do not install singularity, pulsar does not need it

files/pulsar_repo/0.15.14/recursive_rsync.patch

@@ -0,0 +1,52 @@
+--- a/staging/__init__.py    2026-05-05 00:09:44.381594787 +0200
++++ b/staging/__init__.py    2026-05-05 00:12:14.175296482 +0200
+@@ -358,3 +358,18 @@
+         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/staging/down.py     2026-05-05 00:12:46.458249361 +0200
++++ b/staging/down.py     2026-05-05 00:15:54.391439324 +0200
+@@ -118,7 +118,7 @@
+             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/transport/ssh.py    2026-05-04 16:02:17.470665842 +0200
++++ b/transport/ssh.py    2026-05-05 00:19:04.621400669 +0200
+@@ -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

@@ -12,6 +12,7 @@ miniconda_channels:
   - 'bioconda'
   - 'conda-forge'
 csnt_dependency_resolvers: {}
+csnt_use_recursive_rsync: yes
 
 # only galaxyproject.pulsar role vars below
 pulsar_user: "{{ pulsar.user_name }}"

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

@@ -1,7 +1,44 @@
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host_vars/pulsar-re.grid.cesnet.cz/vars.yaml

@@ -1,23 +1,30 @@
 # Galaxy/Pulsar user setup
 pulsar:
-## Specific settings for pulsar-re (needs to be moved into host_vars foder
   user_name: galaxyelixir
   uid:  2469
   gid: 10145
+  group: galaxyelixir
   nfs_home: "brno11-elixir"
   nfs_prefix: pulsar-re
-## Specific settings for pulsar-cz (needs to be moved into host_vars foder
-#  user_name: galaxyeu
-#  uid: 5430
-#  gid:
-#  nfs_home: "praha5-elixir"
-#  nfs_prefix: pulsar-cz
-## Specific settings for pulsar-umsa (needs to be moved into host_vars foder
-#  user_name: galaxyumsa
-#  uid: 10456
-#  gid: 
-#  nfs_home: "brno11-elixir"
-#  nfs_prefix: pulsar-umsa
+
+install_nfs_conda: true
+miniconda_channels: 
+  - 'bioconda'
+  - 'conda-forge'
+  - 'petrnovak'
+miniconda_prefix: "/storage/{{ pulsar.nfs_home }}/home/{{ pulsar.user_name }}/anaconda3"
+miniconda_exec: "{{ miniconda_prefix }}/bin/mamba"
+
+csnt_use_recursive_rsync: yes
+pulsar_package_version: 0.15.14
+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)

pulsar.yml

@@ -40,11 +40,13 @@
         basedir: "{{ pulsar_package_change_dir }}"
         backup: true
         strip: 1
+      when: csnt_use_recursive_rsync
     - name: Restart pulsar service after change
       ansible.builtin.systemd:
         state: restarted
         name: "{{ pulsar_systemd_service_name }}"
       become: yes
+      when: csnt_use_recursive_rsync
 
     - name: Create .drmaa folder in NFS home
       ansible.builtin.file:

roles/metacentrum.krbnfs/tasks/main.yml

@@ -25,7 +25,6 @@
     name:
       - openpbs-client
       - libopenpbs-dev
-      - singularity-ce
       - nfs-common
 
 - name: PBS config

roles/metacentrum.pulsar/tasks/main.yml

@@ -9,7 +9,6 @@
       - libssl-dev
       - virtualenv
       - libgnutls28-dev
-      - squashfs-tools # DEMON: needed by singularity roles
       - rsync
       - tmpreaper
     state: present