Adding pulsar re2

ansible.cfg

@@ -22,3 +22,4 @@ always = True
 
 [ssh_connection]
 pipelining = true
+ssh_args = -o GSSAPIAuthentication=no -o GSSAPIDelegateCredentials=no

files/pulsar_repo/0.15.6/recursive_rsync.patch

@@ -0,0 +1,53 @@
+--- a/staging/down.py  2024-11-15 14:28:46.166714601 +0000
++++ b/staging/down.py  2026-04-27 14:18:40.826792741 +0000
+@@ -103,7 +103,7 @@
+             if output_generated:
+                 self._attempt_collect_output('output', output_file)
+
+-            for galaxy_path, pulsar in self.pulsar_outputs.output_extras(output_file).items():
++            for galaxy_path, pulsar in self.pulsar_outputs.output_extra_files_dir(output_file).items():
+                 self._attempt_collect_output('output', path=galaxy_path, name=pulsar)
+             # else not output generated, do not attempt download.
+
+--- a/staging/__init__.py  2024-11-15 14:28:46.166714601 +0000
++++ b/staging/__init__.py  2026-04-27 14:12:38.332467975 +0000
+@@ -309,3 +309,19 @@
+         files_directory = "{}_files{}".format(basename(output_file)[0:-len(".dat")], self.path_helper.separator)
+         names = filter(lambda o: o.startswith(files_directory), self.output_directory_contents)
+         return dict(map(lambda name: (local_path(name), name), names))
++
++
++    def output_extra_files_dir(self, output_file):
++        """
++        Returns dict mapping local path to remote name.
++        """
++        print(output_file)
++        output_directory = dirname(output_file)
++
++        def local_path(name):
++            return join(output_directory, self.path_helper.local_name(name))
++
++        name = "{}_files{}".format(basename(output_file)[0:-len(".dat")], self.path_helper.separator)
++        edir = dict()
++        edir[local_path(name)] = name
++        return edir
+
+--- a/transport/ssh.py  2024-11-15 14:28:46.166714601 +0000
++++ b/transport/ssh.py  2026-04-27 14:05:24.769565794 +0000
+@@ -7,6 +7,7 @@
+ def rsync_get_file(uri_from, uri_to, user, host, port, key):
+     cmd = [
+         'rsync',
++        '-src',
+         '-e',
+         'ssh -i {} -p {} {}'.format(key, port, ' '.join(SSH_OPTIONS)),
+         '{}@{}:{}'.format(user, host, uri_from),
+@@ -19,6 +20,8 @@
+     _ensure_dir(uri_to, key, port, user, host)
+     cmd = [
+         'rsync',
++        '-src',
++        '--chmod=F664,D775',
+         '-e',
+         'ssh -i {} -p {} {}'.format(key, port, ' '.join(SSH_OPTIONS)),
+         uri_from,

group_vars/pulsarservers.yml

@@ -1,18 +1,30 @@
 drmaa_version: 1.0.19
 pbs_server: pbs-m1.metacentrum.cz
 install_nfs_conda: false
+conda_auto_init: "{{ install_nfs_conda }}"
+pulsar_network_homedir: "/storage/{{ pulsar.nfs_home }}/home/{{ pulsar.user_name }}"
+
+# Miniconda settings
+miniconda_prefix: "{{ pulsar_network_homedir }}/conda"
+miniconda_exec: "{{ miniconda_prefix }}/bin/mamba"
+miniconda_version: 23.1.0
+miniconda_channels:
+  - 'bioconda'
+  - 'conda-forge'
+csnt_dependency_resolvers: {}
 
 # only galaxyproject.pulsar role vars below
+pulsar_user: "{{ pulsar.user_name }}"
 pulsar_root: /opt/pulsar
 pulsar_package_version: "0.15.6"
-pulsar_network_homedir: "/storage/{{ pulsar.nfs_home }}/home/{{ pulsar.user_name }}"
 pulsar_data_dir: "{{ pulsar_network_homedir }}/{{ pulsar.nfs_prefix }}"
 pulsar_staging_dir: "{{ pulsar_data_dir }}/files/staging"
 pulsar_cleanup_dir: "{{ pulsar_data_dir }}/files/cleanup_jobs"
 pulsar_cleanup_delay: "7d" # DEMON: pulsar-re needs this to have over 30d
 pulsar_persistence_dir: "{{ pulsar_root }}/files/persistent"
 pulsar_dependencies_dir: "{{ pulsar_data_dir }}/deps"
 pulsar_singularity_cachedir: "{{ pulsar_network_homedir }}/.singularity"
+pulsar_package_change_dir: "{{ pulsar_root }}/venv/lib/python3.11/site-packages/pulsar/client"
 pulsar_separate_privileges: true
 pulsar_pip_install: true
 pulsar_pycurl_ssl_library: openssl
@@ -52,28 +64,9 @@ pulsar_yaml_config:
   amqp_publish_retry_interval_step: 10
   amqp_publish_retry_interval_max: 60
 
