From 2c90e0aa3db479a311e6812ba20ed9ba4082b7eb Mon Sep 17 00:00:00 2001
From: martindemko <325073@mail.muni.cz>
Date: Thu, 23 Apr 2026 13:30:59 +0200
Subject: [PATCH 01/10] adds neccesarry files

---
 host_vars/pulsar-re2.grid.cesnet.cz/secret.yml | 14 ++++++++++++++
 host_vars/pulsar-re2.grid.cesnet.cz/vars.yml   | 15 +++++++++++++++
 hosts.yml                                      |  2 ++
 3 files changed, 31 insertions(+)
 create mode 100644 host_vars/pulsar-re2.grid.cesnet.cz/secret.yml
 create mode 100644 host_vars/pulsar-re2.grid.cesnet.cz/vars.yml

diff --git a/host_vars/pulsar-re2.grid.cesnet.cz/secret.yml b/host_vars/pulsar-re2.grid.cesnet.cz/secret.yml
new file mode 100644
index 0000000..e1a492d
--- /dev/null
+++ b/host_vars/pulsar-re2.grid.cesnet.cz/secret.yml
@@ -0,0 +1,14 @@
+$ANSIBLE_VAULT;1.1;AES256
+63616434326663326431623131663336323264386666313463643634636630396462626234393730
+3038333563313737343234313633623530316538346634380a323637613733393836653131326564
+61363566383438323334333165363437333133313765353631613232613263653361613931613265
+6638346566313664630a333563346639303061313738373437383161393238343964373564336366
+38343161616433646330643431353137626263636266653331303934616265353233663733633834
+36653063393264346136623436643735636163663638316334386337313661376536316537373966
+31396339323535353066363337626238396464666139303537393034663035373065336335653263
+36663030663461353531373731316133306263373961356335353666393433613166303135666261
+37343965316563303166346366313834393431386336376532363730343432363333383765386337
+32393737336132396363313432323666333737616266656263646164616363633233363466343265
+63336261356362316531353536626437346266353337313735623933373462323937373736653736
+62333331313434353937333437373534643633323437326536363736353234363830393130383062
+6366
diff --git a/host_vars/pulsar-re2.grid.cesnet.cz/vars.yml b/host_vars/pulsar-re2.grid.cesnet.cz/vars.yml
new file mode 100644
index 0000000..93ffa82
--- /dev/null
+++ b/host_vars/pulsar-re2.grid.cesnet.cz/vars.yml
@@ -0,0 +1,15 @@
+# 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
+
+# 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
diff --git a/hosts.yml b/hosts.yml
index ca51026..b5f9e11 100644
--- a/hosts.yml
+++ b/hosts.yml
@@ -15,6 +15,8 @@ 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:

From 5b4ea2b5faef4ec2c3fec5dffe51a5dcf777a0e1 Mon Sep 17 00:00:00 2001
From: martindemko <325073@mail.muni.cz>
Date: Mon, 27 Apr 2026 09:25:05 +0200
Subject: [PATCH 02/10] changes to merge RE stuf to main

---
 group_vars/pulsarservers.yml                  | 51 +++++++-----
 .../pulsar-re2.grid.cesnet.cz/secret.yml      | 56 +++++++++----
 host_vars/pulsar-re2.grid.cesnet.cz/vars.yml  | 21 ++++-
 hosts.yml                                     |  2 +
 pulsar.yml                                    | 41 +++++-----
 roles/galaxyproject.miniconda/README.md       | 69 ----------------
 .../galaxyproject.miniconda/defaults/main.yml | 58 --------------
 .../meta/.galaxy_install_info                 |  2 -
 roles/galaxyproject.miniconda/meta/main.yml   | 27 -------
 .../galaxyproject.miniconda/tasks/install.yml | 26 -------
 roles/galaxyproject.miniconda/tasks/main.yml  | 78 -------------------
 roles/galaxyproject.miniconda/tests/inventory |  2 -
 roles/galaxyproject.miniconda/tests/test.yml  |  7 --
 roles/metacentrum.krbnfs/tasks/main.yml       |  2 +-
