From 26e1fcf16475301783090cf0e9bf95def59652b1 Mon Sep 17 00:00:00 2001
From: martindemko <325073@mail.muni.cz>
Date: Wed, 17 Jun 2026 23:41:38 +0200
Subject: [PATCH 1/3] Fixes cases when tool ID includes spaces

---
 templates/galaxy/config/tpv_rules_meta.yml.j2 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/galaxy/config/tpv_rules_meta.yml.j2 b/templates/galaxy/config/tpv_rules_meta.yml.j2
index 02e0ebc..10655ab 100644
--- a/templates/galaxy/config/tpv_rules_meta.yml.j2
+++ b/templates/galaxy/config/tpv_rules_meta.yml.j2
@@ -344,7 +344,7 @@ destinations:
       ssh_key: |
         {{ pulsar_ssh_key | indent(width=8,first=False) }}
       outputs_to_working_directory: false
-      submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb -l walltime={int(walltime)}:00:00 -q {queue} -N {{ pulsar.nfs_prefix }}_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'}"
+      submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb -l walltime={int(walltime)}:00:00 -q {queue} -N {{ pulsar.nfs_prefix }}_j{job.id}__{(tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]).replace(' ','_')}__{user.username if user and hasattr(user, 'username') else 'anonymous'}"
     env:
       TMPDIR: $SCRATCHDIR
       TMP: $SCRATCHDIR

From 8cb2e0b6c0c3a5bf9b986488c4b5ceacd4778bf5 Mon Sep 17 00:00:00 2001
From: martindemko <325073@mail.muni.cz>
Date: Thu, 18 Jun 2026 12:55:51 +0200
Subject: [PATCH 2/3] fixes more submit_native_specification in TPV config

---
 templates/galaxy/config/tpv_rules_meta.yml.j2 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/templates/galaxy/config/tpv_rules_meta.yml.j2 b/templates/galaxy/config/tpv_rules_meta.yml.j2
index 10655ab..b4833f4 100644
--- a/templates/galaxy/config/tpv_rules_meta.yml.j2
+++ b/templates/galaxy/config/tpv_rules_meta.yml.j2
@@ -401,7 +401,7 @@ destinations:
     inherits: tpv_pulsar
     runner: pulsar_tpv_runner
     params:
-      submit_native_specification: "-l place=exclhost -l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb -l walltime={int(walltime)}:00:00 -q {queue} -N pulsar-re_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'}"
+      submit_native_specification: "-l place=exclhost -l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb -l walltime={int(walltime)}:00:00 -q {queue} -N pulsar-re_j{job.id}__{(tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]).replace(' ','_')}__{user.username if user and hasattr(user, 'username') else 'anonymous'}"
     scheduling:
       require:
         - exclusive
@@ -426,7 +426,7 @@ destinations:
     runner: pulsar_tpv_runner
     params:
       singularity_enabled: false
-      submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb:ngpus={int(gpus)}:gpu_mem={int(gpu_mem)}gb -l walltime={int(walltime)}:00:00 -q galaxy_gpu@pbs-m1.metacentrum.cz -N pulsar_cz_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'}"
+      submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb:ngpus={int(gpus)}:gpu_mem={int(gpu_mem)}gb -l walltime={int(walltime)}:00:00 -q galaxy_gpu@pbs-m1.metacentrum.cz -N pulsar_cz_j{job.id}__{(tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]).replace(' ','_')}__{user.username if user and hasattr(user, 'username') else 'anonymous'}"
     scheduling:
       require:
         - rosettafold
@@ -452,7 +452,7 @@ destinations:
     params:
       singularity_run_extra_arguments: '--nv'
       singularity_volumes: '$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,$SCRATCHDIR,$ALPHAFOLD_DB:/data/2.3:ro'
-      submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb:ngpus={int(gpus)}:gpu_mem={int(gpu_mem)}gb -l walltime={int(walltime)}:00:00 -q {{ pulsar.pbs_gpu_queue }} -N {{ pulsar.nfs_prefix }}_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'}"
+      submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb:ngpus={int(gpus)}:gpu_mem={int(gpu_mem)}gb -l walltime={int(walltime)}:00:00 -q {{ pulsar.pbs_gpu_queue }} -N {{ pulsar.nfs_prefix }}_j{job.id}__{(tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]).replace(' ','_')}__{user.username if user and hasattr(user, 'username') else 'anonymous'}"
     scheduling:
       require:
         - alphafold

