From ffed26f2672e7b0c75aa8901fb7c56c6aa8b5125 Mon Sep 17 00:00:00 2001
From: Shettland <pyblus@gmail.com>
Date: Thu, 19 Oct 2023 16:36:28 +0200
Subject: [PATCH] Included srun_settings fields in scratch_copy

---
 bu_isciii/conf/configuration.json | 89 ++++++++++++++++---------------
 1 file changed, 47 insertions(+), 42 deletions(-)

diff --git a/bu_isciii/conf/configuration.json b/bu_isciii/conf/configuration.json
index f6dd78f9..6acd6990 100755
--- a/bu_isciii/conf/configuration.json
+++ b/bu_isciii/conf/configuration.json
@@ -1,60 +1,65 @@
 {
-    "global":{
-      "data_path": "/data/bi",
-      "archived_path": "/archived/bi",
-      "yaml_conf_path": "~/buisciii_config.yml"
+    "global": {
+        "data_path": "/data/bi",
+        "archived_path": "/archived/bi",
+        "yaml_conf_path": "~/buisciii_config.yml"
     },
     "sftp_copy": {
-      "protocol": "rsync",
-      "options": ["-rlpv", "--update", "-L", "--inplace"],
-      "exclusions": [
-        "'*_NC'",
-        "'lablog'",
-        "'work'",
-        "'00-reads'",
-        "'*.sh'",
-        "'.nextflow*'",
-        "'*_DEL'",
-        "'*.R'",
-        "'*.py'"
-      ]
+        "protocol": "rsync",
+        "options": ["-rlpv", "--update", "-L", "--inplace"],
+        "exclusions": [
+            "'*_NC'",
+            "'lablog'",
+            "'work'",
+            "'00-reads'",
+            "'*.sh'",
+            "'.nextflow*'",
+            "'*_DEL'",
+            "'*.R'",
+            "'*.py'"
+        ]
     },
     "xtutatis_api_settings": {
-      "api_url": "/drylab/api/",
-      "server": "http://iskylimsapi.isciiides.es"
+        "api_url": "/drylab/api/",
+        "server": "http://iskylims.isciiides.es"
     },
     "api_settings": {
         "server": "http://iskylims.isciiides.es",
         "api_url": "/drylab/api/"
     },
     "bioinfo_doc": {
-      "bioinfodoc_path": "/data/bioinfo_doc/",
-      "services_path": "services",
-      "service_folder": ["service_info", "result"],
-      "service_info_template_path_file" : "templates/jinja_template_service_info.j2",
-      "delivery_template_path_file" : "templates/jinja_template_delivery.j2",
-      "html_template_path_file" : "templates/html_service_template.html",
-      "path_to_css" : "assets/css",
-      "wkhtmltopdf_path" : "/data/bi/pipelines/miniconda3/envs/buisciii-tools/bin/wkhtmltopdf",
-      "email_host":"mx2.isciii.es",
-      "email_port" : "587",
-      "email_host_user" : "bioinformatica@isciii.es",
-      "email_use_tls" : "True"
+        "bioinfodoc_path": "/data/bioinfo_doc/",
+        "services_path": "services",
+        "service_folder": ["service_info", "result"],
+        "service_info_template_path_file": "templates/jinja_template_service_info.j2",
+        "delivery_template_path_file": "templates/jinja_template_delivery.j2",
+        "html_template_path_file": "templates/html_service_template.html",
+        "path_to_css": "assets/css",
+        "wkhtmltopdf_path": "/data/bi/pipelines/miniconda3/envs/buisciii-tools/bin/wkhtmltopdf",
+        "email_host": "mx2.isciii.es",
+        "email_port": "587",
+        "email_host_user": "bioinformatica@isciii.es",
+        "email_use_tls": "True"
     },
     "new_service": {
-      "fastq_repo": "/srv/fastq_repo"
+        "fastq_repo": "/srv/fastq_repo"
     },
     "scratch_copy": {
-      "protocol": "rsync",
-      "options": ["-rlpv"],
-      "exclusions": [
-        "'*_NC'",
-        "'service_info.txt'",
-        "'work'"
-      ]
+        "protocol": "rsync",
+        "options": ["-rlpv"],
+        "exclusions": [
+            "'*_NC'",
+            "'service_info.txt'",
+            "'work'"
+        ],
+        "srun_settings": {
+            "--partition": "middle_idx",
+            "--time": "24:00:00",
+            "--chdir": "/scratch/bi/"
+        }
     },
     "archive": {
-      "protocol": "rsync",
-      "options": ["-rv"]
+        "protocol": "rsync",
+        "options": ["-rv"]
     }
-}
\ No newline at end of file
+}