Updating anvil-edge README for edge-24-08-30-06-10-1

anvilproject · Aug 30, 2024 · e1a5e2e · e1a5e2e
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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
@@ -49,11 +49,11 @@
         "date2": "Thu Aug 22 18:43:08 2024"
     },
     "8": {
-        "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-23-06-10-1/results.html",
-        "date1": "Fri Aug 23 06:25:56 2024",
-        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-23-06-10-1/tools.yml",
-        "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-16-06-10-1/results.html",
-        "date2": "Fri Aug 16 06:25:00 2024"
+        "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/results.html",
+        "date1": "Fri Aug 30 06:25:36 2024",
+        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/tools.yml",
+        "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-23-06-10-1/results.html",
+        "date2": "Fri Aug 23 06:25:56 2024"
     },
     "9": {
         "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-23-18-15-1/results.html",

diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/chunk.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/chunk.json
@@ -0,0 +1,7 @@
+{
+    "8": {
+        "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/results.html",
+        "date1": "Fri Aug 30 06:25:36 2024",
+        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/tools.yml"
+    }
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/chunk.txt b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/chunk.txt
@@ -0,0 +1,27 @@
+-t collection_column_join --tool-version 071084070619
+-t collection_column_join --tool-version 58228a4d58fe
+-t deeptools_plot_coverage --tool-version 56bce3c82278
+-t trim_galore --tool-version 084bbd8ba7b8
+-t minimap2 --tool-version f54f5baedfdd
+-t flye --tool-version 3ee0ef312022
+-t poretools_tabular --tool-version 2cb2feb94f0e
+-t hisat2 --tool-version 26371a1df031
+-t hisat2 --tool-version f4af63aaf57a
+-t samtools_merge --tool-version 740ce0a18f0d
+-t samtools_merge --tool-version 36677f429310
+-t bam_to_sam --tool-version 88eedb4abea0
+-t anndata_export --tool-version 707023fa62fe
+-t anndata_export --tool-version 0cb889db0910
+-t alevin --tool-version 04b494623f8e
+-t alevin --tool-version e4c01dcece8b
+-t scanpy_plot --tool-version aa0c474463c2
+-t scanpy_plot --tool-version a8f865950ac4
+-t scanpy_run_pca --tool-version 988edd5fa902
+-t scanpy_run_pca --tool-version ce93e630b55a
+-t table_compute --tool-version 60ff16842fcd
+-t lofreq_viterbi --tool-version aa35ee7f3ab2
+-t bcftools_convert_to_vcf --tool-version fec517907949
+-t bcftools_plugin_fill_an_ac --tool-version 582f8b13873d
+-t vcfaddinfo --tool-version 6ea73d6151ec
+-t vcfleftalign --tool-version 29f9b782727e
+-t ivar_consensus --tool-version 78bbd17d0703
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/05f1cc2cc180b061.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/05f1cc2cc180b061.json
@@ -0,0 +1,132 @@
+{
+    "model_class": "Job",
+    "id": "05f1cc2cc180b061",
+    "history_id": "436da20d1fd8461d",
+    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0",
+    "state": "error",
+    "exit_code": null,
+    "create_time": "2024-08-30T07:18:05.746212",
+    "update_time": "2024-08-30T07:18:24.999336",
+    "galaxy_version": "24.1",
