Mercurial > repos > rnateam > blockclust_workflow
changeset 1:25afbac62e0d draft
Uploaded
author | rnateam |
---|---|
date | Wed, 07 May 2014 04:59:28 -0400 (2014-05-07) |
parents | b2040467dad2 |
children | 0c393c9d3756 |
files | blockclust_workflow.ga blockclust_workflow_clustering.ga blockclust_workflow_complete.ga readme.rst |
diffstat | 4 files changed, 744 insertions(+), 739 deletions(-) [+] |
line wrap: on
line diff
--- a/blockclust_workflow.ga Tue May 06 12:51:51 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,461 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "", - "format-version": "0.1", - "name": "BlockClustWorkflow", - "steps": { - "0": { - "annotation": "", - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Input BAM file" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 267, - "top": 257.5 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"Input BAM file\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "1": { - "annotation": "", - "id": 1, - "input_connections": { - "tool_mode|reads_bam": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "name": "BlockClust", - "outputs": [ - { - "name": "tags_bed", - "type": "bed" - }, - { - "name": "hclust_plot", - "type": "pdf" - }, - { - "name": "clusters", - "type": "bed" - }, - { - "name": "model_based_pred_bed", - "type": "bed" - }, - { - "name": "nearest_neighbour_pred_bed", - "type": "bed" - }, - { - "name": "sim_tab_out", - "type": "tabular" - }, - { - "name": "cluster_dist", - "type": "pdf" - }, - { - "name": "cluster_hclust", - "type": "pdf" - } - ], - "position": { - "left": 524, - "top": 323 - }, - "post_job_actions": { - "HideDatasetActioncluster_dist": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "cluster_dist" - }, - "HideDatasetActioncluster_hclust": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "cluster_hclust" - }, - "HideDatasetActionclusters": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "clusters" - }, - "HideDatasetActionhclust_plot": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "hclust_plot" - }, - "HideDatasetActionmodel_based_pred_bed": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "model_based_pred_bed" - }, - "HideDatasetActionnearest_neighbour_pred_bed": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "nearest_neighbour_pred_bed" - }, - "HideDatasetActionsim_tab_out": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "sim_tab_out" - }, - "HideDatasetActiontags_bed": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "tags_bed" - } - }, - "tool_errors": null, - "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", - "tool_state": "{\"tool_mode\": \"{\\\"operation\\\": \\\"pre\\\", \\\"reads_bam\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"operation\\\": \\\"pre\\\", \\\"reads_bam\\\": null, \\\"__current_case__\\\": 0}\", \"__page__\": 0}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "2": { - "annotation": "", - "id": 2, - "input_connections": { - "input": { - "id": 1, - "output_name": "tags_bed" - } - }, - "inputs": [], - "name": "Sort", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 797, - "top": 355 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "sort1", - "tool_state": "{\"__page__\": 0, \"style\": \"\\\"alpha\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"ASC\\\"\", \"input\": \"null\", \"column_set\": \"[{\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 0, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"6\\\"}, \\\"other_style\\\": \\\"alpha\\\"}, {\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 1, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}, \\\"other_style\\\": \\\"num\\\"}, {\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 2, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"3\\\"}, \\\"other_style\\\": \\\"num\\\"}]\"}", - "tool_version": "1.0.3", - "type": "tool", - "user_outputs": [] - }, - "3": { - "annotation": "", - "id": 3, - "input_connections": { - "input": { - "id": 2, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "blockbuster", - "outputs": [ - { - "name": "output", - "type": "tabular" - } - ], - "position": { - "left": 970, - "top": 225 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1", - "tool_state": "{\"distance\": \"\\\"40\\\"\", \"scale\": \"\\\"0.5\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"print\": \"\\\"2\\\"\", \"tagFilter\": \"\\\"0\\\"\", \"merge\": \"\\\"0\\\"\", \"minBlockHeight\": \"\\\"1.0\\\"\", \"input\": \"null\", \"minClusterHeight\": \"\\\"50.0\\\"\"}", - "tool_version": "0.1", - "type": "tool", - "user_outputs": [] - }, - "4": { - "annotation": "", - "id": 