 14 files changed, 119 insertions(+), 323 deletions(-)
 delete mode 100644 roles/galaxyproject.miniconda/README.md
 delete mode 100644 roles/galaxyproject.miniconda/defaults/main.yml
 delete mode 100644 roles/galaxyproject.miniconda/meta/.galaxy_install_info
 delete mode 100644 roles/galaxyproject.miniconda/meta/main.yml
 delete mode 100644 roles/galaxyproject.miniconda/tasks/install.yml
 delete mode 100644 roles/galaxyproject.miniconda/tasks/main.yml
 delete mode 100644 roles/galaxyproject.miniconda/tests/inventory
 delete mode 100644 roles/galaxyproject.miniconda/tests/test.yml

diff --git a/group_vars/pulsarservers.yml b/group_vars/pulsarservers.yml
index 33b1b7f..c4253e3 100644
--- a/group_vars/pulsarservers.yml
+++ b/group_vars/pulsarservers.yml
@@ -1,11 +1,25 @@
 drmaa_version: 1.0.19
 pbs_server: pbs-m1.metacentrum.cz
 install_nfs_conda: false
+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'
+  - 'iuc'
+  - 'r'
+  - 'anaconda'
+  - 'defaults'
+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"
@@ -57,23 +71,24 @@ pulsar_yaml_config:
   ## 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
+  dependency_resolution:
+    resolvers: "{{ csnt_dependency_resolvers }}"
+#    resolvers:
+#      - type: conda
+#        auto_init: true
+#        auto_install: true
+#        ensure_channels: "{{ miniconda_channels|join(',') }}"
+#        exec: "{{ miniconda_exec }}"
+#        prefix: "{{ miniconda_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
   managers:
     _default_:
       type: queued_drmaa
diff --git a/host_vars/pulsar-re2.grid.cesnet.cz/secret.yml b/host_vars/pulsar-re2.grid.cesnet.cz/secret.yml
index e1a492d..e3cb3aa 100644
--- a/host_vars/pulsar-re2.grid.cesnet.cz/secret.yml
+++ b/host_vars/pulsar-re2.grid.cesnet.cz/secret.yml
@@ -1,14 +1,44 @@
 $ANSIBLE_VAULT;1.1;AES256
-63616434326663326431623131663336323264386666313463643634636630396462626234393730
-3038333563313737343234313633623530316538346634380a323637613733393836653131326564
-61363566383438323334333165363437333133313765353631613232613263653361613931613265
-6638346566313664630a333563346639303061313738373437383161393238343964373564336366
-38343161616433646330643431353137626263636266653331303934616265353233663733633834
-36653063393264346136623436643735636163663638316334386337313661376536316537373966
-31396339323535353066363337626238396464666139303537393034663035373065336335653263
-36663030663461353531373731316133306263373961356335353666393433613166303135666261
-37343965316563303166346366313834393431386336376532363730343432363333383765386337
-32393737336132396363313432323666333737616266656263646164616363633233363466343265
-63336261356362316531353536626437346266353337313735623933373462323937373736653736
-62333331313434353937333437373534643633323437326536363736353234363830393130383062
-6366
+38363034333061383832316233613735333633653034643435663733663064323331646137633130
+6133613965393661663934646639353833656432313532630a666234396134303866303735636533
+64613538373265323631316339366335353161313937663663386633356466643533656531333136
+3735383133373535300a353731366138333731666462636261393632386263616666366466333738
+37323161303563393636616134333132306261613562323930383439343131663265326134346562
+32633732363435313935373234666532393261396237396563623830643266633936633661346632
