John Chilton jmchilton
jmchilton
/ gist:e84f91cf2646057e5cd25781ba7d422b
Last active
August 11, 2024 14:18
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| Found 4 test cases to validate for tool shasta / 0.6.0+galaxy0 (@ /Users/jxc755/workspace/tools-iuc/tools/shasta/shasta.xml) | |
| Test Case 1: validated | |
| Test Case 2: validated | |
| Test Case 3: validated | |
| Test Case 4: validation failed - Invalid parameter name found kmers|enrichmentThreshold | |
| Found 3 test cases to validate for tool bg_diamond_view / 2.0.8 (@ /Users/jxc755/workspace/tools-iuc/tools/diamond/diamond_view.xml) | |
| Test Case 1: validated | |
| Test Case 2: validated | |
| Test Case 3: validation failed - 1 validation error for DynamicModelForTool | |
| forwardonly |
jmchilton
/ gist:651dad1289cb897cfaa92a86a39a184e
Created
September 13, 2021 21:16
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| toolshed.g2.bx.psu.edu/repos/devteam/cummerbund_to_tabular/cummerbund_to_cuffdiff | |
| toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_coverage_distributions | |
| toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_population_structure |
jmchilton
/ gist:320fc4de3e6db1df098edf0d1f4f9319
Created
July 9, 2020 17:12
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| Server running... press ctrl-c to stop. | |
| Regenerating: 1 file(s) changed at 2020-07-09 12:50:54 | |
| topics/dev/images/core_plugins_overview.plantuml.txt | |
| Warning: Empty `slug` generated for ''. | |
| Warning: Empty `slug` generated for ''. | |
| [2020-07-09 12:57:05] ERROR Errno::ECONNRESET: Connection reset by peer @ io_fillbuf - fd:17 | |
| /Users/john/miniconda3/envs/galaxy_training_material/lib/ruby/2.4.0/webrick/httpserver.rb:82:in `eof?' | |
| /Users/john/miniconda3/envs/galaxy_training_material/lib/ruby/2.4.0/webrick/httpserver.rb:82:in `run' | |
| /Users/john/miniconda3/envs/galaxy_training_material/lib/ruby/2.4.0/webrick/server.rb:308:in `block in start_thread' |
jmchilton
/ gist:6a9dee80fb676db8029c49a3578d9c7b
Created
May 18, 2017 18:11
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| >>> import galaxy.tools.parser | |
| >>> import galaxy.tools.parser.factory | |
| >>> tool_source = galaxy.tools.parser.factory.get_tool_source("bwa.xml") | |
| >>> reqs, _ = tool_source.parse_requirements_and_containers() | |
| >>> from galaxy.tools.deps.conda_util import CondaTarget | |
| >>> from galaxy.tools.deps.conda_util import hash_conda_packages | |
| >>> hash_conda_packages([CondaTarget(req.name, req.version) for req in reqs]) | |
| '28bd91abdde0d474ee5121c1db757e2fe25984a7b393b5288912c68b29b67e02' |
jmchilton
/ gist:00b6a9cad4a78207c5075d2f584838a7
Created
September 27, 2016 19:59
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| $ mulled-build --recipes-dir ../bioconda-recipes --targets 'samtools=1.3.1,bedtools=2.22' build | |
| ./involucro -v=3 -f /home/john/workspace/galaxy-lib/galaxy/tools/deps/mulled/invfile.lua -set CHANNELS='bioconda,conda-forge,r' -set TEST='true' -set TARGETS='samtools=1.3.1,bedtools=2.22' -set REPO='quay.io/mulled/mulled-v1-a93fa17175d6f093a6423535399b7ad4ac06ceed' build | |
| [Sep 27 15:58:40] DEBU Run file [/home/john/workspace/galaxy-lib/galaxy/tools/deps/mulled/invfile.lua] | |
| [Sep 27 15:58:40] STEP Run image [continuumio/miniconda:latest] with command [[rm -rf /data/dist]] | |
| [Sep 27 15:58:40] DEBU Creating container [step-4ff4f7eeac] | |
| [Sep 27 15:58:40] DEBU Created container [eb5cdfab2b12 step-4ff4f7eeac], starting it | |
| [Sep 27 15:58:40] DEBU Container [eb5cdfab2b12 step-4ff4f7eeac] started, waiting for completion | |
| [Sep 27 15:58:40] DEBU Container [eb5cdfab2b12 step-4ff4f7eeac] completed with exit code [0] as expected | |
| [Sep 27 15:58:40] DEBU Container [eb5cdfab2b12 step-4ff4f7eeac] removed | |
| [Sep 27 15:58:40] STEP Run image [ |
jmchilton
/ gist:b4911039b2c7a6acd0b4
Created
February 4, 2016 20:39
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| class: CommandLineTool | |
| cwlVersion: "cwl:draft-3" | |
| baseCommand: python | |
| arguments: | |
| - valueFrom: input.txt | |
| position: 1 | |
| requirements: | |
| - class: CreateFileRequirement | |
| fileDef: | |
| - filename: input.txt |
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| ab1 | format_2333 | Binary format | Binary format. | |
|---|---|---|---|---|
| acedb | format_2330 | Textual format | Textual format. | |
| affybatch | format_2331 | HTML | HTML format. | |
| afg | format_2561 | Sequence assembly format (text) | Text format for sequence assembly data. | |
| arff | format_2330 | Textual format | Textual format. | |
| asn1 | format_2330 | Textual format | Textual format. | |
| asn1-binary | format_2333 | Binary format | Binary format. | |
| axt | format_2330 | Textual format | Textual format. | |
| bam | format_2572 | BAM | BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data. | |
| bcf | format_3020 | BCF | BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation). |
jmchilton
/ gx_edam.tsv
Created
December 15, 2015 15:42
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| acedb | format_2330 | Textual format | Textual format. | |
|---|---|---|---|---|
| affybatch | format_2331 | HTML | HTML format. | |
| afg | format_2561 | Sequence assembly format (text) | Text format for sequence assembly data. | |
| arff | format_2330 | Textual format | Textual format. | |
| asn1 | format_2330 | Textual format | Textual format. | |
| asn1-binary | format_2333 | Binary format | Binary format. | |
| axt | format_2330 | Textual format | Textual format. | |
| bam | format_2572 | BAM | BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data. | |
| bcf | format_3020 | BCF | BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation). |
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| Overview: bit.ly/gcc2014workflows | |
| Tool Authors: http://planemo.readthedocs.org/en/latest/writing_standalone.html#collections | |
| History Management: https://wiki.galaxyproject.org/Histories#Dataset_Collections | |
| An Analysis (RNA-seq): | |
| 1. https://vimeo.com/128265983 | |
| 2. https://vimeo.com/128268401 |
jmchilton
/ history_context.xml
Created
May 5, 2015 19:11
Get the history name and encoded id from inside a Galaxy tool.
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| <tool id="history_context" name="history_context" version="1.0.0"> | |
| <command> | |
| #set $history_id=$__app__.security.encode_id($output_dataset.creating_job.history.id) | |
| #set $history_name=$output_dataset.creating_job.history.name | |
| echo $history_id > $output_dataset; | |
| echo $history_name >> $output_dataset; | |
| </command> | |
| <inputs> | |
| <param name="ignored" type="integer" value="0" /> | |
| </inputs> |
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