diff galaxy_integration.org @ 0:dd46956ff61f draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_integration.org	Fri Dec 08 09:57:17 2017 -0500
@@ -0,0 +1,41 @@
+#+TITLE: Building galaxy tools
+#+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 |
+
+file must be manually edited
+
+# create toolshed configuration
+#+BEGIN_SRC bash
+planemo shed_init --name=long_reads_sampling \
+                    --owner=repeatexplorer \
+                    --description=long_reads_sampling \
+                    --long_description="Create sample of long reads" \
+                    --category="Fasta Manipulation"
+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