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diff --git a/host_vars/pulsar-re2.grid.cesnet.cz/vars.yml b/host_vars/pulsar-re2.grid.cesnet.cz/vars.yml
index 93ffa82..907556a 100644
--- a/host_vars/pulsar-re2.grid.cesnet.cz/vars.yml
+++ b/host_vars/pulsar-re2.grid.cesnet.cz/vars.yml
@@ -1,6 +1,5 @@
 # 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
@@ -8,6 +7,26 @@ pulsar:
   nfs_home: "brno11-elixir"
   nfs_prefix: pulsar-re
 
+miniconda_channels: 
+  - 'conda-forge'
+  - 'bioconda'
+  - 'iuc'
+  - 'r'
+  - 'anaconda'
+  - 'petrnovak'
+  - 'defaults'
+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
diff --git a/hosts.yml b/hosts.yml
index b5f9e11..c00295d 100644
--- a/hosts.yml
+++ b/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:
diff --git a/pulsar.yml b/pulsar.yml
index 23c316f..33eb8f3 100644
--- a/pulsar.yml
+++ b/pulsar.yml
@@ -4,22 +4,21 @@
       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'
+#  vars:
+#    pulsar_user: "{{ pulsar.user_name }}"
+#    pbs_drmaa_version: "1.0.19"
+#
+#    # Miniconda settings
+#    miniconda_prefix: "{{ pulsar_network_homedir }}/conda"
+#    miniconda_exec: "{{ miniconda_prefix }}/bin/mamba"
+#    miniconda_version: 23.1.0
+#    miniconda_channels:
+#      - 'bioconda'
+#      - 'conda-forge'
+#      - 'iuc'
+#      - 'r'
+#      - 'anaconda'
+#      - 'defaults'
 
   pre_tasks:
     - group:
@@ -52,11 +51,11 @@
 
   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: 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: Create .drmaa folder in NFS home
       ansible.builtin.file:
         path: "{{ pulsar_network_homedir }}/.drmaa"
diff --git a/roles/galaxyproject.miniconda/README.md b/roles/galaxyproject.miniconda/README.md
deleted file mode 100644
index 51dc2ab..0000000
--- a/roles/galaxyproject.miniconda/README.md
+++ /dev/null
@@ -1,69 +0,0 @@
-galaxyproject.miniconda
-=======================
-
-An [Ansible][ansible] role for installing and managing [Miniconda][miniconda] installation. Additionally, the role can
-manage the creation of a [Conda][conda] environment that can be used to create a [venv][venv] for [Galaxy][galaxy].
-
-[ansible]: https://www.ansible.com/
-[miniconda]: https://docs.conda.io/en/latest/miniconda.html
-[conda]: https://docs.conda.io/en/latest/
-[venv]: https://docs.python.org/3/tutorial/venv.html
-[galaxy]: https://galaxyproject.org/
-
-Requirements
-------------
-
-A [Conda][conda]-compatible version of Linux or macOS is required.
-
-Role Variables
---------------
-
-See [defaults/main.yml](defaults/main.yml) for a full list.
-
-The only required variable is `miniconda_prefix`, the root of the Conda installation.
-
-To create arbitrary conda environments, use the variable `miniconda_conda_environments` as shown in the defaults, or the
-example below. The role will also run `conda install` to update these environments if you change their list of packages
-or package versions.
-
-To create an env named `_galaxy_` for creating a venv for [Galaxy][galaxy], set `galaxy_conda_create_env` to `true`. You
-can then use `{{ miniconda_prefix }}/envs/_galaxy_/bin/virtualenv` as the value to `galaxy_virtualenv_command` in
-[galaxyproject.galaxy][galaxy-role]. This is particularly useful if you need a cross-platform copy of Python and
-Galaxy's venv to be deployed on a shared filesystem between a Galaxy server and cluster that may not have matching OS
-distributions and versions.
