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workflow-install #1

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6 changes: 6 additions & 0 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,12 @@ ENV GALAXY_CONFIG_BRAND EOSC-Life_D4
ADD tool_list.yml $GALAXY_ROOT/tool_list.yml
RUN install-tools $GALAXY_ROOT/tool_list.yml

# Install the workflow
ADD galaxy-workflow.ga $GALAXY_ROOT/galaxy-workflow.ga
RUN startup_lite && \
galaxy-wait && \
workflow-install --workflow_path $GALAXY_ROOT/galaxy-workflow.ga -g http://localhost:8080 -u $GALAXY_DEFAULT_ADMIN_USER -p $GALAXY_DEFAULT_ADMIN_PASSWORD

# Container Style
ADD welcome.html $GALAXY_CONFIG_DIR/web/welcome.html

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198 changes: 198 additions & 0 deletions galaxy-workflow.ga
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@@ -0,0 +1,198 @@
{
"a_galaxy_workflow": "true",
"annotation": "",
"format-version": "0.1",
"name": "Last",
"steps": {
"0": {
"annotation": "",
"content_id": "last_db",
"errors": null,
"id": 0,
"input_connections": {},
"inputs": [
{
"description": "runtime parameter for tool LASTdb",
"name": "input_files"
}
],
"label": null,
"name": "LASTdb",
"outputs": [
{
"name": "outfile",
"type": "lastdb"
}
],
"position": {
"left": 227,
"top": 183.5
},
"post_job_actions": {},
"tool_id": "last_db",
"tool_state": "{\"input_files\": {\"__class__\": \"RuntimeValue\"}, \"lastdb\": {\"sequences_type\": {\"protein\": \"\", \"__current_case__\": 0, \"a\": \"ACGT\"}, \"repeats\": {\"uppercase\": \"1\", \"simple_repeat\": \"1\", \"sm_lower\": \"true\"}, \"lastdb_advanced\": {\"S\": \"1\", \"seeds\": {\"u\": \"NEAR\", \"__current_case__\": 5, \"w\": \"1\", \"W\": \"1\", \"m\": \"1\"}, \"i\": \"0\", \"C\": \"0\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1021+galaxy1",
"type": "tool",
"uuid": "4fef6daf-3a5c-44a7-9262-09591628c8c8",
"workflow_outputs": []
},
"1": {
"annotation": "",
"content_id": "last_maf_convert",
"errors": null,
"id": 1,
"input_connections": {},
"inputs": [
{
"description": "runtime parameter for tool MAF-convert",
"name": "maf_file"
}
],
"label": null,
"name": "MAF-convert",
"outputs": [
{
"name": "outfile",
"type": "maf"
}
],
"position": {
"left": 1196,
"top": 227.5
},
"post_job_actions": {},
"tool_id": "last_maf_convert",
"tool_state": "{\"maf_convert\": {\"noheader\": \"false\", \"output_type\": {\"output_format\": \"psl\", \"__current_case__\": 2, \"protein\": \"false\", \"j\": \"1\"}}, \"maf_file\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1021+galaxy0",
"type": "tool",
"uuid": "3d613b41-11c6-4165-89e9-d3d865929b0a",
"workflow_outputs": []
},
"2": {
"annotation": "",
"content_id": "last_train",
"errors": null,
"id": 2,
"input_connections": {
"db_opts|lastdatabase": {
"id": 0,
"output_name": "outfile"
}
},
"inputs": [
{
"description": "runtime parameter for tool LAST-train",
"name": "db_opts"
},
{
"description": "runtime parameter for tool LAST-train",
"name": "query_fasta"
}
],
"label": null,
"name": "LAST-train",
"outputs": [
{
"name": "outfile",
"type": "txt"
}
],
"position": {
"left": 434,
"top": 361.5
},
"post_job_actions": {},
"tool_id": "last_train",
