annotate galaxy_integration.org @ 1:5596bafd2119 draft

Uploaded

#+TITLE: Building galaxy tools
* Long reads sampling
#+BEGIN_SRC sh
# require planemo
if [ -e "long_reads_sampling.xml" ]
then
   echo "backing up original file"
   cp long_reads_sampling.xml long_reads_sampling.xml.backup
fi
planemo tool_init --force  --id 'long_reads_sampling' \
--name 'Create sample of long reads' \
--requirement biopython \
--example_command 'long_reads_sampling.py -i input_seq.fasta -o output_seq.fasta -l total_length -s seed' \
--example_input 'input_seq.fasta' \
--example_output 'output_seq.fasta'

#+END_SRC

#+RESULTS:
| backing         | up      | original | file                         |
| Tool | written | to       | long_reads_sampling.xml |




* Short read simulator
#+BEGIN_SRC sh
# require planemo
if [ -e "long2short.xml" ]
then
   echo "backing up original file"
   cp long2short.xml long2short.xml.backup
fi
/home/petr/anaconda3/bin/planemo tool_init --force  --id 'long2short' \
--name 'Get pseudo short paired end reads from long reads' \
--requirement biopython \
--requirement python@3.6 \
--example_command 'long2short.py -i input_seq.fasta -o output_seq.fasta -cov coverage -L insert_length -l read_length' \
--example_input 'input_seq.fasta' \
--example_output 'output_seq.fasta'

#+END_SRC

#+RESULTS:
: Tool written to long2short.xml

file must be manually edited


* create planemo repo with all tools
# create toolshed configuration
#+BEGIN_SRC bash
/home/petr/anaconda3/bin/planemo shed_init --name=long_reads_sampling \
                    --owner=repeatexplorer \
                    --description=long_reads_sampling \
                    --long_description="Create sample of long reads" \
                    --category="Fasta Manipulation"
/home/petr/anaconda3/bin/planemo shed_lint --tools
#+END_SRC

#+RESULTS:

# creating repository - once

#+BEGIN_SRC bash
# it requires planemo server running!
planemo shed_create --shed_target local
#+END_SRC