-
-[galaxy-role]: https://github.com/galaxyproject/ansible-galaxy
-
-Dependencies
-------------
-
-None
-
-Example Playbook
-----------------
-
-```yaml
-- hosts: localhost
-  vars:
-    miniconda_prefix: /conda
-    miniconda_conda_environments:
-      python@3.9:
-        channels:  # optional, defaults to miniconda_channels
-          - conda-forge
-          - defaults
-        packages:
-          - python=3.9
-  connection: local
-  roles:
-     - galaxyproject.miniconda
-```
-
-License
--------
-
-MIT
-
-Author Information
-------------------
-
-[View contributors on GitHub](https://github.com/galaxyproject/ansible-miniconda/graphs/contributors)
diff --git a/roles/galaxyproject.miniconda/defaults/main.yml b/roles/galaxyproject.miniconda/defaults/main.yml
deleted file mode 100644
index ae43fef..0000000
--- a/roles/galaxyproject.miniconda/defaults/main.yml
+++ /dev/null
@@ -1,58 +0,0 @@
----
-
-# Installers are not released for every version of conda, you can use this to
-# `conda install conda={{ miniconda_version }}` a specific version of conda. If set to `latest` then the role will
-# perform a `conda update conda` instead.
-miniconda_version: latest
-
-# If you wish to install e.g. a conda-forge version of conda you can do so by setting channels. This causes
-# `--override-channels --channel <channel> [--channel <channel> ...]` to be specified on the call to
-# `conda install conda...` or `conda update conda`.
-miniconda_channels: []
-
-# Use a specific installer version and python version. The default is to use the latest installer. If you specify a
-# version, it must exist in https://repo.anaconda.com/miniconda/
-#
-# The Python major and minor version e.g. '3.9' (or '39') of the installer
-miniconda_installer_python: null
-# The conda version of the installer
-miniconda_installer_version: latest
-
-# List packages to install into conda's base environment
-# e.g.
-# miniconda_base_env_packages: ['mamba']
-miniconda_base_env_packages: []
-
-# Create environments using the provided description. e.g.:
-#
-# miniconda_conda_environments:
-#   python@3.9:
-#     channels:  # optional, defaults to miniconda_channels
-#       - conda-forge
-#       - defaults
-#     packages:
-#       - python=3.9
-miniconda_conda_environments: {}
-
-# Automatically create a conda env using virtualenv from conda-forge for Galaxy (https://galaxyproject.org/)
-galaxy_conda_create_env: false
-galaxy_conda_env: _galaxy_
-galaxy_conda_env_channels:
-  - conda-forge
-  - defaults
-galaxy_conda_env_packages:
-  - python=3.6
-  - pip>=9
-  - virtualenv>=16
-
-# You generally should not need to set these yourself
-#
-# ansible_distribution is 'MacOSX' if ansible_system is 'Darwin'
-# ansible_system is 'Linux' on Linux
-miniconda_installer_os: "{{ ansible_distribution if ansible_system == 'Darwin' else ansible_system }}"
-miniconda_installer_arch: "{{ ansible_architecture }}"
-# The installer filename on https://repo.anaconda.com/miniconda/ to fetch and run
-miniconda_installer: >-
-  Miniconda3-{{ 'py' ~ (miniconda_python | replace('.', '')) ~ '_' ~ miniconda_version if miniconda_installer_version != 'latest' else 'latest' }}-{{ miniconda_installer_os }}-{{ miniconda_installer_arch }}.sh
-# The shell to call the downloaded installer script with
-miniconda_installer_shell: /bin/sh
diff --git a/roles/galaxyproject.miniconda/meta/.galaxy_install_info b/roles/galaxyproject.miniconda/meta/.galaxy_install_info
deleted file mode 100644