4, - "input_connections": { - "tool_mode|input_bbo": { - "id": 3, - "output_name": "output" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool BlockClust", - "name": "tool_mode" - } - ], - "name": "BlockClust", - "outputs": [ - { - "name": "tags_bed", - "type": "bed" - }, - { - "name": "hclust_plot", - "type": "pdf" - }, - { - "name": "clusters", - "type": "bed" - }, - { - "name": "model_based_pred_bed", - "type": "bed" - }, - { - "name": "nearest_neighbour_pred_bed", - "type": "bed" - }, - { - "name": "sim_tab_out", - "type": "tabular" - }, - { - "name": "cluster_dist", - "type": "pdf" - }, - { - "name": "cluster_hclust", - "type": "pdf" - } - ], - "position": { - "left": 1232, - "top": 321 - }, - "post_job_actions": { - "HideDatasetActioncluster_dist": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "cluster_dist" - }, - "HideDatasetActioncluster_hclust": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "cluster_hclust" - }, - "HideDatasetActionclusters": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "clusters" - }, - "HideDatasetActionnearest_neighbour_pred_bed": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "nearest_neighbour_pred_bed" - }, - "HideDatasetActionsim_tab_out": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "sim_tab_out" - }, - "HideDatasetActiontags_bed": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "tags_bed" - } - }, - "tool_errors": null, - "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", - "tool_state": "{\"tool_mode\": \"{\\\"pred\\\": {\\\"pred_mode\\\": \\\"model_based\\\", \\\"enable_pred\\\": \\\"yes\\\", \\\"__current_case__\\\": 0}, \\\"operation\\\": \\\"clust\\\", \\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"input_bbo\\\": null}\", \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"operation\\\": \\\"clust\\\", \\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"input_bbo\\\": null}\", \"__page__\": 0}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "5": { - "annotation": "", - "id": 5, - "input_connections": { - "input": { - "id": 4, - "output_name": "clusters" - } - }, - "inputs": [], - "name": "Extract Genomic DNA", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 1495, - "top": 248 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "Extract genomic DNA 1", - "tool_state": "{\"out_format\": \"\\\"fasta\\\"\", \"__page__\": 0, \"interpret_features\": \"\\\"yes\\\"\", \"__rerun_remap_job_id__\": null, \"seq_source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\"}", - "tool_version": "2.2.3", - "type": "tool", - "user_outputs": [] - }, - "6": { - "annotation": "", - "id": 6, - "input_connections": { - "seqdb": { - "id": 5, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "Search covariance model(s)", - "outputs": [ - { - "name": "outfile", - "type": "tabular" - }, - { - "name": "multiple_alignment_output", - "type": "tabular" - } - ], - "position": { - "left": 1753, - "top": 247 - }, - "post_job_actions": { - "HideDatasetActionmultiple_alignment_output": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "multiple_alignment_output" - }, - "HideDatasetActionoutfile": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "outfile" - } - }, - "tool_errors": null, - "tool_id": "testtoolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.0.2", - "tool_state": "{\"A\": \"\\\"False\\\"\", \"nohmm\": \"\\\"False\\\"\", \"--acyk\": \"\\\"False\\\"\", \"bottomonly\": \"\\\"False\\\"\", \"g\": \"\\\"False\\\"\", \"inclusion_thresholds_opts\": \"{\\\"inclusion_thresholds_selector\\\": \\\"\\\", \\\"__current_case__\\\": 3}\", \"__page__\": 0, \"max\": \"\\\"False\\\"\", \"notrunc\": \"\\\"False\\\"\", \"mid\": \"\\\"False\\\"\", \"seqdb\": \"null\", \"toponly\": \"\\\"False\\\"\", \"cm_opts\": \"{\\\"database\\\": null, \\\"__current_case__\\\": 0, \\\"cm_opts_selector\\\": \\\"db\\\"}\", \"reporting_thresholds_opts\": \"{\\\"reporting_thresholds_selector\\\": \\\"\\\", \\\"__current_case__\\\": 3}\", \"cyk\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.0.2", - "type": "tool", - "user_outputs": [] - }, - "7": { - "annotation": "", - "id": 7, - "input_connections": { - "tool_mode|clusters_bed": { - "id": 4, - "output_name": "clusters" - }, - "tool_mode|cmsearch_out": { - "id": 