Skip to content

Commit

Permalink
Updating anvil-edge README for edge-24-10-05-06-10-1
Browse files Browse the repository at this point in the history
  • Loading branch information
@actions-user
actions-user committed Oct 5, 2024
1 parent 298ce51 commit a157f07
Show file tree
Hide file tree
Showing 25 changed files with 25,080 additions and 6 deletions.
2 changes: 1 addition & 1 deletion reports/anvil-edge/README.md
View file

Large diffs are not rendered by default.

10 changes: 5 additions & 5 deletions reports/anvil-edge/tool-tests/chunks.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -63,11 +63,11 @@
"date2": "Fri Sep 27 18:32:42 2024"
},
"10": {
"run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-28-06-10-1/results.html",
"date1": "Sat Sep 28 06:25:48 2024",
"tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-28-06-10-1/tools.yml",
"run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-21-06-10-1/results.html",
"date2": "Sat Sep 21 06:25:16 2024"
"run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/results.html",
"date1": "Sat Oct 05 06:25:14 2024",
"tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/tools.yml",
"run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-28-06-10-1/results.html",
"date2": "Sat Sep 28 06:25:48 2024"
},
"12": {
"run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-29-06-10-1/results.html",
Expand Down
7 changes: 7 additions & 0 deletions reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/chunk.json
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
{
"10": {
"run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/results.html",
"date1": "Sat Oct 05 06:25:14 2024",
"tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/tools.yml"
}
}
25 changes: 25 additions & 0 deletions reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/chunk.txt
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
-t datamash_transpose --tool-version ac092723240d
-t deeptools_plot_fingerprint --tool-version 2da482e408b8
-t umi_tools_extract --tool-version 6a675c3aa610
-t umi_tools_extract --tool-version 99aea37a7ff7
-t umi_tools_extract --tool-version f3759eec3018
-t bwa --tool-version 3fe632431b68
-t medaka_variant_pipeline --tool-version 336b3def9b2b
-t poretools_qualdist --tool-version ae9060e764b5
-t featurecounts --tool-version 38b6d12edc68
-t featurecounts --tool-version f3a5f075498f
-t samtools_fixmate --tool-version bc0cc7bfbfe9
-t sam_to_bam --tool-version cf1ffd88f895
-t chromeister --tool-version e483be1014b6
-t slice_image --tool-version 8856a7c85e4c
-t scanpy_read_10x --tool-version c8391a25dee3
-t scanpy_read_10x --tool-version d92e6f12b790
-t scanpy_run_tsne --tool-version 384cacc40611
-t scanpy_run_tsne --tool-version 8eff7ec034e3
-t add_input_name_as_column --tool-version 3284b72eef56
-t lofreq_filter --tool-version 7dfca164d2e3
-t bcftools_query_list_samples --tool-version ed4ea9de1791
-t bcftools_isec --tool-version 02f349bdbf96
-t vcfannotate --tool-version 01e0321aca98
-t vcfrandomsample --tool-version 6257ee3b50d3
-t ivar_getmasked --tool-version 2cf4a1cafc16
47 changes: 47 additions & 0 deletions reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/066e0eaa4712a55e.json
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,47 @@
{
"model_class": "Job",
"id": "066e0eaa4712a55e",
"history_id": "779d4cab783f0ad5",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0",
"state": "error",
"exit_code": null,
"create_time": "2024-10-05T06:45:26.565484",
"update_time": "2024-10-05T06:45:32.749018",
"galaxy_version": "24.1",
"external_id": "gxy-zmnpq",
"handler": null,
"job_runner_name": null,
"command_line": "poretools qualdist '/galaxy/server/database/objects/a/7/4/dataset_a74e2bbb-94df-4176-bcac-cda666391a8a.dat' > '/galaxy/server/database/objects/6/b/b/dataset_6bb58ad4-0dd4-44b1-a170-0b2e6aac5738.dat'",
"user_email": "tests@fake.org",
"command_version": null,
"params": {
"__input_ext": "\"fast5.tar\"",
"dbkey": "\"?\"",
"chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""
},
"inputs": {
"input": {
"id": "40224001529b2140",
"src": "hda",
"uuid": "a74e2bbb-94df-4176-bcac-cda666391a8a"
}
},
"outputs": {
"output": {
"id": "4b7e4165841ed691",
"src": "hda",
"uuid": "6bb58ad4-0dd4-44b1-a170-0b2e6aac5738"
}
},
"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": []
}
65 changes: 65 additions & 0 deletions reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/2704ccb375827a9b.json