index 3b859ac..0000000
--- a/roles/galaxyproject.miniconda/meta/.galaxy_install_info
+++ /dev/null
@@ -1,2 +0,0 @@
-install_date: Mon Mar 27 12:26:27 2023
-version: 0.3.1
diff --git a/roles/galaxyproject.miniconda/meta/main.yml b/roles/galaxyproject.miniconda/meta/main.yml
deleted file mode 100644
index 474e62f..0000000
--- a/roles/galaxyproject.miniconda/meta/main.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-galaxy_info:
-  namespace: galaxyproject
-  role_name: miniconda
-  author: The Galaxy Project
-  description: |
-    Install and maintain a Miniconda (https://docs.conda.io/en/latest/miniconda.html) installation, and optionally, for Galaxy (https://galaxyproject.org/)
-  company: The Galaxy Project
-  license: MIT
-  min_ansible_version: 2.7
-  github_branch: main
-  platforms:
-    - name: GenericLinux
-      versions:
-        - all
-    - name: macOS
-      versions:
-        - all
-    - name: MacOSX
-      versions:
-        - 10.13
-        - 10.14
-  galaxy_tags:
-    - system
-    - galaxy
-    - conda
-    - miniconda
-dependencies: []
diff --git a/roles/galaxyproject.miniconda/tasks/install.yml b/roles/galaxyproject.miniconda/tasks/install.yml
deleted file mode 100644
index 8d39383..0000000
--- a/roles/galaxyproject.miniconda/tasks/install.yml
+++ /dev/null
@@ -1,26 +0,0 @@
----
-
-- name: Create miniconda installer tempfile
-  tempfile:
-    prefix: ansible-miniconda-installer.
-    suffix: .sh
-  register: miniconda_installer_tempfile
-
-- name: Collect miniconda installer
-  get_url:
-    url: "https://repo.anaconda.com/miniconda/{{ miniconda_installer }}"
-    dest: "{{ miniconda_installer_tempfile.path }}"
-    force: true
-
-- name: miniconda installer block
-  block:
-
-    - name: Run miniconda installer
-      command: "{{ miniconda_installer_shell }} {{ miniconda_installer_tempfile.path }} -b -p {{ miniconda_prefix }}"
-
-  always:
-
-    - name: Remove minicoda installer
-      file:
-        path: "{{ miniconda_installer_tempfile.path }}"
-        state: absent
diff --git a/roles/galaxyproject.miniconda/tasks/main.yml b/roles/galaxyproject.miniconda/tasks/main.yml
deleted file mode 100644
index 180bbdd..0000000
--- a/roles/galaxyproject.miniconda/tasks/main.yml
+++ /dev/null
@@ -1,78 +0,0 @@
----
-
-- name: Check for miniconda existence
-  stat:
-    path: "{{ miniconda_prefix }}/bin/conda"
-  register: miniconda_exists
-
-- name: Include install tasks
-  include_tasks: install.yml
-  when: not miniconda_exists.stat.exists
-
-- name: Collect miniconda version
-  command: "{{ miniconda_prefix }}/bin/conda -V"
-  register: miniconda_installed_version
-  changed_when: false
-
-- name: Update miniconda version (exact)
-  command: >-
-    {{ miniconda_prefix }}/bin/conda install --yes
-    {{ '--override-channels --channel' if miniconda_channels else '' }}
-    {{ miniconda_channels | join(' --channel ') }}
-    conda={{ miniconda_version }}
-  when: miniconda_version != 'latest' and (miniconda_installed_version.stdout.split() | last) != miniconda_version
-
-- name: Update miniconda version (latest)
-  command: >-
-    {{ miniconda_prefix }}/bin/conda update --yes
-    {{ '--override-channels --channel' if miniconda_channels else '' }}
-    {{ miniconda_channels | join(' --channel ') }}
-    conda
-  register: __miniconda_conda_update_conda_output
-  changed_when: "'All requested packages already installed' not in __miniconda_conda_update_conda_output.stdout"
