Repository revision
42:6cd09d7b5f37

Repository 'jbrowse'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/jbrowse

JBrowse - Data Directory to Standalone tool metadata
Miscellaneous
upgrades the bare data directory to a full JBrowse instance
jbrowse_to_standalone
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.10+galaxy0
1.16.10+galaxy0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.10+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.9+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.8+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.8+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.5+galaxy7
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.5+galaxy6
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.5+galaxy5
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.5+galaxy4
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.5+galaxy3
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.4+galaxy3
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.4+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.2+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.2+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.2+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.1+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.12.5+galaxy3
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.12.5+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.12.5+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/0.7.0
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/0.5.3
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/0.5.2
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/0.5.1
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/0.4
jbrowse_to_standalone
Requirements (dependencies defined in the <requirements> tag set)
name version type
jbrowse 1.16.10 package
python 2.7 package
biopython 1.72 package
bcbiogff 0.6.4 package
samtools 1.9 package
pyyaml 3.13 package
tabix 0.2.6 package
findutils 4.6.0 package
Additional information about this tool
## Create output directory
mkdir -p $output.files_path &&

export JBROWSE_SOURCE_DIR=\$(dirname \$(command -v prepare-refseqs.pl))/../opt/jbrowse  &&

## Copy in jbrowse
cp -R \${JBROWSE_SOURCE_DIR}/* $output.files_path/ &&

## Copy in data directory
cp -R $input.dataset.extra_files_path/data/ $output.files_path/ &&
cp $output.files_path/index.html $output
None
False
Functional tests
No functional tests defined