6, - "output_name": "outfile" - }, - "tool_mode|sim_tab_in": { - "id": 4, - "output_name": "sim_tab_out" - } - }, - "inputs": [], - "name": "BlockClust", - "outputs": [ - { - "name": "tags_bed", - "type": "bed" - }, - { - "name": "hclust_plot", - "type": "pdf" - }, - { - "name": "clusters", - "type": "bed" - }, - { - "name": "model_based_pred_bed", - "type": "bed" - }, - { - "name": "nearest_neighbour_pred_bed", - "type": "bed" - }, - { - "name": "sim_tab_out", - "type": "tabular" - }, - { - "name": "cluster_dist", - "type": "pdf" - }, - { - "name": "cluster_hclust", - "type": "pdf" - } - ], - "position": { - "left": 2049, - "top": 433 - }, - "post_job_actions": { - "HideDatasetActionclusters": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "clusters" - }, - "HideDatasetActionhclust_plot": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "hclust_plot" - }, - "HideDatasetActionmodel_based_pred_bed": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "model_based_pred_bed" - }, - "HideDatasetActionnearest_neighbour_pred_bed": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "nearest_neighbour_pred_bed" - }, - "HideDatasetActionsim_tab_out": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "sim_tab_out" - }, - "HideDatasetActiontags_bed": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "tags_bed" - } - }, - "tool_errors": null, - "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", - "tool_state": "{\"tool_mode\": \"{\\\"cmsearch_out\\\": null, \\\"operation\\\": \\\"post\\\", \\\"clusters_bed\\\": null, \\\"__current_case__\\\": 2, \\\"sim_tab_in\\\": null}\", \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"cmsearch_out\\\": null, \\\"operation\\\": \\\"post\\\", \\\"clusters_bed\\\": null, \\\"__current_case__\\\": 2, \\\"sim_tab_in\\\": null}\", \"__page__\": 0}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - } - } -} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/blockclust_workflow_clustering.ga Wed May 07 04:59:28 2014 -0400 @@ -0,0 +1,282 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "Until clustering step. No post processing included.", + "format-version": "0.1", + "name": "BlockClustWorkflow_clustering", + "steps": { + "0": { + "annotation": "", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Input BAM file" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 217, + "top": 282.5 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Input BAM file\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "1": { + "annotation": "", + "id": 1, + "input_connections": { + "tool_mode|reads_bam": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "BlockClust", + "outputs": [ + { + "name": "tags_bed", + "type": "bed" + }, + { + "name": "hclust_plot", + "type": "pdf" + }, + { + "name": "clusters", + "type": "bed" + }, + { + "name": "model_based_pred_bed", + "type": "bed" + }, + { + "name": "nearest_neighbour_pred_bed", + "type": "bed" + }, + { + "name": "sim_tab_out", + "type": "tabular" + }, + { + "name": "cluster_dist", + "type": "pdf" + }, + { + "name": "cluster_hclust", + "type": "pdf" + } + ], + "position": { + "left": 446.5, + "top": 239.5 + }, + "post_job_actions": { + "HideDatasetActioncluster_dist": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "cluster_dist" + }, + "HideDatasetActioncluster_hclust": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "cluster_hclust" + }, + "HideDatasetActionclusters": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "clusters" + }, + "HideDatasetActionhclust_plot": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "hclust_plot" + }, + "HideDatasetActionmodel_based_pred_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "model_based_pred_bed" + }, + "HideDatasetActionnearest_neighbour_pred_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "nearest_neighbour_pred_bed" + }, + "HideDatasetActionsim_tab_out": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "sim_tab_out" + }, + "HideDatasetActiontags_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "tags_bed" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", + "tool_state": "{\"tool_mode\": \"{\\\"operation\\\": \\\"pre\\\", \\\"reads_bam\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "2": { + "annotation": "", + "id": 2, + "input_connections": { + "input": { + "id": 1, + "output_name": "tags_bed" + } + }, + "inputs": [], + "name": "Sort", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 740, + "top": 