New blast+interproscan branch (merging issues with refactor_blast_interproscan_workflow)

constants_phaeo.py

@@ -8,7 +8,8 @@ import constants
 
 WORKFLOWS_PATH = "workflows_phaeoexplorer/"
 
-WF_LOAD_GFF_JB_1_ORG_FILE = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v7.ga"
+# Workflow to load the genome and annotations into chado, create/update organisms in a jbrowse instance
+WF_LOAD_GFF_JB_1_ORG_FILE = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v6.ga"
 WF_LOAD_GFF_JB_1_ORG_INPUT_GENOME = "0"
 WF_LOAD_GFF_JB_1_ORG_INPUT_GFF = "1"
 WF_LOAD_GFF_JB_1_ORG_INPUT_PROTEINS = "2"
@@ -16,37 +17,64 @@ WF_LOAD_GFF_JB_1_ORG_STEP_LOAD_FASTA = "3"
 WF_LOAD_GFF_JB_1_ORG_STEP_JBROWSE = "4"
 WF_LOAD_GFF_JB_1_ORG_STEP_LOAD_GFF = "5"
 WF_LOAD_GFF_JB_1_ORG_STEP_JB_TO_CONTAINER = "6"
-WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_FEATURE = "7"
-WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_ORG = "8"
-WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_GENOME_ANALYSIS = "9"
-WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_OGS_ANALYSIS = "10"
-WF_LOAD_GFF_JB_1_ORG_STEP_POPULATE_VIEWS = "11"
-WF_LOAD_GFF_JB_1_ORG_STEP_INDEX = "12"
+WF_LOAD_GFF_JB_1_ORG_STEP_FEATURE_SYNC = "7"
+WF_LOAD_GFF_JB_1_ORG_STEP_POPULATE_VIEWS = "8"
+WF_LOAD_GFF_JB_1_ORG_STEP_INDEX = "9"
 