+    "external_id": "gxy-dltns",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "mkdir ./index && mkdir ./output && salmon index -i ./index --kmerLen '31' --gencode --transcripts '/galaxy/server/database/objects/6/b/2/dataset_6b225a08-de2e-4ffc-8cdd-52a766782281.dat' && cp '/galaxy/server/database/objects/d/4/7/dataset_d478885a-4e93-45c0-b833-35a1871257f0.dat' ./mate1.fastq.gz && gunzip ./mate1.fastq.gz && cp '/galaxy/server/database/objects/f/1/1/dataset_f11bdbe6-877d-4608-9a9f-4897fa921a3a.dat' ./mate2.fastq.gz && gunzip ./mate2.fastq.gz  && ln -s '/galaxy/server/database/objects/e/f/b/dataset_efb5abf0-017c-45c6-a694-2548c0bf2885.dat' ./alevinmap.tsv && salmon alevin -l A -i ./index -1 ./mate1.fastq -2 ./mate2.fastq -o ./output -p \"${GALAXY_SLOTS:-4}\" --chromium --tgMap ./alevinmap.tsv --numCellBootstraps '2' --keepCBFraction '1.0'   --dumpFeatures  --dumpMtx --freqThreshold '5'  && gunzip output/alevin/quants_mat.mtx.gz  && gunzip output/alevin/quants_tier_mat.gz && gunzip output/alevin/quants_mean_mat.gz && gunzip output/alevin/quants_var_mat.gz  && gunzip output/aux_info/fld.gz && gunzip output/aux_info/observed_bias.gz && gunzip output/aux_info/observed_bias_3p.gz",
+    "user_email": "tests@fake.org",
+    "command_version": null,
+    "params": {
+        "__input_ext": "\"input\"",
+        "dbkey": "\"?\"",
+        "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+        "optional": "{\"dumpBfh\": false, \"dumpFeatures\": true, \"dumpMtx\": true, \"dumpUmiGraph\": false, \"expectCells\": \"\", \"forceCells\": \"\", \"freqThreshold\": \"5\", \"keepCBFraction\": \"1.0\", \"lowRegionMinNumBarcodes\": \"\", \"maxNumBarcodes\": \"\", \"minScoreFraction\": \"\", \"mrna\": null, \"noDedup\": false, \"numCellBootstraps\": \"2\", \"rrna\": null, \"whitelist\": null}",
+        "allout": "false",
+        "protocol": "\"--chromium\"",
+        "pairstraight": "{\"__current_case__\": 0, \"file1\": {\"values\": [{\"id\": 307, \"src\": \"hda\"}]}, \"file2\": {\"values\": [{\"id\": 308, \"src\": \"hda\"}]}, \"libtype\": {\"__current_case__\": 0, \"strandedness\": \"A\"}, \"readselect\": \"paired\"}",
+        "refTranscriptSource": "{\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"values\": [{\"id\": 306, \"src\": \"hda\"}]}, \"kmer\": \"31\", \"phash\": false}}"
+    },
+    "inputs": {
+        "tgmap": {
+            "id": "9e7b4465e6d5f5e7",
+            "src": "hda",
+            "uuid": "efb5abf0-017c-45c6-a694-2548c0bf2885"
+        },
+        "pairstraight|file2": {
+            "id": "fda5818e8a5af745",
+            "src": "hda",
+            "uuid": "f11bdbe6-877d-4608-9a9f-4897fa921a3a"
+        },
+        "pairstraight|file1": {
+            "id": "626a64c6bb868c48",
+            "src": "hda",
+            "uuid": "d478885a-4e93-45c0-b833-35a1871257f0"
+        },
+        "refTranscriptSource|s_index|fasta": {
+            "id": "ade34174ea908ec9",
+            "src": "hda",
+            "uuid": "6b225a08-de2e-4ffc-8cdd-52a766782281"
+        }
+    },
+    "outputs": {
+        "quants_mat_cols_txt": {
+            "id": "388a4dbdf6225b5e",
+            "src": "hda",
+            "uuid": "1a811432-4941-4735-89b6-0b87a7d26d61"
+        },
+        "quants_mat_rows_txt": {
+            "id": "016a9ecab36a8a33",
+            "src": "hda",
+            "uuid": "c7f8267e-25a2-43e5-a3f4-10e21ab11301"
+        },
+        "quants_mat_mtx": {
+            "id": "c8642ef18f13529c",
+            "src": "hda",
+            "uuid": "4671a059-2f13-4e16-8224-26fb87dbe063"
+        },
+        "raw_cb_frequency_txt": {
+            "id": "a201e7513402edc5",
+            "src": "hda",
+            "uuid": "94e23446-c99d-4f28-a2cb-5fa9f42586a3"
+        },
+        "quants_tier_mat": {
+            "id": "bfc105b661dbaf2b",
+            "src": "hda",
+            "uuid": "40387756-8171-4ba3-8458-7ab7a2278eae"
+        },
+        "featureDump_txt": {
+            "id": "37bf2b8aff708392",
+            "src": "hda",
+            "uuid": "5d1ce308-ef04-4307-9e22-c8afb94d4dd3"
+        },
+        "whitelist_txt": {
+            "id": "6c555ae15f749b36",
+            "src": "hda",
+            "uuid": "a6c6b15d-d965-42c7-90f5-7facba229951"
+        },
