Skip to content

Instantly share code, notes, and snippets.

Avatar

John Chilton jmchilton

75 followers · 17 following
  • Penn State University
  • Pittsburgh, PA
  • Twitter @jmchilton
View GitHub Profile
@jmchilton
jmchilton / gist:651dad1289cb897cfaa92a86a39a184e
Created Sep 13, 2021
View gist:651dad1289cb897cfaa92a86a39a184e
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
jmchilton / gist:320fc4de3e6db1df098edf0d1f4f9319
Created Jul 9, 2020
View gist:320fc4de3e6db1df098edf0d1f4f9319
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
jmchilton / gist:6a9dee80fb676db8029c49a3578d9c7b
Created May 18, 2017
View gist:6a9dee80fb676db8029c49a3578d9c7b
>>> 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
jmchilton / gist:00b6a9cad4a78207c5075d2f584838a7
Created Sep 27, 2016
View gist:00b6a9cad4a78207c5075d2f584838a7
$ 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
jmchilton / gist:b4911039b2c7a6acd0b4
Created Feb 4, 2016
View gist:b4911039b2c7a6acd0b4
class: CommandLineTool
cwlVersion: "cwl:draft-3"
baseCommand: python
arguments:
- valueFrom: input.txt
position: 1
requirements:
- class: CreateFileRequirement
fileDef:
- filename: input.txt
@jmchilton
jmchilton / gx_edam.tsv
Created Dec 15, 2015
View gx_edam.tsv
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
jmchilton / gx_edam.tsv
Created Dec 15, 2015
View gx_edam.tsv
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
jmchilton / gist:ee87de7c7eac001b9081
Created Jun 11, 2015
Collections Docs
View gist:ee87de7c7eac001b9081
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
jmchilton / history_context.xml
Created May 5, 2015
Get the history name and encoded id from inside a Galaxy tool.
View history_context.xml
<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>
@jmchilton
jmchilton / gist:89db5844d72ae8326499
Created Jan 29, 2015
Cleaning up Docker...
View gist:89db5844d72ae8326499
# Remove stopped images...
sudo bash -c 'docker rm $(docker ps -a -q)'
sudo bash -c 'docker images -q --filter "dangling=true" | xargs docker rmi'