"tool_state": "{\"db_opts\": {\"db_opts_input\": \"lastdb\", \"__current_case__\": 1, \"lastdatabase\": {\"__class__\": \"RuntimeValue\"}}, \"init_options\": {\"Q\": \"0\", \"__current_case__\": 0, \"r\": \"5\", \"q\": \"5\", \"cost_opt\": {\"a\": \"15\", \"b\": \"3\", \"A\": \"15\", \"B\": \"3\"}}, \"last_train_opt\": {\"align_opt\": {\"D\": \"1000000\", \"E\": \"10\", \"s\": \"1\", \"S\": \"1\", \"T\": \"0\", \"m\": \"10\", \"k\": \"1\", \"X\": \"0\"}}, \"query_fasta\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1021+galaxy1",
"type": "tool",
"uuid": "6889f6cb-3bd2-496c-8fee-88fb05a18892",
"workflow_outputs": []
},
"3": {
"annotation": "",
"content_id": "last_al",
"errors": null,
"id": 3,
"input_connections": {
"db_opts|lastdatabase": {
"id": 0,
"output_name": "outfile"
}
},
"inputs": [
{
"description": "runtime parameter for tool LASTal",
"name": "db_opts"
},
{
"description": "runtime parameter for tool LASTal",
"name": "query_seq"
}
],
"label": null,
"name": "LASTal",
"outputs": [
{
"name": "outfile",
"type": "maf"
}
],
"position": {
"left": 722,
"top": 205.5
},
"post_job_actions": {},
"tool_id": "last_al",
"tool_state": "{\"db_opts\": {\"db_opts_input\": \"lastdb\", \"__current_case__\": 1, \"lastdatabase\": {\"__class__\": \"RuntimeValue\"}}, \"lastal\": {\"f\": \"MAF\", \"j\": \"3\", \"isprotein\": {\"lastal_protein\": \"dna\", \"__current_case__\": 0, \"schoring_schemes\": {\"score_matrix\": \"scoreFile\", \"__current_case__\": 10, \"scoreMatrixFile\": {\"__class__\": \"RuntimeValue\"}}, \"s\": \"2\"}, \"repeats_misc\": {\"uppercase_misc\": \"1\", \"simple_repeat_misc\": \"0\"}, \"evalue_opt\": {\"D\": \"1000000\"}, \"init_match_opt\": {\"m\": \"10\", \"l\": \"1\", \"L\": \"999999999\", \"k\": \"1\", \"W\": \"1\"}, \"misc_opt\": {\"S\": \"0\", \"K\": \"0\", \"C\": \"0\", \"T\": \"0\", \"n\": \"10\", \"u\": \"0\", \"w\": \"1000\", \"G\": \"1\", \"g\": \"1\"}}, \"query_seq\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1021+galaxy1",
"type": "tool",
"uuid": "e13efc25-165f-4b73-8931-ad5fac874273",
"workflow_outputs": []
},
"4": {
"annotation": "",
"content_id": "last_split",
"errors": null,
"id": 4,
"input_connections": {
"db_opts|lastdatabase": {
"id": 2,
"output_name": "outfile"
}
},
"inputs": [
{
"description": "runtime parameter for tool LAST-split",
"name": "db_opts"
},
{
"description": "runtime parameter for tool LAST-split",
"name": "last_align"
}
],
"label": null,
"name": "LAST-split",
"outputs": [
{
"name": "outfile",
"type": "maf"
}
],
"position": {
"left": 967,
"top": 408.5
},
"post_job_actions": {},
"tool_id": "last_split",
"tool_state": "{\"db_opts\": {\"db_opts_input\": \"lastdb\", \"__current_case__\": 1, \"lastdatabase\": {\"__class__\": \"RuntimeValue\"}}, \"last_align\": {\"__class__\": \"RuntimeValue\"}, \"lastsplit_opt\": {\"d\": \"1\", \"c\": \"0.004\", \"t\": \"1e-05\", \"M\": \"7.0\", \"S\": \"1.7\", \"m\": \"1.0\", \"no_split\": \"false\"}, \"output_format\": \"MAF+\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1021+galaxy0",
"type": "tool",
"uuid": "a1b4f3c2-1d2f-42d7-9c59-221b9989926e",
"workflow_outputs": []
}
},
"tags": [],
"uuid": "0453396e-524c-4709-8d89-db2c67022f51",
"version": 1
}