-  ## DEMON: this setting is specific for RE Galaxy and pulsar-re cause usegalaxy.cz and galaxy-umsa depends only on singu;arity images
-  #
-  ## We also need to create the dependency resolvers configuration so pulsar knows how to find and install dependencies
-  ## for the tools we ask it to run. The simplest method which covers 99% of the use cases is to use conda auto installs
-  ## similar to how Galaxy works.
-  #dependency_resolution:
-  #  resolvers:
-  #    - type: conda
-  #      auto_init: true
-  #      auto_install: true
-  #      ensure_channels: "{{ conda_channels|join(',') }}"
-  #      exec: "{{ conda_exec }}"
-  #      prefix: "{{ conda_prefix }}"
-  container_resolvers:
-    -   type: explicit_singularity
-    -   cache_directory: /cvmfs/singularity.galaxyproject.org/all/
-        type: cached_mulled_singularity
-    -   auto_install: true
-        type: mulled_singularity
-    -   auto_install: false
-        cache_directory: /cvmfs/singularity.galaxyproject.org/all/
-        type: build_mulled_singularity
+  ## DEMON: resolvers is an empty list in most cases (for Galaxy supporting Singularity images over CVMFS instead of Conda)
+  dependency_resolution:
+    resolvers: "{{ csnt_dependency_resolvers }}"
   managers:
     _default_:
       type: queued_drmaa

host_vars/pulsar-re2.grid.cesnet.cz/secret.yml

@@ -0,0 +1,44 @@
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host_vars/pulsar-re2.grid.cesnet.cz/vars.yml

@@ -0,0 +1,30 @@
+# Galaxy/Pulsar user setup
+pulsar:
+  user_name: galaxyelixir
+  uid:  2469
+  gid: 10145
+  group: galaxyelixir
+  nfs_home: "brno11-elixir"
+  nfs_prefix: pulsar-re
+
+miniconda_channels: 
+  - 'bioconda'
+  - 'conda-forge'
+  - 'petrnovak'
+miniconda_prefix: "/storage/{{ pulsar.nfs_home }}/home/{{ pulsar.user_name }}/anaconda3"
+miniconda_exec: "{{ miniconda_prefix }}/bin/mamba"
+
+pulsar_cleanup_delay: "40d" # DEMON: pulsar-re* need this to have over 30d
+csnt_dependency_resolvers:
+  - type: conda
+    auto_init: true
+    auto_install: true
+    ensure_channels: "{{ miniconda_channels|join(',') }}"
+    exec: "{{ miniconda_exec }}"
+    prefix: "{{ miniconda_prefix }}"
+
+# Put your Galaxy server's fully qualified domain name (FQDN) (or the FQDN of the RabbitMQ server) above.
+rabbitmq_hostname: "galaxy-re.grid.cesnet.cz" # DEMON: Important to have proper FQDN of connected Galaxy server (or at least RabbitMQ server)
+rabbitmq_vhost: "pulsar2" # DEMON: must be the same rabbitmq vhost set for communication between Galaxy and Pulsar set on Galaxy side
+rabbitmq_user: "{{ pulsar.user_name }}" # DEMON: must be user running connected Galaxy server
+rabbitmq_port: 5671 # DEMON: must be port where to contact RabbitMQ server

hosts.yml

@@ -4,6 +4,8 @@ nometapuppet:
       ansible_user: debian
     pulsar-qa2.galaxy.cloud.e-infra.cz:
       ansible_user: debian
+    pulsar-re2.grid.cesnet.cz:
+      ansible_user: debian
 
 pulsarservers:
   hosts:
@@ -15,6 +17,8 @@ pulsarservers:
       ansible_user: debian
     pulsar-re.grid.cesnet.cz:
       ansible_user: root
+    pulsar-re2.grid.cesnet.cz:
+      ansible_user: debian
     pulsar-cz.grid.cesnet.cz:
       ansible_user: debian
     pulsar-eu.grid.cesnet.cz:

pulsar.yml

@@ -4,23 +4,6 @@
       become: yes
 
 - hosts: pulsarservers
-  vars:
-    pulsar_user: "{{ pulsar.user_name }}"
-    pbs_drmaa_version: "1.0.19"
-
-    # Miniconda settings
-    miniconda_prefix: "{{ pulsar_network_homedir }}/conda"
-    miniconda_version: 23.1.0
-    miniconda_base_env_packages: ['mamba']
-    miniconda_channels:
-      - 'conda-forge'
-      - 'bioconda'
-      - 'iuc'
-      - 'r'
-      - 'anaconda'
-      - 'petrnovak' # DEMON: this is pecific for RE Galaxy and pulsar-re but could be usefull also for usegalaxy.cz if using RE tools
-      - 'defaults'
-
   pre_tasks:
     - group:
         name: "{{ pulsar.group }}"
@@ -51,12 +34,13 @@
       become_user: "{{ pulsar.user_name }}"
 
   post_tasks:
-    ## DEMON: This task might be necessary to comment out for pulsar-re
-    - name: copy dependency_resolvers_config into pulsar config folder
-      ansible.builtin.copy:
-        src: dependency_resolvers_conf.xml
-        dest: "{{ pulsar_root }}/config/dependency_resolvers_conf.xml"
-      become: yes
+    - name: Apply recursive rsync changes in pulsar package
+      ansible.posix.patch:
+        src: "files/pulsar_repo/{{ pulsar_package_version }}/recursive_rsync.patch"
+        basedir: "{{ pulsar_package_change_dir }}"
+        backup: true
+        strip: 1
+
     - name: Create .drmaa folder in NFS home
       ansible.builtin.file:
         path: "{{ pulsar_network_homedir }}/.drmaa"