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,65 @@
{
"model_class": "Job",
"id": "2704ccb375827a9b",
"history_id": "779d4cab783f0ad5",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2",
"state": "error",
"exit_code": null,
"create_time": "2024-10-05T06:40:17.162455",
"update_time": "2024-10-05T06:40:23.333336",
"galaxy_version": "24.1",
"external_id": "gxy-7nbzx",
"handler": null,
"job_runner_name": null,
"command_line": "ln -s '/galaxy/server/database/objects/b/9/9/dataset_b99998c9-5079-466a-bd90-6b4ac47ef392.dat' input_read1.gz && ln -s '/galaxy/server/database/objects/e/f/d/dataset_efd26cbf-3208-4678-be8b-be73c00f4356.dat' input_read2.gz && umi_tools extract --extract-method='string' --bc-pattern='NNNNNNCCCCCC' --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log2stderr && mv out1.gz '/galaxy/server/database/objects/5/1/b/dataset_51bc75bf-3db8-4f22-9b83-0177410c5511.dat' && mv out2.gz '/galaxy/server/database/objects/c/8/5/dataset_c850d4a7-42a1-430b-81e0-4ea7da635e32.dat'",
"user_email": "tests@fake.org",
"command_version": null,
"params": {
"__input_ext": "\"input\"",
"dbkey": "\"?\"",
"chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
"log": "false",
"quality": "{\"__current_case__\": 0, \"quality_selector\": \"false\"}",
"error_correct_cell": "false",
"blacklist": null,
"whitelist": null,
"ignore_read_pair_suffixes": "false",
"extract_method_cond": "{\"__current_case__\": 0, \"extract_method\": \"string\", \"prime3\": false}",
"input_type_cond": "{\"__current_case__\": 1, \"bc_pattern\": \"NNNNNNCCCCCC\", \"bc_pattern2\": \"\", \"input_read1\": {\"values\": [{\"id\": 87, \"src\": \"hda\"}]}, \"input_read2\": {\"values\": [{\"id\": 88, \"src\": \"hda\"}]}, \"input_type\": \"paired\", \"reconcile_pairs\": false}"
},
"inputs": {
"input_type_cond|input_read1": {
"id": "75502bcd39344a71",
"src": "hda",
"uuid": "b99998c9-5079-466a-bd90-6b4ac47ef392"
},
"input_type_cond|input_read2": {
"id": "20a79f958a1ad4a1",
"src": "hda",
"uuid": "efd26cbf-3208-4678-be8b-be73c00f4356"
}
},
"outputs": {
"out": {
"id": "db5a2d4573973b22",
"src": "hda",
"uuid": "51bc75bf-3db8-4f22-9b83-0177410c5511"
},
"out2": {
"id": "1901d0f883d04f28",
"src": "hda",
"uuid": "c850d4a7-42a1-430b-81e0-4ea7da635e32"
}
},
"copied_from_job_id": null,
"output_collections": {},
"tool_stdout": "",
"tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by extract --extract-method=string --bc-pattern=NNNNNNCCCCCC --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log2stderr\n# job started at Sat Oct 5 06:40:20 2024 on gxy-7nbzx-6thqk -- c21d894e-39dc-4938-a87d-12180e793794\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 10 16:12:02 UTC 2024 x86_64\n# blacklist : None\n# compresslevel : 6\n# correct_umi_threshold : 0\n# either_read : False\n# either_read_resolve : discard\n# error_correct_cell : False\n# extract_method : string\n# filter_cell_barcode : None\n# filter_cell_barcodes : False\n# filter_umi : None\n# filtered_out : None\n# filtered_out2 : None\n# ignore_suffix : False\n# log2stderr : True\n# loglevel : 1\n# pattern : NNNNNNCCCCCC\n# pattern2 : None\n# prime3 : None\n# quality_encoding : None\n# quality_filter_mask : None\n# quality_filter_threshold : None\n# random_seed : None\n# read2_in : input_read2.gz\n# read2_out : out2.gz\n# read2_stdout : False\n# reads_subset : None\n# reconcile : False\n# retain_umi : None\n# short_help : None\n# stderr : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'>\n# stdlog : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='out1.gz' encoding='ascii'>\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_correct_log : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# whitelist : None\n2024-10-05 06:40:20,721 INFO Starting barcode extraction\n2024-10-05 06:40:20,728 INFO Input Reads: 50\n2024-10-05 06:40:20,729 INFO Reads output: 50\n# job finished in 0 seconds at Sat Oct 5 06:40:20 2024 -- 1.35 0.22 0.00 0.00 -- c21d894e-39dc-4938-a87d-12180e793794\n",
"job_stdout": null,
"job_stderr": null,
"stdout": "",
