jmchilton

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

  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

<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

>>> 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

# Setup Galaxy instance and dataset for testing...
from bioblend import galaxy
gi = galaxy.GalaxyInstance("localhost:8080", "1957431058be3aa3c57ca312f4a05521")
history = gi.histories.create_history(name="TestRandomLines")
dataset_id = gi.tools.paste_content("1\n2\n3", history["id"])['outputs'][0]["id"]

# Prepare tool inputs.
from bioblend.galaxy.tools.inputs import inputs, dataset
random_lines_inputs = inputs().set("num_lines", 1).set("input", dataset(dataset_id))

jmchilton

# Remove stopped images...
sudo bash -c 'docker rm $(docker ps -a -q)'
sudo bash -c 'docker images -q --filter "dangling=true" | xargs docker rmi'

jmchilton

$ 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

#!/bin/bash                                                                                                           

SOURCE="${BASH_SOURCE[0]}"
app_dir="$( dirname "$SOURCE" )"
while [ -h "$SOURCE" ]
do
  SOURCE="$(readlink "$SOURCE")"
  [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
  app_dir="$( cd -P "$( dirname "$SOURCE"  )" && pwd )"
done

jmchilton

class: CommandLineTool
cwlVersion: "cwl:draft-3"
baseCommand: python
arguments:
  - valueFrom: input.txt
    position: 1
requirements:
  - class: CreateFileRequirement
    fileDef:
      - filename: input.txt

jmchilton

11:56 < jmchilton> I am trying to understand hda.children - is the only for an hda to have a child if a tool output is 
                   specified this way. Is anything else a parent/child (implicit conversions, etc...)?
11:57 < jmchilton> And more specifically - should it possible for a parent to be 'deleted' but not the child?
....
13:22 < jmchilton> Well you cannot purge datasets with children because of a bug in user.quota_amount. I am assuming this 
                   feature doesn't get used much :)
13:27 < natefoo> galaxy_main=> select count(*) from history_dataset_association where parent_id is not null;
13:27 < natefoo>  count
13:27 < natefoo> -------
13:27 < natefoo>     30