From 961458024ad01d43f580bfe3d01037b4a344e8d2 Mon Sep 17 00:00:00 2001
From: martindemko <325073@mail.muni.cz>
Date: Thu, 18 Jun 2026 15:27:54 +0200
Subject: [PATCH 3/3] rearranges submit_native_specifications in TPV config

---
 templates/galaxy/config/tpv_rules_meta.yml.j2 | 25 ++++++++++++++++---
 1 file changed, 21 insertions(+), 4 deletions(-)

diff --git a/templates/galaxy/config/tpv_rules_meta.yml.j2 b/templates/galaxy/config/tpv_rules_meta.yml.j2
index b4833f4..a968594 100644
--- a/templates/galaxy/config/tpv_rules_meta.yml.j2
+++ b/templates/galaxy/config/tpv_rules_meta.yml.j2
@@ -344,7 +344,11 @@ destinations:
       ssh_key: |
         {{ pulsar_ssh_key | indent(width=8,first=False) }}
       outputs_to_working_directory: false
-      submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb -l walltime={int(walltime)}:00:00 -q {queue} -N {{ pulsar.nfs_prefix }}_j{job.id}__{(tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]).replace(' ','_')}__{user.username if user and hasattr(user, 'username') else 'anonymous'}"
+      submit_native_specification: >-
+        -l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb
+        -l walltime={int(walltime)}:00:00
+        -q {queue}
+        -N {{ pulsar.nfs_prefix }}_j{job.id}__{(tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]).replace(' ','_')}__{user.username if user and hasattr(user, 'username') else 'anonymous'}
     env:
       TMPDIR: $SCRATCHDIR
       TMP: $SCRATCHDIR
@@ -401,7 +405,12 @@ destinations:
     inherits: tpv_pulsar
     runner: pulsar_tpv_runner
     params:
-      submit_native_specification: "-l place=exclhost -l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb -l walltime={int(walltime)}:00:00 -q {queue} -N pulsar-re_j{job.id}__{(tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]).replace(' ','_')}__{user.username if user and hasattr(user, 'username') else 'anonymous'}"
+      submit_native_specification: >-
+        -l place=exclhost
+        -l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb
+        -l walltime={int(walltime)}:00:00
+        -q {queue}
+        -N {{ pulsar.nfs_prefix }}_j{job.id}__{(tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]).replace(' ','_')}__{user.username if user and hasattr(user, 'username') else 'anonymous'}
     scheduling:
       require:
         - exclusive
@@ -426,7 +435,11 @@ destinations:
     runner: pulsar_tpv_runner
     params:
       singularity_enabled: false
-      submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb:ngpus={int(gpus)}:gpu_mem={int(gpu_mem)}gb -l walltime={int(walltime)}:00:00 -q galaxy_gpu@pbs-m1.metacentrum.cz -N pulsar_cz_j{job.id}__{(tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]).replace(' ','_')}__{user.username if user and hasattr(user, 'username') else 'anonymous'}"
+      submit_native_specification: >-
+        -l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb:ngpus={int(gpus)}:gpu_mem={int(gpu_mem)}gb
+        -l walltime={int(walltime)}:00:00
+        -q {{ pulsar.pbs_gpu_queue }}
+        -N {{ pulsar.nfs_prefix }}_j{job.id}__{(tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]).replace(' ','_')}__{user.username if user and hasattr(user, 'username') else 'anonymous'}
     scheduling:
       require:
         - rosettafold
@@ -452,7 +465,11 @@ destinations:
     params:
       singularity_run_extra_arguments: '--nv'
       singularity_volumes: '$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,$SCRATCHDIR,$ALPHAFOLD_DB:/data/2.3:ro'
-      submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb:ngpus={int(gpus)}:gpu_mem={int(gpu_mem)}gb -l walltime={int(walltime)}:00:00 -q {{ pulsar.pbs_gpu_queue }} -N {{ pulsar.nfs_prefix }}_j{job.id}__{(tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]).replace(' ','_')}__{user.username if user and hasattr(user, 'username') else 'anonymous'}"
+      submit_native_specification: >-
+        -l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb:ngpus={int(gpus)}:gpu_mem={int(gpu_mem)}gb
+        -l walltime={int(walltime)}:00:00
+        -q {{ pulsar.pbs_gpu_queue }}
+        -N {{ pulsar.nfs_prefix }}_j{job.id}__{(tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]).replace(' ','_')}__{user.username if user and hasattr(user, 'username') else 'anonymous'}
     scheduling:
       require:
         - alphafold