"stderr": "# UMI-tools version: 1.1.2\n# output generated by extract --extract-method=string --bc-pattern=NNNNNNCCCCCC --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz False --log2stderr\n# job started at Sat Oct 5 06:40:20 2024 on gxy-7nbzx-6thqk -- c21d894e-39dc-4938-a87d-12180e793794\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 10 16:12:02 UTC 2024 x86_64\n# blacklist : None\n# compresslevel : 6\n# correct_umi_threshold : 0\n# either_read : False\n# either_read_resolve : discard\n# error_correct_cell : False\n# extract_method : string\n# filter_cell_barcode : None\n# filter_cell_barcodes : False\n# filter_umi : None\n# filtered_out : None\n# filtered_out2 : None\n# ignore_suffix : False\n# log2stderr : True\n# loglevel : 1\n# pattern : NNNNNNCCCCCC\n# pattern2 : None\n# prime3 : None\n# quality_encoding : None\n# quality_filter_mask : None\n# quality_filter_threshold : None\n# random_seed : None\n# read2_in : input_read2.gz\n# read2_out : out2.gz\n# read2_stdout : False\n# reads_subset : None\n# reconcile : False\n# retain_umi : None\n# short_help : None\n# stderr : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'>\n# stdlog : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='out1.gz' encoding='ascii'>\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_correct_log : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# whitelist : None\n2024-10-05 06:40:20,721 INFO Starting barcode extraction\n2024-10-05 06:40:20,728 INFO Input Reads: 50\n2024-10-05 06:40:20,729 INFO Reads output: 50\n# job finished in 0 seconds at Sat Oct 5 06:40:20 2024 -- 1.35 0.22 0.00 0.00 -- c21d894e-39dc-4938-a87d-12180e793794\n",
"job_messages": null,
"dependencies": [],
"job_metrics": []
}
45 changes: 45 additions & 0 deletions reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/39a53760c56001e8.json
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,45 @@
{
"model_class": "Job",
"id": "39a53760c56001e8",
"history_id": "779d4cab783f0ad5",
"tool_id": "upload1",
"state": "error",
"exit_code": null,
"create_time": "2024-10-05T06:28:02.222110",
"update_time": "2024-10-05T06:28:15.264725",
"galaxy_version": "24.1",
"external_id": "gxy-qdt55",
"handler": null,
"job_runner_name": null,
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/6/registry.xml' '/galaxy/server/database/jobs_directory/000/6/upload_params.json' '6:/galaxy/server/database/objects/1/e/0/dataset_1e05d2ac-55d6-446f-9ea8-ca6f9edfd74f_files:/galaxy/server/database/objects/1/e/0/dataset_1e05d2ac-55d6-446f-9ea8-ca6f9edfd74f.dat'",
"user_email": "tests@fake.org",
"command_version": null,
"params": {
"paramfile": "\"/galaxy/server/database/tmp/upload_params_a0kkzha3\"",
"files_metadata": "{\"__current_case__\": 36, \"file_type\": \"bam\"}",
"dbkey": "\"?\"",
"force_composite": "\"false\"",
"files": "[{\"NAME\": \"bowtie2 test1.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_tmkk73t3\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
"file_count": "\"auto\"",
"file_type": "\"bam\""
},
"inputs": {},
"outputs": {
"output0": {
"id": "39a53760c56001e8",
"src": "hda",
"uuid": "1e05d2ac-55d6-446f-9ea8-ca6f9edfd74f"
}
},
"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": []
}
45 changes: 45 additions & 0 deletions reports/anvil-edge/tool-tests/edge-24-10-05-06-10-1/errors/3bdef6d60132b40e.json
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,45 @@
{
"model_class": "Job",
"id": "3bdef6d60132b40e",
"history_id": "779d4cab783f0ad5",
"tool_id": "upload1",
"state": "error",
"exit_code": null,
"create_time": "2024-10-05T06:53:35.229647",
"update_time": "2024-10-05T06:53:47.319910",
"galaxy_version": "24.1",
"external_id": "gxy-nlk7h",
"handler": null,
"job_runner_name": null,
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/116/registry.xml' '/galaxy/server/database/jobs_directory/000/116/upload_params.json' '160:/galaxy/server/database/objects/5/5/8/dataset_55886639-e887-4ce9-a9d5-0619bc31ea48_files:/galaxy/server/database/objects/5/5/8/dataset_55886639-e887-4ce9-a9d5-0619bc31ea48.dat'",
"user_email": "tests@fake.org",
"command_version": null,
"params": {
"paramfile": "\"/galaxy/server/database/tmp/upload_params_6tbgvd3j\"",
"files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
"dbkey": "\"?\"",
"force_composite": "\"false\"",
"files": "[{\"NAME\": \"3_reverse_read_pp_lt.sam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_w_rdbek2\", \"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": "6d0793221f983d04",
"src": "hda",
"uuid": "55886639-e887-4ce9-a9d5-0619bc31ea48"
}
},
"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": []
}
Loading

0 comments on commit a157f07

Please sign in to comment.