271 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "sort1", + "tool_state": "{\"__page__\": 0, \"style\": \"\\\"alpha\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"ASC\\\"\", \"input\": \"null\", \"column_set\": \"[{\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 0, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"6\\\"}, \\\"other_style\\\": \\\"alpha\\\"}, {\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 1, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}, \\\"other_style\\\": \\\"num\\\"}, {\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 2, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"3\\\"}, \\\"other_style\\\": \\\"num\\\"}]\"}", + "tool_version": "1.0.3", + "type": "tool", + "user_outputs": [] + }, + "3": { + "annotation": "", + "id": 3, + "input_connections": { + "input": { + "id": 2, + "output_name": "out_file1" + } + }, + "inputs": [], + "name": "blockbuster", + "outputs": [ + { + "name": "output", + "type": "tabular" + } + ], + "position": { + "left": 961.5, + "top": 219.5 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1", + "tool_state": "{\"distance\": \"\\\"40\\\"\", \"scale\": \"\\\"0.5\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"print\": \"\\\"2\\\"\", \"tagFilter\": \"\\\"0\\\"\", \"merge\": \"\\\"0\\\"\", \"minBlockHeight\": \"\\\"1.0\\\"\", \"input\": \"null\", \"minClusterHeight\": \"\\\"50.0\\\"\"}", + "tool_version": "0.1", + "type": "tool", + "user_outputs": [] + }, + "4": { + "annotation": "", + "id": 4, + "input_connections": { + "tool_mode|input_bbo": { + "id": 3, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool BlockClust", + "name": "tool_mode" + } + ], + "name": "BlockClust", + "outputs": [ + { + "name": "tags_bed", + "type": "bed" + }, + { + "name": "hclust_plot", + "type": "pdf" + }, + { + "name": "clusters", + "type": "bed" + }, + { + "name": "model_based_pred_bed", + "type": "bed" + }, + { + "name": "nearest_neighbour_pred_bed", + "type": "bed" + }, + { + "name": "sim_tab_out", + "type": "tabular" + }, + { + "name": "cluster_dist", + "type": "pdf" + }, + { + "name": "cluster_hclust", + "type": "pdf" + } + ], + "position": { + "left": 1220.5, + "top": 375.5 + }, + "post_job_actions": { + "HideDatasetActioncluster_dist": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "cluster_dist" + }, + "HideDatasetActioncluster_hclust": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "cluster_hclust" + }, + "HideDatasetActionsim_tab_out": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "sim_tab_out" + }, + "HideDatasetActiontags_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "tags_bed" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", + "tool_state": "{\"tool_mode\": \"{\\\"pred\\\": {\\\"pred_mode\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"enable_pred\\\": \\\"yes\\\", \\\"__current_case__\\\": 0}, \\\"operation\\\": \\\"clust\\\", \\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"input_bbo\\\": null}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + } + } +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/blockclust_workflow_complete.ga Wed May 07 04:59:28 2014 -0400 @@ -0,0 +1,462 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "BlockClustWorkflow_clustering", + "steps": { + "0": { + "annotation": "", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Input BAM file" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 217, + "top": 276.5 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Input BAM file\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "1": { + "annotation": "", + "id": 1, + "input_connections": { + "tool_mode|reads_bam": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "BlockClust", + "outputs": [ + { + "name": "tags_bed", + "type": "bed" + }, + { + "name": "hclust_plot", + "type": "pdf" + }, + { + "name": "clusters", + "type": "bed" + }, + { + "name": "model_based_pred_bed", + "type": "bed" + }, + { + "name": "nearest_neighbour_pred_bed", + "type": "bed" + }, + { + "name": "sim_tab_out", + "type": "tabular" + }, + { + "name": "cluster_dist", + "type": "pdf" + }, + { + "name": "cluster_hclust", + "type": "pdf" + } + ], + "position": { + "left": 446.5, + "top": 233.5 + }, + "post_job_actions": { + "HideDatasetActioncluster_dist": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "cluster_dist" + }, + "HideDatasetActioncluster_hclust": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "cluster_hclust" + }, + "HideDatasetActionclusters": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "clusters" + }, + "HideDatasetActionhclust_plot": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "hclust_plot" + }, + "HideDatasetActionmodel_based_pred_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "model_based_pred_bed" + }, + "HideDatasetActionnearest_neighbour_pred_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "nearest_neighbour_pred_bed" + }, + "HideDatasetActionsim_tab_out": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "sim_tab_out" + }, + "HideDatasetActiontags_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "tags_bed" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", + "tool_state": "{\"tool_mode\": \"{\\\"operation\\\": \\\"pre\\\", \\\"reads_bam\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "2": { + "annotation": "", + "id": 2, + "input_connections": { + "input": { + "id": 1, + "output_name": "tags_bed" + } + }, + "inputs": [], + "name": "Sort", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 740, + "top": 265 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "sort1", + "tool_state": "{\"__page__\": 0, \"style\": \"\\\"alpha\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"ASC\\\"\", \"input\": \"null\", \"column_set\": \"[{\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 0, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"6\\\"}, \\\"other_style\\\": \\\"alpha\\\"}, {\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 1, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}, \\\"other_style\\\": \\\"num\\\"}, {\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 2, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"3\\\"}, \\\"other_style\\\": \\\"num\\\"}]\"}", + "tool_version": "1.0.3", + "type": "tool", + "user_outputs": [] + }, + "3": { + "annotation": "", + "id": 3, + "input_connections": { + "input": { + "id": 2, + "output_name": "out_file1" + } + }, + "inputs": [], + "name": "blockbuster", + "outputs": [ + { + "name": "output", + "type": "tabular" + } + ], + "position": { + "left": 961.5, + "top": 213.5 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1", + "tool_state": "{\"distance\": \"\\\"40\\\"\", \"scale\": \"\\\"0.5\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"print\": \"\\\"2\\\"\", \"tagFilter\": \"\\\"0\\\"\", \"merge\": \"\\\"0\\\"\", \"minBlockHeight\": \"\\\"1.0\\\"\", \"input\": \"null\", \"minClusterHeight\": \"\\\"50.0\\\"\"}", + "tool_version": "0.1", + "type": "tool", + "user_outputs": [] + }, + "4": { + "annotation": "", + "id": 4, + "input_connections": { + "tool_mode|input_bbo": { + "id": 3, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool BlockClust", + "name": "tool_mode" + } + ], + "name": "BlockClust", + "outputs": [ + { + "name": "tags_bed", + "type": "bed" + }, + { + "name": "hclust_plot", + "type": "pdf" + }, + { + "name": "clusters", + "type": "bed" + }, + { + "name": "model_based_pred_bed", + "type": "bed" + }, + { + "name": "nearest_neighbour_pred_bed", + "type": "bed" + }, + { + "name": "sim_tab_out", + "type": "tabular" + }, + { + "name": "cluster_dist", + "type": "pdf" + }, + { + "name": "cluster_hclust", + "type": "pdf" + } + ], + "position": { + "left": 1220.5, + "top": 369.5 + }, + "post_job_actions": { + "HideDatasetActioncluster_dist": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "cluster_dist" + }, + "HideDatasetActioncluster_hclust": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "cluster_hclust" + }, + "HideDatasetActionsim_tab_out": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "sim_tab_out" + }, + "HideDatasetActiontags_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "tags_bed" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", + "tool_state": "{\"tool_mode\": \"{\\\"pred\\\": {\\\"pred_mode\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"enable_pred\\\": \\\"yes\\\", \\\"__current_case__\\\": 0}, \\\"operation\\\": \\\"clust\\\", \\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"input_bbo\\\": null}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "5": { + "annotation": "", + "id": 5, + "input_connections": { + "input": { + "id": 4, + "output_name": "clusters" + } + }, + "inputs": [], + "name": "Extract Genomic DNA", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 1562, + "top": 204 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "Extract genomic DNA 