From 88e9823e0f7a048149399a2b021d7bfbfe956241 Mon Sep 17 00:00:00 2001
From: Martin Demko <325073@mail.muni.cz>
Date: Mon, 27 May 2024 01:59:02 +0200
Subject: [PATCH 1/2] Update destinations.yml.j2

---
 files/galaxy/tpv/destinations.yml.j2 | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/files/galaxy/tpv/destinations.yml.j2 b/files/galaxy/tpv/destinations.yml.j2
index fa12c2554..a19ee5e6b 100644
--- a/files/galaxy/tpv/destinations.yml.j2
+++ b/files/galaxy/tpv/destinations.yml.j2
@@ -244,12 +244,13 @@ destinations:
     inherits: pulsar_default
     runner: pulsar_eu_cz01
     max_accepted_cores: 32
-    max_accepted_mem: 128
+    max_accepted_mem: 256
     min_accepted_gpus: 0
     max_accepted_gpus: 0
     env:
       LC_ALL: C
-      SINGULARITY_CACHEDIR: "/storage/praha5-elixir/home/galaxyeu/singularity"
+      #SINGULARITY_CACHEDIR: "/storage/praha5-elixir/home/galaxyeu/singularity"
+      SINGULARITY_CACHEDIR: "/cvmfs/singularity.galaxyproject.org/all/"
       SINGULARITY_TMPDIR: "$SCRATCHDIR"
       TMPDIR: "$SCRATCHDIR"
       TMP: "$SCRATCHDIR"
@@ -260,6 +261,7 @@ destinations:
       persistence_directory: "/opt/pulsar/files/persistent"
       singularity_volumes: "$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/cvmfs/data.galaxyproject.org:ro,$SCRATCHDIR,/storage/praha5-elixir/home/galaxyeu:/home/galaxyeu,/cvmfs/data.galaxyproject.org/managed/:/data/db/data_managers/:ro"
       singularity_run_extra_arguments: --env "_JAVA_OPTIONS=\"-Djava.io.tmpdir=$SCRATCHDIR\""
+      submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local=100gb -l walltime=24:00:00 -q galaxyeu@pbs-m1.metacentrum.cz -N pulsar_eu_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}"
     scheduling:
       require:
         - cz-pulsar
@@ -273,7 +275,8 @@ destinations:
     max_accepted_gpus: 1
     env:
       LC_ALL: C
-      SINGULARITY_CACHEDIR: "/storage/praha5-elixir/home/galaxyeu/singularity"
+      #SINGULARITY_CACHEDIR: "/storage/praha5-elixir/home/galaxyeu/singularity"
+      SINGULARITY_CACHEDIR: "/cvmfs/singularity.galaxyproject.org/all/"
       SINGULARITY_TMPDIR: "$SCRATCHDIR"
       TMPDIR: "$SCRATCHDIR"
       TMP: "$SCRATCHDIR"
@@ -286,6 +289,7 @@ destinations:
       persistence_directory: "/opt/pulsar/files/persistent"
       singularity_volumes: "$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/cvmfs/data.galaxyproject.org:ro,$SCRATCHDIR,/storage/praha5-elixir/home/galaxyeu:/home/galaxyeu,$ALPHAFOLD_DB:/data:ro"
       singularity_run_extra_arguments: "--nv --env ALPHAFOLD_USE_GPU=True"
+      submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local=100gb:ngpus=1:gpu_mem=8gb -l walltime=24:00:00 -q gpu@pbs-m1.metacentrum.cz -N pulsar_eu_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}"
     scheduling:
       require:
         - cz-pulsar

From 1f4075be7d5a6af6b0a6f34d7217fad25d263441 Mon Sep 17 00:00:00 2001
From: Martin Demko <325073@mail.muni.cz>
Date: Mon, 27 May 2024 02:05:15 +0200
Subject: [PATCH 2/2] Update job_conf.yml

no need to use two runners anymore
---
 templates/galaxy/config/job_conf.yml | 12 ------------
 1 file changed, 12 deletions(-)

diff --git a/templates/galaxy/config/job_conf.yml b/templates/galaxy/config/job_conf.yml
index 95d75ffd8..7261a3176 100644
--- a/templates/galaxy/config/job_conf.yml
+++ b/templates/galaxy/config/job_conf.yml
@@ -178,18 +178,6 @@ galaxy_jobconf:
       params:
         amqp_url: "pyamqp://galaxy_cz01:{{ rabbitmq_password_galaxy_cz01 }}@mq.galaxyproject.eu:5671//pulsar/galaxy_cz01?ssl=1"
         galaxy_url: "https://usegalaxy.eu"
-        manager: production
-        amqp_acknowledge: "true"
-        amqp_ack_republish_time: 300
-        amqp_consumer_timeout: 2.0
-        amqp_publish_retry: "true"
-        amqp_publish_retry_max_retries: 60
-    - id: pulsar_eu_cz02
-      load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
-      params:
-        amqp_url: "pyamqp://galaxy_cz01:{{ rabbitmq_password_galaxy_cz01 }}@mq.galaxyproject.eu:5671//pulsar/galaxy_cz01?ssl=1"
-        galaxy_url: "https://usegalaxy.eu"
-        manager: gpu
         amqp_acknowledge: "true"
         amqp_ack_republish_time: 300
         amqp_consumer_timeout: 2.0