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Updating anvil-edge README for edge-24-10-10-06-12-1
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7 changes: 7 additions & 0 deletions
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reports/anvil-edge/tool-tests/edge-24-10-10-06-12-1/chunk.json
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,7 @@ | ||
| { | ||
| "6": { | ||
| "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-10-10-06-12-1/results.html", | ||
| "date1": "Thu Oct 10 06:28:11 2024", | ||
| "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-10-10-06-12-1/tools.yml" | ||
| } | ||
| } |
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reports/anvil-edge/tool-tests/edge-24-10-10-06-12-1/chunk.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,23 @@ | ||
| -t split_file_to_collection --tool-version 6cbe2f30c2d7 | ||
| -t deeptools_multi_bigwig_summary --tool-version 3c9f0c486cca | ||
| -t fastq_paired_end_interlacer --tool-version 2ccb8dcabddc | ||
| -t jbrowse --tool-version 4542035c1075 | ||
| -t jbrowse --tool-version a6e57ff585c0 | ||
| -t mummer_delta_filter --tool-version b3acbb3a6af0 | ||
| -t poretools_winner --tool-version 79c1ac92f31b | ||
| -t edger --tool-version 334ce9b1bac5 | ||
| -t qualimap_multi_bamqc --tool-version e38af83df163 | ||
| -t samtools_sort --tool-version e613c1ad4c4c | ||
| -t 10x_bamtofastq --tool-version f71fd828c126 | ||
| -t raceid_trajectory --tool-version 72979cac22b2 | ||
| -t raceid_trajectory --tool-version c92d0f9338c5 | ||
| -t scanpy_inspect --tool-version c5d3684f7c4c | ||
| -t scanpy_find_variable_genes --tool-version 0edb75c411a4 | ||
| -t scanpy_find_variable_genes --tool-version 5c62f39aab8f | ||
| -t concatenate_multiple_datasets --tool-version 201c568972c3 | ||
| -t snpfreqplot --tool-version e362b3143cde | ||
| -t bcftools_gtcheck --tool-version 672b6c02fbc7 | ||
| -t bcftools_reheader --tool-version 9ef52d95114b | ||
| -t bcftools_plugin_tag2tag --tool-version bdfdf5f6e950 | ||
| -t vcfgenotypes --tool-version a60ae8af21a1 | ||
| -t ivar_removereads --tool-version ee2beb764a7b |
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reports/anvil-edge/tool-tests/edge-24-10-10-06-12-1/errors/09a0a60a0d4cfd6b.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "09a0a60a0d4cfd6b", | ||
| "history_id": "90345f6386454b4c", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-10-10T07:28:17.022529", | ||
| "update_time": "2024-10-10T07:28:26.942208", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-kdcvw", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/218/registry.xml' '/galaxy/server/database/jobs_directory/000/218/upload_params.json' '297:/galaxy/server/database/objects/b/c/2/dataset_bc2e90b4-4bb2-4dfb-b244-c9d5969bf15e_files:/galaxy/server/database/objects/b/c/2/dataset_bc2e90b4-4bb2-4dfb-b244-c9d5969bf15e.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_tzz0424o\"", | ||
| "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"krumsiek11.h5ad\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_eyd1t8_t\", \"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": "3877bfd1c458fe0b", | ||
| "src": "hda", | ||
| "uuid": "bc2e90b4-4bb2-4dfb-b244-c9d5969bf15e" | ||
| } | ||
| }, | ||
| "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
45
reports/anvil-edge/tool-tests/edge-24-10-10-06-12-1/errors/1a67d59c0bcef107.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "1a67d59c0bcef107", | ||
| "history_id": "90345f6386454b4c", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-10-10T06:39:30.632979", | ||
| "update_time": "2024-10-10T06:39:40.640655", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-j55s5", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/39/registry.xml' '/galaxy/server/database/jobs_directory/000/39/upload_params.json' '86:/galaxy/server/database/objects/f/b/7/dataset_fb7c1c8c-e862-4a31-9331-5982f0ad2353_files:/galaxy/server/database/objects/f/b/7/dataset_fb7c1c8c-e862-4a31-9331-5982f0ad2353.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_3asmyts2\"", | ||
| "files_metadata": "{\"__current_case__\": 325, \"file_type\": \"tabular\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"test.tabular\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_jahtcies\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