1", + "tool_state": "{\"out_format\": \"\\\"fasta\\\"\", \"__page__\": 0, \"interpret_features\": \"\\\"yes\\\"\", \"__rerun_remap_job_id__\": null, \"seq_source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\"}", + "tool_version": "2.2.3", + "type": "tool", + "user_outputs": [] + }, + "6": { + "annotation": "", + "id": 6, + "input_connections": { + "seqdb": { + "id": 5, + "output_name": "out_file1" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Search covariance model(s)", + "name": "cm_opts" + } + ], + "name": "Search covariance model(s)", + "outputs": [ + { + "name": "outfile", + "type": "tabular" + }, + { + "name": "multiple_alignment_output", + "type": "tabular" + } + ], + "position": { + "left": 1857, + "top": 256.5 + }, + "post_job_actions": { + "HideDatasetActionmultiple_alignment_output": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "multiple_alignment_output" + }, + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.0.2", + "tool_state": "{\"A\": \"\\\"False\\\"\", \"nohmm\": \"\\\"False\\\"\", \"--acyk\": \"\\\"False\\\"\", \"bottomonly\": \"\\\"False\\\"\", \"g\": \"\\\"False\\\"\", \"inclusion_thresholds_opts\": \"{\\\"inclusion_thresholds_selector\\\": \\\"--incE\\\", \\\"__current_case__\\\": 1, \\\"incE\\\": \\\"0.1\\\"}\", \"__page__\": 0, \"max\": \"\\\"False\\\"\", \"notrunc\": \"\\\"False\\\"\", \"mid\": \"\\\"False\\\"\", \"seqdb\": \"null\", \"toponly\": \"\\\"False\\\"\", \"cm_opts\": \"{\\\"database\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"cm_opts_selector\\\": \\\"db\\\"}\", \"reporting_thresholds_opts\": \"{\\\"reporting_thresholds_selector\\\": \\\"-E\\\", \\\"E\\\": \\\"0.1\\\", \\\"__current_case__\\\": 1}\", \"cyk\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null}", + "tool_version": "1.1.0.2", + "type": "tool", + "user_outputs": [] + }, + "7": { + "annotation": "", + "id": 7, + "input_connections": { + "tool_mode|clusters_bed": { + "id": 4, + "output_name": "clusters" + }, + "tool_mode|cmsearch_out": { + "id": 6, + "output_name": "outfile" + }, + "tool_mode|sim_tab_in": { + "id": 4, + "output_name": "sim_tab_out" + } + }, + "inputs": [], + "name": "BlockClust", + "outputs": [ + { + "name": "tags_bed", + "type": "bed" + }, + { + "name": "hclust_plot", + "type": "pdf" + }, + { + "name": "clusters", + "type": "bed" + }, + { + "name": "model_based_pred_bed", + "type": "bed" + }, + { + "name": "nearest_neighbour_pred_bed", + "type": "bed" + }, + { + "name": "sim_tab_out", + "type": "tabular" + }, + { + "name": "cluster_dist", + "type": "pdf" + }, + { + "name": "cluster_hclust", + "type": "pdf" + } + ], + "position": { + "left": 2165.5, + "top": 313.5 + }, + "post_job_actions": { + "HideDatasetActionclusters": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "clusters" + }, + "HideDatasetActionhclust_plot": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "hclust_plot" + }, + "HideDatasetActionmodel_based_pred_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "model_based_pred_bed" + }, + "HideDatasetActionnearest_neighbour_pred_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "nearest_neighbour_pred_bed" + }, + "HideDatasetActionsim_tab_out": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "sim_tab_out" + }, + "HideDatasetActiontags_bed": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "tags_bed" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", + "tool_state": "{\"tool_mode\": \"{\\\"cmsearch_out\\\": null, \\\"operation\\\": \\\"post\\\", \\\"clusters_bed\\\": null, \\\"__current_case__\\\": 2, \\\"sim_tab_in\\\": null}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + } + } +} \ No newline at end of file
--- a/readme.rst Tue May 06 12:51:51 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,278 +0,0 @@ - - -This package is a Galaxy workflow for BlockClust pipeline. - - -====== -Galaxy -====== - -`Galaxy <http://galaxyproject.org/>`_ is an open, web-based platform for data intensive research. -All tools can be combined in workflows without any need of programming skills. -Furthermore the platform can be extended with more tools at any time. -Each tool has its own information about what it does and how the input is supposed to look like. -You can make data available for Galaxy by uploading local files or downloading online content. -Inputfiles, workflowsteps and results are stored in a history where you can view them or reaccess them later. -It is possible to share workflows and