+        "quants_mean_mat": {
+            "id": "8e3bc46515971f80",
+            "src": "hda",
+            "uuid": "6792f8c2-0020-42fd-88a6-5e3b7636f0cc"
+        },
+        "quants_var_mat": {
+            "id": "9e66f7e372adc5d1",
+            "src": "hda",
+            "uuid": "c93c16f0-360c-41cc-861d-e1487fada4f7"
+        },
+        "quants_boot_rows_txt": {
+            "id": "fa46b69b3b6eb2d0",
+            "src": "hda",
+            "uuid": "48ae43a8-3804-451f-a40b-b5aecb38069a"
+        },
+        "expected_bias": {
+            "id": "ef008abdd885cd3a",
+            "src": "hda",
+            "uuid": "ffa68773-a1bf-4d2f-9216-17af90d27a79"
+        },
+        "observed_bias": {
+            "id": "9157b567b4405058",
+            "src": "hda",
+            "uuid": "a86985fb-67bf-41e0-998e-a27b9b05cfa5"
+        },
+        "observed_bias_3p": {
+            "id": "787f20cab39ce662",
+            "src": "hda",
+            "uuid": "8b2746d8-9a97-45ef-ae2e-c59c49c368c3"
+        },
+        "flenDist_txt": {
+            "id": "91ee28930f1e2eb4",
+            "src": "hda",
+            "uuid": "3fe922e2-673c-42a8-beee-075481887097"
+        }
+    },
+    "copied_from_job_id": null,
+    "output_collections": {},
+    "tool_stdout": "",
+    "tool_stderr": "",
+    "job_stdout": null,
+    "job_stderr": null,
+    "stdout": "",
+    "stderr": "",
+    "job_messages": [],
+    "dependencies": [],
+    "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/0c5fa726f67a9d66.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/0c5fa726f67a9d66.json
@@ -0,0 +1,45 @@
+{
+    "model_class": "Job",
+    "id": "0c5fa726f67a9d66",
+    "history_id": "436da20d1fd8461d",
+    "tool_id": "upload1",
+    "state": "error",
+    "exit_code": null,
+    "create_time": "2024-08-30T08:08:57.544623",
+    "update_time": "2024-08-30T08:09:08.432695",
+    "galaxy_version": "24.1",
+    "external_id": "gxy-gbnn4",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/428/registry.xml' '/galaxy/server/database/jobs_directory/000/428/upload_params.json' '575:/galaxy/server/database/objects/6/2/f/dataset_62fe37e2-b0b2-480f-b892-54951abafd69_files:/galaxy/server/database/objects/6/2/f/dataset_62fe37e2-b0b2-480f-b892-54951abafd69.dat'",
+    "user_email": "tests@fake.org",
+    "command_version": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_wbhaifrf\"",
+        "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"examples.7.tsv\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_bm5uwcw3\", \"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": "3f4b647bf56e33ca",
+            "src": "hda",
+            "uuid": "62fe37e2-b0b2-480f-b892-54951abafd69"
+        }
+    },
+    "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-24-08-30-06-10-1/errors/1a18e3937393327c.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/1a18e3937393327c.json
@@ -0,0 +1,45 @@
+{
+    "model_class": "Job",
+    "id": "1a18e3937393327c",
+    "history_id": "436da20d1fd8461d",
+    "tool_id": "upload1",
+    "state": "error",
+    "exit_code": null,
+    "create_time": "2024-08-30T07:10:09.396045",
+    "update_time": "2024-08-30T07:10:21.898947",
+    "galaxy_version": "24.1",
+    "external_id": "gxy-vjp9c",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/215/registry.xml' '/galaxy/server/database/jobs_directory/000/215/upload_params.json' '252:/galaxy/server/database/objects/f/b/3/dataset_fb332dc3-820f-46f1-8eea-4845812e8cc6_files:/galaxy/server/database/objects/f/b/3/dataset_fb332dc3-820f-46f1-8eea-4845812e8cc6.dat'",
+    "user_email": "tests@fake.org",
+    "command_version": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_p0t1tx49\"",