| "file_count": "\"auto\"", | ||
| "file_type": "\"tabular\"" | ||
| }, | ||
| "inputs": {}, | ||
| "outputs": { | ||
| "output0": { | ||
| "id": "a49e08336e05c66c", | ||
| "src": "hda", | ||
| "uuid": "fb7c1c8c-e862-4a31-9331-5982f0ad2353" | ||
| } | ||
| }, | ||
| "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": [] | ||
| } |
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reports/anvil-edge/tool-tests/edge-24-10-10-06-12-1/errors/24075871b4f5b976.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "24075871b4f5b976", | ||
| "history_id": "90345f6386454b4c", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-10-10T06:58:11.511143", | ||
| "update_time": "2024-10-10T06:58:22.054534", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-wdcbj", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/90/registry.xml' '/galaxy/server/database/jobs_directory/000/90/upload_params.json' '143:/galaxy/server/database/objects/a/4/e/dataset_a4eb3fa1-77bf-496d-86cf-3e4d70a40b04_files:/galaxy/server/database/objects/a/4/e/dataset_a4eb3fa1-77bf-496d-86cf-3e4d70a40b04.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_953wzag8\"", | ||
| "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"merlin.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_cwtjef5g\", \"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": "61634d51334de09f", | ||
| "src": "hda", | ||
| "uuid": "a4eb3fa1-77bf-496d-86cf-3e4d70a40b04" | ||
| } | ||
| }, | ||
| "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": [] | ||
| } |
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reports/anvil-edge/tool-tests/edge-24-10-10-06-12-1/errors/375c9a5e2c3002cf.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "375c9a5e2c3002cf", | ||
| "history_id": "90345f6386454b4c", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-10-10T07:33:42.005607", | ||
| "update_time": "2024-10-10T07:33:53.349471", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-6vldf", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/236/registry.xml' '/galaxy/server/database/jobs_directory/000/236/upload_params.json' '323:/galaxy/server/database/objects/e/6/d/dataset_e6dd71a4-9546-4f07-970e-fa7e0d28297b_files:/galaxy/server/database/objects/e/6/d/dataset_e6dd71a4-9546-4f07-970e-fa7e0d28297b.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_3tpu6kz7\"", | ||
| "files_metadata": "{\"__current_case__\": 325, \"file_type\": \"tabular\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"input437.tabular\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_elzggoj6\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
| "file_count": "\"auto\"", | ||
| "file_type": "\"tabular\"" | ||
| }, | ||
| "inputs": {}, | ||
| "outputs": { | ||
| "output0": { | ||
| "id": "4c6fd33063266c41", | ||
| "src": "hda", | ||
| "uuid": "e6dd71a4-9546-4f07-970e-fa7e0d28297b" | ||
| } | ||
| }, | ||
| "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
45
reports/anvil-edge/tool-tests/edge-24-10-10-06-12-1/errors/3df9b402e57be778.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "3df9b402e57be778", | ||
| "history_id": "90345f6386454b4c", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-10-10T07:42:26.194048", | ||
| "update_time": "2024-10-10T07:42:37.173450", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-sd22d", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/292/registry.xml' '/galaxy/server/database/jobs_directory/000/292/upload_params.json' '379:/galaxy/server/database/objects/d/0/3/dataset_d030b506-7df7-4ddd-a1d7-1f05ec35ef22_files:/galaxy/server/database/objects/d/0/3/dataset_d030b506-7df7-4ddd-a1d7-1f05ec35ef22.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_v70k0t54\"", | ||
| "files_metadata": "{\"__current_case__\": 342, \"file_type\": \"vcf\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"reheader.vcf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_3bl3fqew\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
| "file_count": "\"auto\"", | ||
| "file_type": "\"vcf\"" | ||
| }, | ||
| "inputs": {}, | ||
| "outputs": { | ||
| "output0": { | ||
| "id": "c1ea69fda62862ce", | ||