histories with other users or make the public available. -Saved workflows can be used with new input files or just to rerun an analyses which ensures repeatability. - - - -Getting Started -=============== - -BlockClust can be installed on all common Unix systems. -However, it is developed on Linux and I don't have access to OS X. You are welcome to help improving this documentation, just contact_ me. - -For any additional information, especially cluster configuration or general Galaxy_ questions, -please have a look at the Galaxy Wiki. - -- http://wiki.galaxyproject.org/ - -- http://wiki.galaxyproject.org/Admin/ - -- http://galaxyproject.org/search/web/ - -.. _contact: https://github.com/bgruening -.. _Galaxy: http://galaxyproject.org/ - -Prerequisites:: - -* Python 2.6 or 2.7 -* standard C compiler, C++ and Fortran compiler -* Autotools -* CMake -* cairo development files (used for PNG depictions) -* python development files -* Java Runtime Environment (JRE, used by OPSIN and NPLS) - -To install all of the prerequisites you can run the following command, depending on your OS: - -- Debian based systems: apt-get install build-essential gfortran cmake mercurial libcairo2-dev python-dev -- Fedora: yum install make automake gcc gcc-c++ gcc-gfortran cmake mercurial libcairo2-devel python-devel -- OS X (MacPorts_): port install gcc cmake automake mercurial cairo-devel - -.. _MacPorts: http://www.macports.org/ - - -=================== -Galaxy installation -=================== - - -0. Create a sand-boxed Python using virtualenv_ (not necessary but recommended):: - - wget https://raw.github.com/pypa/virtualenv/master/virtualenv.py - python ./virtualenv.py --no-site-packages galaxy_env - . ./galaxy_env/bin/activate - -.. _virtualenv: http://www.virtualenv.org/ - - -1. Clone the latest `Galaxy platform`_:: - - hg clone https://bitbucket.org/galaxy/galaxy-central/ - -.. _Galaxy platform: http://wiki.galaxyproject.org/Admin/Get%20Galaxy - -2. Navigate to the galaxy-central folder and update it:: - - cd ~/galaxy-central - hg pull - hg update - - This step is not necessary if you have a fresh checkout. Anyway, it is good to know ;) - -3. Create folders for toolshed and dependencies:: - - mkdir ~/shed_tools - mkdir ~/galaxy-central/tool_deps - -4. Create configuration file:: - - cp ~/galaxy-central/universe_wsgi.ini.sample ~/galaxy-central/universe_wsgi.ini - -5. Open universe_wsgi.ini and change the dependencies directory:: - - LINUX: gedit ~/galaxy-central/universe_wsgi.ini - OS X: open -a TextEdit ~/galaxy-central/universe_wsgi.ini - -6. Search for ``tool_dependency_dir = None`` and change it to ``tool_dependency_dir = ./tool_deps``, remove the ``#`` if needed - -7. Remove the ``#`` in front of ``tool_config_file`` and ``tool_path`` - -8. (Re-)Start the galaxy daemon:: - - sh run.sh --reload - - In deamon mode all logs will be written to main.log in your Galaxy Home directory. You can also use:: - - run.sh - - During the first startup Galaxy will prepare your database. That can take some time. Have a look at the log file if you want to know what happens. - -After launching galaxy is accessible via the browser at ``http://localhost:8080/``. - - - -======================= -Tool Shed configuration -======================= - -- Register a new user account in your Galaxy instance: Top Panel → User → Register -- Become an admin - - open ``universe_wsgi.ini`` in your favourite text editor (gedit universe_wsgi.ini) - - search ``admin_users = None`` and change it to ``admin_users = EMAIL_ADDRESS`` (your Galaxy Username) - - remove the ``#`` if needed -- restart Galaxy - -:: - - sh run.sh --reload - - -======================= -BlockClust installation -======================= - -BlockClust will automatically download and compile all requirements, -like EDeN, samtools and so on. It can take up to 1-2 hours. - - -Installation via Galaxy API (recommended) -========================================= - -- Generate an `API Key`_ -- Run the installation script:: - - python ./scripts/api/install_tool_shed_repositories.py --api YOUR_API_KEY -l http://localhost:8080 --url http://toolshed.g2.bx.psu.edu/ -o rnateam -r e9b2400cc569 --name blockclust_workflow --tool-deps --repository-deps --panel-section-name ChemicalToolBoX - -The -r argument specifies the version of ChemicalToolBoX. You can get the latest revsion number from the -`test tool shed`_ or with the following command:: - - hg identify