From 6ee6fafbec245727ea4e8704ef78688e6915a472 Mon Sep 17 00:00:00 2001
From: lgueguen <lgueguen@sb-roscoff.fr>
Date: Mon, 3 May 2021 21:00:41 +0200
Subject: [PATCH] Rename WF dir. Add jinja2 template for input yaml
---
templates/organisms.yml.j2 | 38 +++++++++++++++++++
.../Blast_Diamond.ga | 0
.../Chado_load_Tripal_synchronize.ga | 0
.../Chado_load_Tripal_synchronize.ga.bak | 0
...load_tripal_synchronize_jbrowse_1org_v1.ga | 0
...load_tripal_synchronize_jbrowse_1org_v2.ga | 0
...load_tripal_synchronize_jbrowse_2org_v1.ga | 0
...load_tripal_synchronize_jbrowse_2org_v2.ga | 0
.../Interproscan.ga | 0
.../Jbrowse.ga | 0
10 files changed, 38 insertions(+)
create mode 100644 templates/organisms.yml.j2
rename {workflows => workflows_phaeoexplorer}/Blast_Diamond.ga (100%)
rename {workflows => workflows_phaeoexplorer}/Chado_load_Tripal_synchronize.ga (100%)
rename {workflows => workflows_phaeoexplorer}/Chado_load_Tripal_synchronize.ga.bak (100%)
rename {workflows => workflows_phaeoexplorer}/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v1.ga (100%)
rename {workflows => workflows_phaeoexplorer}/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v2.ga (100%)
rename {workflows => workflows_phaeoexplorer}/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v1.ga (100%)
rename {workflows => workflows_phaeoexplorer}/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v2.ga (100%)
rename {workflows => workflows_phaeoexplorer}/Interproscan.ga (100%)
rename {workflows => workflows_phaeoexplorer}/Jbrowse.ga (100%)
diff --git a/templates/organisms.yml.j2 b/templates/organisms.yml.j2
new file mode 100644
index 0000000..98ce0e4
--- /dev/null
+++ b/templates/organisms.yml.j2
@@ -0,0 +1,38 @@
+{{ name }}: # Dummy value to designate the species (isn't used by the script)
+ description:
+ # Species description, leave blank if unknown or you don't want it to be used
+ # These parameters are used to set up the various urls and adresses in different containers
+ # The script requires at least the genus to be specified
+ genus: {{ genus }} # Mandatory!
+ species: {{ species }} # Mandatory!
+ sex: {{ sex }}
+ strain: {{ strain }}
+ common_name: {{ common_name }}
+ origin: {{ origin }}
+ # the sex and strain, the script will look for files containing the genus, species, sex and strain of the species)
+ # If no file corresponding to the description is found, this path will be considered empty and the script will
+ # proceed to the next step (create the directory tree for the GGA docker stack)
+ data:
+ # Sequence of paths to the different datasets to copy and import into the galaxy container (as a shared library)
+ # Must be absolute paths to the dataset
+ genome_path: {{ genome_path }} # Mandatory!
+ transcripts_path: {{ transcripts_path }} # Mandatory!
+ proteins_path: {{ proteins_path }} # Mandatory!
+ gff_path: {{ gff_path }} # Mandatory!
+ interpro_path: {{ interpro_path }}
+ orthofinder_path: {{ orthofinder_path }}
+ blastp_path: {{ blastp_path }}
+ blastx_path: {{ blastx_path }}
+ # If the user has several datasets of the same 'nature' (gff, genomes, ...) to upload to galaxy, the next scalar is used by the script to differentiate
+ # between these different versions and name directories according to it and not overwrite the existing data
+ # If left empty, the genome will be considered version "1.0"
+ genome_version: {{ genome_version }}
+ # Same as genome version, but for the OGS analysis
+ ogs_version: {{ ogs_version }}
+ performed_by: {{ performed_by }}
+ services:
+ # Describe what optional services to deploy for the stack
+ # By default, only tripal, tripaldb and galaxy services will be deployed
+ blast: {{ blast }}
+ wiki: {{ wiki }}
+ apollo: {{ apollo }}
diff --git a/workflows/Blast_Diamond.ga b/workflows_phaeoexplorer/Blast_Diamond.ga
similarity index 100%
rename from workflows/Blast_Diamond.ga
rename to workflows_phaeoexplorer/Blast_Diamond.ga
diff --git a/workflows/Chado_load_Tripal_synchronize.ga b/workflows_phaeoexplorer/Chado_load_Tripal_synchronize.ga
similarity index 100%
rename from workflows/Chado_load_Tripal_synchronize.ga
rename to workflows_phaeoexplorer/Chado_load_Tripal_synchronize.ga
diff --git a/workflows/Chado_load_Tripal_synchronize.ga.bak b/workflows_phaeoexplorer/Chado_load_Tripal_synchronize.ga.bak
similarity index 100%
rename from workflows/Chado_load_Tripal_synchronize.ga.bak
rename to workflows_phaeoexplorer/Chado_load_Tripal_synchronize.ga.bak
diff --git a/workflows/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v1.ga b/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v1.ga
similarity index 100%
rename from workflows/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v1.ga
rename to workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v1.ga
diff --git a/workflows/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v2.ga b/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v2.ga
similarity index 100%
rename from workflows/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v2.ga
rename to workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v2.ga
diff --git a/workflows/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v1.ga b/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v1.ga
similarity index 100%
rename from workflows/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v1.ga
rename to workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v1.ga
diff --git a/workflows/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v2.ga b/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v2.ga
similarity index 100%
rename from workflows/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v2.ga
rename to workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v2.ga
diff --git a/workflows/Interproscan.ga b/workflows_phaeoexplorer/Interproscan.ga
similarity index 100%
rename from workflows/Interproscan.ga
rename to workflows_phaeoexplorer/Interproscan.ga
diff --git a/workflows/Jbrowse.ga b/workflows_phaeoexplorer/Jbrowse.ga
similarity index 100%
rename from workflows/Jbrowse.ga
rename to workflows_phaeoexplorer/Jbrowse.ga
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