| "src": "hda", | ||
| "uuid": "d030b506-7df7-4ddd-a1d7-1f05ec35ef22" | ||
| } | ||
| }, | ||
| "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": [] | ||
| } |
55 changes: 55 additions & 0 deletions
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reports/anvil-edge/tool-tests/edge-24-10-10-06-12-1/errors/50e423fd8ea29b4d.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "50e423fd8ea29b4d", | ||
| "history_id": "90345f6386454b4c", | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-10-10T07:03:39.403635", | ||
| "update_time": "2024-10-10T07:03:45.195696", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-gh7br", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "mkdir -p /galaxy/server/database/objects/2/2/5/dataset_22550930-15f6-4803-a9e9-4cb5a8c8ceb3_files && cp /galaxy/server/database/jobs_directory/000/119/configs/tmpq41_cx2o /galaxy/server/database/objects/2/2/5/dataset_22550930-15f6-4803-a9e9-4cb5a8c8ceb3_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/2/2/5/dataset_22550930-15f6-4803-a9e9-4cb5a8c8ceb3_files /galaxy/server/database/jobs_directory/000/119/configs/tmpq41_cx2o && cp /galaxy/server/database/jobs_directory/000/119/configs/tmpiz8_fe6l /galaxy/server/database/objects/2/2/5/dataset_22550930-15f6-4803-a9e9-4cb5a8c8ceb3.dat; cp /galaxy/server/database/jobs_directory/000/119/configs/tmpq41_cx2o /galaxy/server/database/objects/2/2/5/dataset_22550930-15f6-4803-a9e9-4cb5a8c8ceb3.dat", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "__input_ext": "\"fasta\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "uglyTestingHack": "\"enabled\"", | ||
| "plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", | ||
| "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", | ||
| "track_groups": "[{\"__index__\": 0, \"category\": \"External endpoints\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 5, \"data_format_select\": \"rest\", \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"Hit_titles\", \"style_height\": \"600px\", \"style_label\": \"description\"}, \"label\": \"Rest api\", \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_visibility\": \"default_off\", \"url\": \"http://example.org.external/rest_api/\"}}, {\"__index__\": 1, \"data_format\": {\"__current_case__\": 6, \"data_format_select\": \"sparql\", \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"Hit_titles\", \"style_height\": \"600px\", \"style_label\": \"description\"}, \"label\": \"Sparql endpoint\", \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"query\": \" DEFINE sql:select-option 'order' prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> select ?start, ?end, IF( ?faldo_type = faldo:ForwardStrandPosition, 1, IF( ?faldo_type = faldo:ReverseStrandPosition, -1, 0 ) ) as ?strand, str(?obj_type_name) as ?type, str(?label) as ?name, str(?obj_name) as ?description, ?obj as ?uniqueID, ?parent as ?parentUniqueID where { values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition } }\", \"track_visibility\": \"default_off\", \"url\": \"http://example.org.external/sparql/\"}}]}]", | ||
| "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", | ||
| "gencode": "\"11\"", | ||
| "standalone": "\"data\"", | ||
| "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 171, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}" | ||
| }, | ||
| "inputs": { | ||
| "reference_genome|genome": { | ||
| "id": "cc0f4d7e673557f7", | ||
| "src": "hda", | ||
| "uuid": "3294d2b8-53ec-413d-9e7f-dc0c0f0df47b" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "output": { | ||
| "id": "abd630a4cb3f30ec", | ||
| "src": "hda", | ||
| "uuid": "22550930-15f6-4803-a9e9-4cb5a8c8ceb3" | ||
| } | ||
| }, | ||
| "copied_from_job_id": null, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "INFO:jbrowse:Processing External endpoints / Rest api\nINFO:jbrowse:Processing External endpoints / Sparql endpoint\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stdout": "", | ||
| "stderr": "INFO:jbrowse:Processing External endpoints / Rest api\nINFO:jbrowse:Processing External endpoints / Sparql endpoint\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "job_metrics": [] | ||
| } |
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