diff --git a/Dockerfile b/Dockerfile index 43735af..6ad0b5a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -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 diff --git a/galaxy-workflow.ga b/galaxy-workflow.ga new file mode 100644 index 0000000..01d5037 --- /dev/null +++ b/galaxy-workflow.ga @@ -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 +} \ No newline at end of file