http://toolshed.g2.bx.psu.edu/repos/bgruening/chemicaltoolbox - -You can watch the installation status under: Top Panel → Admin → Manage installed tool shed repositories - - -.. _API Key: http://wiki.galaxyproject.org/Admin/API#Generate_the_Admin_Account_API_Key -.. _`test tool shed`: http://testtoolshed.g2.bx.psu.edu/ - - -Installation via webbrowser -=========================== - -- go to the `admin page`_ -- select *Search and browse tool sheds* -- Galaxy test tool shed > Sequence Analysis > blockclust_workflow -- install chemicaltoolbox - -.. _admin page: http://localhost:8080/admin - - - -=============== -Troubleshooting -=============== - -If you have any trouble or the installation did not finish properly, do not hesitate to contact me. However, if the -installation fails during the Galaxy installation, you can have a look at the `Galaxy wiki`_. If the ChemicalToolBoX installation fails, -you can try to run:: - - python ./scripts/api/repair_tool_shed_repository.py --api YOUR_API_KEY -l http://localhost:8080 --url http://toolshed.g2.bx.psu.edu/ -o rnateam -r e9b2400cc569 --name blockclust_workflow - -That will rerun all failed installation routines. Alternatively, you can navigate to the ChemicalToolBoX repository in -your browser and repair manually: -Top Panel → Admin → Manage installed tool shed repositories → chemicaltoolbox → Repository Actions → Repair repository - ------- - - -On slow computers and during the compilation of large software libraries, like R, -the Tool Shed can run into a timeout and kills the installation. -That problem is known and should be fixed in the near future. - -If you encouter a timeout or 'hung' during the installation you can increase the ``threadpool_kill_thread_limit`` in your universe_wsgi.ini file. - - ------- - -**Database locking errors** - -Please note that Galaxy per default uses a SQLite database. Sqlite is not intended for production use. -With multiple users or complex components, like that workflow, you will see database locking errors. -We highly recommend to use PostgreSQL for any kind of production system. - - -.. _Galaxy wiki: http://wiki.galaxyproject.org/ - - -Workflows -========= - -An example workflow is located in the `Tool Shed`:: - - http://testtoolshed.g2.bx.psu.edu/view/rnateam/blockclust_workflow - -You can install the workflow with the API:: - - python ./scripts/api/install_tool_shed_repositories.py --api YOUR_API_KEY -l http://localhost:8080 --url http://toolshed.g2.bx.psu.edu/ -o rnateam -r e9b2400cc569 --name blockclust_workflow --tool-deps --repository-deps --panel-section-name BlockClust - -or as described above via webbrowser. You have now successfully installed the workflow, -to import it to all your users you need to go to the admin panel, choose the worklow and import it. -For more information have a look at the Galaxy wiki:: - - http://wiki.galaxyproject.org/ToolShedWorkflowSharing#Finding_workflows_in_tool_shed_repositories - -Please **note** that Galaxy per default uses a SQLite database. Sqlite is not intended for production use. -With multiple users or complex components, like that workflow, you will see database locking errors. -We highly recommend to use PostgreSQL for any kind of production system. - - - -Sample Data -=========== - - - -Citation -======== - -If you use this workflow directly, or a derivative of it, or the associated -wrappers for Galaxy, in work leading to a scientific publication, -please cite: - -P. Videm at al... - - - -Additional References -===================== - - - -Availability -============ - -This workflow is available on the main Galaxy Tool Shed: - - http://testtoolshed.g2.bx.psu.edu/view/rnateam/blockclust_workflow - -Development is being done on github: - -https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust - - -Dependencies -============ - -These dependencies should be resolved automatically via the Galaxy Tool Shed: - -* http://testtoolshed.g2.bx.psu.edu/view/iuc/package_samtools_0_1_19 -* http://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_0_1 -* http://testtoolshed.g2.bx.psu.edu/view/rnateam/package_segemehl_0_1_6 -* http://testtoolshed.g2.bx.psu.edu/view/iuc/msa_datatypes -* http://testtoolshed.g2.bx.psu.edu/view/iuc/package_infernal_1_1rc4 -* http://testtoolshed.g2.bx.psu.edu/view/rnateam/blockbuster -* http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_eden_1_1 -* http://testtoolshed.g2.bx.psu.edu/view/iuc/package_mcl_12_135