+        "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"test_input_1_a.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_24plaftt\", \"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": "fbce319d75744a7b",
+            "src": "hda",
+            "uuid": "fb332dc3-820f-46f1-8eea-4845812e8cc6"
+        }
+    },
+    "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-24-08-30-06-10-1/errors/1d8f058f735ff10d.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/1d8f058f735ff10d.json
@@ -0,0 +1,45 @@
+{
+    "model_class": "Job",
+    "id": "1d8f058f735ff10d",
+    "history_id": "436da20d1fd8461d",
+    "tool_id": "upload1",
+    "state": "error",
+    "exit_code": null,
+    "create_time": "2024-08-30T08:12:30.055518",
+    "update_time": "2024-08-30T08:12:41.098379",
+    "galaxy_version": "24.1",
+    "external_id": "gxy-8qrrf",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/441/registry.xml' '/galaxy/server/database/jobs_directory/000/441/upload_params.json' '588:/galaxy/server/database/objects/9/8/e/dataset_98ed1a65-6b35-4a0a-ac5d-7b298e0ec81c_files:/galaxy/server/database/objects/9/8/e/dataset_98ed1a65-6b35-4a0a-ac5d-7b298e0ec81c.dat'",
+    "user_email": "tests@fake.org",
+    "command_version": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_rml7sg47\"",
+        "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"examples.1.tsv\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_4qijso58\", \"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": "030993b6c9043e4c",
+            "src": "hda",
+            "uuid": "98ed1a65-6b35-4a0a-ac5d-7b298e0ec81c"
+        }
+    },
+    "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-24-08-30-06-10-1/errors/21b4b2693acea78a.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/21b4b2693acea78a.json
@@ -0,0 +1,55 @@
+{
+    "model_class": "Job",
+    "id": "21b4b2693acea78a",
+    "history_id": "436da20d1fd8461d",
+    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+    "state": "error",
+    "exit_code": null,
+    "create_time": "2024-08-30T07:46:42.485838",
+    "update_time": "2024-08-30T07:46:50.637279",
+    "galaxy_version": "24.1",
+    "external_id": "gxy-tkf98",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "cp '/galaxy/server/database/objects/0/2/8/dataset_028d334c-30f9-4a11-bf97-1c28532bdb15.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/348/configs/tmpm3gqvmnt' > '/galaxy/server/database/objects/4/f/f/dataset_4ff53f62-2edd-4994-9b63-8c6fdba8fa14.dat' && python '/galaxy/server/database/jobs_directory/000/348/configs/tmpm3gqvmnt' >> '/galaxy/server/database/objects/4/f/f/dataset_4ff53f62-2edd-4994-9b63-8c6fdba8fa14.dat' && ls . >> '/galaxy/server/database/objects/4/f/f/dataset_4ff53f62-2edd-4994-9b63-8c6fdba8fa14.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__\": 11, \"log\": false, \"method\": \"pl.pca_variance_ratio\", \"n_pcs\": \"5\"}",
+        "format": "\"png\""
+    },
+    "inputs": {
+        "adata": {
+            "id": "c948ff00108a577e",
+            "src": "hda",
+            "uuid": "028d334c-30f9-4a11-bf97-1c28532bdb15"
+        }
+    },
+    "outputs": {
+        "hidden_output": {
+            "id": "4503b172d2db2f67",
+            "src": "hda",
+            "uuid": "4ff53f62-2edd-4994-9b63-8c6fdba8fa14"
+        },
+        "out_png": {
+            "id": "ede55d2d793e0163",
+            "src": "hda",
+            "uuid": "01f05daa-b8de-4d7b-9289-78fff472829d"
+        }
+    },
+    "copied_from_job_id": null,
+    "output_collections": {},
+    "tool_stdout": "",
+    "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file pca_variance_ratio.png\n",
+    "job_stdout": null,
+    "job_stderr": null,
+    "stdout": "",
+    "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file pca_variance_ratio.png\n",
+    "job_messages": null,
+    "dependencies": [],
+    "job_metrics": []
+}