.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt'  | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\"  | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n-    \\2|g' | sed 's|, |\\n-    |g'",
+    "user_email": "tests@fake.org",
+    "command_version": null,
+    "params": {
+        "__input_ext": "\"input\"",
+        "dbkey": "\"?\"",
+        "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+        "advanced_common": "{\"show_log\": true}",
+        "method": "{\"__current_case__\": 0, \"filter\": {\"__current_case__\": 3, \"filter\": \"max_genes\", \"max_genes\": \"100\"}, \"method\": \"pp.filter_cells\"}"
+    },
+    "inputs": {
+        "adata": {
+            "id": "da8dabdc7a6c9084",
+            "src": "hda",
+            "uuid": "31560881-ef28-4f42-9279-93241afca87a"
+        }
+    },
+    "outputs": {
+        "anndata_out": {
+            "id": "bec25e6b1a0850d8",
+            "src": "hda",
+            "uuid": "850fcd68-6380-4967-b7ab-508770596108"
+        },
+        "hidden_output": {
+            "id": "ae6bb488985fa333",
+            "src": "hda",
+            "uuid": "9871714f-f2ce-4a0f-bd7c-dba53bbd7541"
+        }
+    },
+    "copied_from_job_id": null,
+    "output_collections": {},
+    "tool_stdout": "[n_obs \u00d7 n_vars]\n-    640 \u00d7 11\n[obs]\n-    cell_type\n-    n_genes\n[uns]\n-    cell_type_colors\n-    highlights\n-    iroot\n",
+    "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\n",
+    "job_stdout": null,
+    "job_stderr": null,
+    "stdout": "[n_obs \u00d7 n_vars]\n-    640 \u00d7 11\n[obs]\n-    cell_type\n-    n_genes\n[uns]\n-    cell_type_colors\n-    highlights\n-    iroot\n",
+    "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\n",
+    "job_messages": null,
+    "dependencies": [],
+    "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/25718ce0aef57e36.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/25718ce0aef57e36.json
@@ -0,0 +1,69 @@
+{
+    "model_class": "Job",
+    "id": "25718ce0aef57e36",
+    "history_id": "3cbec5b19229f469",
+    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.3.2.0.0",
+    "state": "error",
+    "exit_code": null,
+    "create_time": "2024-09-04T18:32:57.803959",
+    "update_time": "2024-09-04T18:33:03.041702",
+    "galaxy_version": "24.1",
+    "external_id": "gxy-gjv5d",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "ln -s '/galaxy/server/database/objects/0/7/b/dataset_07b5eeaf-5a1b-4dc7-ade8-b80f34b1e0f9.dat' './0.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/2/6/4/metadata_2641dd70-609b-4f94-9c42-2b30489ecfa6.dat' './0.bam.bai' && ln -s '/galaxy/server/database/objects/0/7/b/dataset_07b5eeaf-5a1b-4dc7-ade8-b80f34b1e0f9.dat' './1.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/2/6/4/metadata_2641dd70-609b-4f94-9c42-2b30489ecfa6.dat' './1.bam.bai' &&   multiBamSummary BED-file --numberOfProcessors \"${GALAXY_SLOTS:-4}\"  --outFileName '/galaxy/server/database/objects/5/f/5/dataset_5f516eee-0a8b-4a48-997f-5c7961be38d6.dat' --bamfiles '0.bam' '1.bam' --labels 'bowtie2 test1.bam' 'bowtie2 test1.bam'    --BED /galaxy/server/database/objects/1/6/8/dataset_168b8377-1770-4dce-ba17-7aecf99d7738.dat",
+    "user_email": "tests@fake.org",
+    "command_version": null,
+    "params": {
+        "__input_ext": "\"bam\"",
+        "dbkey": "\"?\"",
+        "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+        "scalingFactors": "false",
+        "outRawCounts": "false",
+        "advancedOpt": "{\"__current_case__\": 0, \"showAdvancedOpt\": \"no\"}",
+        "region": "\"\"",
+        "mode": "{\"__current_case__\": 1, \"modeOpt\": \"BED-file\", \"region_file\": {\"values\": [{\"id\": 4, \"src\": \"hda\"}]}}",
+        "custom_sample_labels_conditional": "{\"__current_case__\": 0, \"custom_labels_select\": \"No\"}",
+        "multibam_conditional": "{\"__current_case__\": 0, \"bamfiles\": {\"values\": [{\"id\": 3, \"src\": \"hda\"}, {\"id\": 3, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}"
+    },
+    "inputs": {
+        "multibam_conditional|bamfiles": {
+            "id": "2e44e9ff029c6820",
+            "src": "hda",
+            "uuid": "07b5eeaf-5a1b-4dc7-ade8-b80f34b1e0f9"
+        },
+        "multibam_conditional|bamfiles1": {
+            "id": "2e44e9ff029c6820",
+            "src": "hda",
+            "uuid": "07b5eeaf-5a1b-4dc7-ade8-b80f34b1e0f9"
+        },
+        "multibam_conditional|bamfiles2": {
+            "id": "2e44e9ff029c6820",
+            "src": "hda",
+            "uuid": "07b5eeaf-5a1b-4dc7-ade8-b80f34b1e0f9"
+        },
+        "mode|region_file": {
+            "id": "7c84d18633e694f0",
+            "src": "hda",
+            "uuid": "168b8377-1770-4dce-ba17-7aecf99d7738"
+        }
+    },
+    "outputs": {
+        "outFile": {
+            "id": "25718ce0aef57e36",
+            "src": "hda",
+            "uuid": "5f516eee-0a8b-4a48-997f-5c7961be38d6"
+        }
+    },
+    "copied_from_job_id": null,
+    "output_collections": {},
+    "tool_stdout": "",
+    "tool_stderr": "Number of bins found: 3\n",
+    "job_stdout": null,
+    "job_stderr": null,
+    "stdout": "",
+    "stderr": "Number of bins found: 3\n",
+    "job_messages": null,
+    "dependencies": [],
+    "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/36df2befc514ba6e.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/36df2befc514ba6e.json
@@ -0,0 +1,45 @@
+{
+    "model_class": "Job",
+    "id": "36df2befc514ba6e",
+    "history_id": "3cbec5b19229f469",
+    "tool_id": "upload1",
+    "state": "error",
+    "exit_code": null,
+    "create_time": "2024-09-04T18:59:31.848577",
+    "update_time": "2024-09-04T18:59:42.998921",
+    "galaxy_version": "24.1",
+    "external_id": "gxy-lpclb",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/106/registry.xml' '/galaxy/server/database/jobs_directory/000/106/upload_params.json' '153:/galaxy/server/database/objects/b/d/d/dataset_bdde608d-979e-40e8-a5aa-5d94e8e598a5_files:/galaxy/server/database/objects/b/d/d/dataset_bdde608d-979e-40e8-a5aa-5d94e8e598a5.dat'",
+    "user_email": "tests@fake.org",
+    "command_version": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_3_kfdxpb\"",
+        "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"matrix.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_0yincmgu\", \"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": {},
+    "outputs": {
+        "output0": {
+            "id": "ce798158709471b6",
+            "src": "hda",
+            "uuid": "bdde608d-979e-40e8-a5aa-5d94e8e598a5"
+        }
+    },
+    "copied_from_job_id": null,
+    "output_collections": {},
+    "tool_stdout": "",
+    "tool_stderr": "",
+    "job_stdout": null,
+    "job_stderr": null,
+    "stdout": "",
+    "stderr": "",
+    "job_messages": null,
+    "dependencies": [],
+    "job_metrics": []
+}