John Chilton jmchilton
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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| # Remove stopped images... | |
| sudo bash -c 'docker rm $(docker ps -a -q)' | |
| sudo bash -c 'docker images -q --filter "dangling=true" | xargs docker rmi' |
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| library(mzR) | |
| library(msdata) | |
| library(jsonlite) | |
| library("RSQLite") | |
| z <- openMSfile("iTRAQ_Erwinia.mzML") | |
| x <- openIDfile("iTRAQ_Erwinia.mzid") | |
| p <- psms(x) | |
| m <- modifications(x) | |
| s <- score(x) | |
| ## add a column for the scanNum by parsing |
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| #!/bin/sh | |
| tags=" | |
| latest_2013.06.03:/tmp/old.patch | |
| latest_2013.08.12:/tmp/old.patch | |
| latest_2013.11.04:/tmp/old.patch | |
| latest_2014.02.10:/tmp/new.patch | |
| latest_2014.04.14:/tmp/new.patch | |
| latest_2014.06.02:/tmp/new.patch | |
| latest_2014.08.11:/tmp/new.patch |
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| # Is dataset an image? | |
| image = check_image( dataset.path ) | |
| if image: | |
| if not PIL: | |
| image = None | |
| # get_image_ext() returns None if nor a supported Image type | |
| ext = get_image_ext( dataset.path, image ) | |
| data_type = ext | |
| # Is dataset content multi-byte? | |
| elif dataset.is_multi_byte: |