-WF_LOAD_GFF_JB_2_ORG_FILE = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v7.ga"
-WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG1 = "4"
-WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG1 = "2"
-WF_LOAD_GFF_JB_2_ORG_INPUT_PROTEINS_ORG1 = "0"
-WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG2 = "1"
-WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG2 = "3"
+WF_LOAD_GFF_JB_2_ORG_FILE = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v6.ga"
+WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG1 = "0"
+WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG1 = "1"
+WF_LOAD_GFF_JB_2_ORG_INPUT_PROTEINS_ORG1 = "2"
+WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG2 = "3"
+WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG2 = "4"
 WF_LOAD_GFF_JB_2_ORG_INPUT_PROTEINS_ORG2 = "5"
-WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_FASTA_ORG1 = "7"
-WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG1 = "8"
-WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG2 = "6"
+WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_FASTA_ORG1 = "6"
+WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG1 = "7"
+WF_LOAD_GFF_JB_2_ORG_STEP_JRBOWSE_ORG2 = "8"
 WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_GFF_ORG1 = "9"
 WF_LOAD_GFF_JB_2_ORG_STEP_JB_TO_CONTAINER = "10"
-WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_FEATURE_ORG1 = "11"
+WF_LOAD_GFF_JB_2_ORG_STEP_FEATURE_SYNC_ORG1 = "11"
 WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_FASTA_ORG2 = "12"
 WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_GFF_ORG2 = "13"
-WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_FEATURE_ORG2 = "14"
-WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_ORG1 = "15"
-WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_ORG2 = "16"
-WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_GENOME_ANALYSIS_ORG1 = "17"
-WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_OGS_ANALYSIS_ORG1 = "18"
-WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_GENOME_ANALYSIS_ORG2 = "19"
-WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_OGS_ANALYSIS_ORG2 = "20"
-WF_LOAD_GFF_JB_2_ORG_STEP_POPULATE_VIEWS = "21"
-WF_LOAD_GFF_JB_2_ORG_STEP_INDEX = "22"
+WF_LOAD_GFF_JB_2_ORG_STEP_FEATURE_SYNC_ORG2 = "14"
+WF_LOAD_GFF_JB_2_ORG_STEP_POPULATE_VIEWS = "15"
+WF_LOAD_GFF_JB_2_ORG_STEP_INDEX = "16"
+
+# Workflow to load blastp, blastx and interproscan into chado and tripal
+WF_BLAST_INTERPRO_1_ORG_FILE = "Galaxy-Workflow-load_blast_interproscan_results_1org_v1.ga"
+WF_BLAST_INTERPRO_1_ORG_INPUT_BLASTP = "0"
+WF_BLAST_INTERPRO_1_ORG_INPUT_BLASTX = "1"
+WF_BLAST_INTERPRO_1_ORG_INPUT_INTERPRO = "2"
+WF_BLAST_INTERPRO_1_ORG_LOAD_BLASTP = "3"
+WF_BLAST_INTERPRO_1_ORG_LOAD_BLASTX = "4"
+WF_BLAST_INTERPRO_1_ORG_LOAD_INTERPRO = "5"
+WF_BLAST_INTERPRO_1_ORG_POPULATE_MAT_VIEWS = "6"
+WF_BLAST_INTERPRO_1_ORG_INDEX_TRIPAL_DATA = "7"
+WF_BLAST_INTERPRO_1_ORG_SYNC_BLASTP_ANALYSIS = "8"
+WF_BLAST_INTERPRO_1_ORG_SYNC_BLASTX_ANALYSIS = "9"
+WF_BLAST_INTERPRO_1_ORG_SYNC_INTERPRO_ANALYSIS = "10"
+
+WF_BLAST_INTERPRO_2_ORG_FILE = "Galaxy-Workflow-load_blast_interproscan_results_2org_v1.ga"
+WF_BLAST_INTERPRO_2_ORG_INPUT_BLASTP_ORG1 = "0"
+WF_BLAST_INTERPRO_2_ORG_INPUT_BLASTP_ORG2 = "1"
+WF_BLAST_INTERPRO_2_ORG_INPUT_BLASTX_ORG1 = "2"
+WF_BLAST_INTERPRO_2_ORG_INPUT_BLASTX_ORG2 = "3"
+WF_BLAST_INTERPRO_2_ORG_INPUT_INTERPRO_ORG1 = "4"
+WF_BLAST_INTERPRO_2_ORG_INPUT_INTERPRO_ORG2 = "5"
+WF_BLAST_INTERPRO_2_ORG_LOAD_BLASTP_ORG1 = "6"
+WF_BLAST_INTERPRO_2_ORG_LOAD_BLASTP_ORG2 = "7"
+WF_BLAST_INTERPRO_2_ORG_LOAD_BLASTX_ORG1 = "8"
+WF_BLAST_INTERPRO_2_ORG_LOAD_BLASTX_ORG2 = "9"
+WF_BLAST_INTERPRO_2_ORG_LOAD_INTERPRO_ORG1 = "10"
+WF_BLAST_INTERPRO_2_ORG_LOAD_INTERPRO_ORG2 = "11"
+WF_BLAST_INTERPRO_2_ORG_POPULATE_MAT_VIEWS = "12"
+WF_BLAST_INTERPRO_2_ORG_INDEX_TRIPAL_DATA = "13"
+WF_BLAST_INTERPRO_2_ORG_SYNC_BLASTP_ANALYSIS_ORG1 = "14"
+WF_BLAST_INTERPRO_2_ORG_SYNC_BLASTX_ANALYSIS_ORG1 = "15"
+WF_BLAST_INTERPRO_2_ORG_SYNC_INTERPRO_ANALYSIS_ORG1 = "16"
+WF_BLAST_INTERPRO_2_ORG_SYNC_BLASTP_ANALYSIS_ORG2 = "17"
+WF_BLAST_INTERPRO_2_ORG_SYNC_BLASTX_ANALYSIS_ORG2 = "18"
+WF_BLAST_INTERPRO_2_ORG_SYNC_INTERPRO_ANALYSIS_ORG2 = "19"
 
 
 ### Galaxy tools