-  when: miniconda_version == 'latest'
-
-- name: Install packages to conda base environment
-  command: >-
-    {{ miniconda_prefix }}/bin/conda install --yes
-    {{ '--override-channels --channel' if (miniconda_channels) else '' }}
-    {{ miniconda_channels | join(' --channel ') }}
-    {{ miniconda_base_env_packages | join(' ') }}
-  when: miniconda_base_env_packages
-
-# Apparently item.value.copy always refers to the built-in copy method of the dict, whereas item.value['copy'] only does
-# if the key 'copy' is not defined
-- name: Create conda envs
-  command: >-
-    {{ miniconda_prefix }}/bin/conda create --yes
-    {{ '--override-channels --channel' if (item.value.channels | default(miniconda_channels)) else '' }}
-    {{ (item.value.channels | default(miniconda_channels)) | join(' --channel ') }}
-    {{ '--name ' ~ item.key if not item.key.startswith('/') else '--prefix ' ~ item.key }}
-    {{ '--copy' if (item.value['copy'] is boolean and item.value['copy']) else '' }}
-    {{ item.value.packages | join(' ') }}
-  args:
-    creates: "{{ miniconda_prefix ~ '/envs/' ~ item.key if not item.key.startswith('/') else item.key }}"
-  loop: "{{ miniconda_conda_environments | dict2items }}"
-
-- name: Update conda envs
-  command: >-
-    {{ miniconda_prefix }}/bin/conda install --yes
-    {{ '--override-channels --channel' if (item.value.channels | default(miniconda_channels)) else '' }}
-    {{ (item.value.channels | default(miniconda_channels)) | join(' --channel ') }}
-    {{ '--name ' ~ item.key if not item.key.startswith('/') else '--prefix ' ~ item.key }}
-    {{ '--copy' if (item.value['copy'] is boolean and item.value['copy']) else '' }}
-    {{ item.value.packages | join(' ') }}
-  register: __miniconda_conda_install_output
-  changed_when: "'All requested packages already installed' not in __miniconda_conda_install_output.stdout"
-  loop: "{{ miniconda_conda_environments | dict2items }}"
-
-- name: Create Galaxy conda env
-  command: >-
-    {{ miniconda_prefix }}/bin/conda create --yes
-    {{ '--override-channels --channel' if galaxy_conda_env_channels else '' }}
-    {{ galaxy_conda_env_channels | join(' --channel ') }}
-    --name {{ galaxy_conda_env }}
-    {{ galaxy_conda_env_packages | join(' ') }}
-  args:
-    creates: "{{ miniconda_prefix }}/envs/{{ galaxy_conda_env }}"
-  when: galaxy_conda_create_env
diff --git a/roles/galaxyproject.miniconda/tests/inventory b/roles/galaxyproject.miniconda/tests/inventory
deleted file mode 100644
index 878877b..0000000
--- a/roles/galaxyproject.miniconda/tests/inventory
+++ /dev/null
@@ -1,2 +0,0 @@
-localhost
-
diff --git a/roles/galaxyproject.miniconda/tests/test.yml b/roles/galaxyproject.miniconda/tests/test.yml
deleted file mode 100644
index 3a39277..0000000
--- a/roles/galaxyproject.miniconda/tests/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
----
-- hosts: localhost
-  remote_user: root
-  vars:
-    miniconda_prefix: "{{ lookup('env', 'TRAVIS_BUILD_DIR') }}/conda"
-  roles:
-    - ansible-miniconda
diff --git a/roles/metacentrum.krbnfs/tasks/main.yml b/roles/metacentrum.krbnfs/tasks/main.yml
index 780aa98..8db0889 100644
--- a/roles/metacentrum.krbnfs/tasks/main.yml
+++ b/roles/metacentrum.krbnfs/tasks/main.yml
@@ -10,7 +10,7 @@
 - name: Metacentrum repo key
   apt_key:
     url: https://repo.metacentrum.cz/key.asc
-    id: F11383F552848522E4EACA443573FD94A385CDB0
+#    id: F11383F552848522E4EACA443573FD94A385CDB0
   when: ansible_os_family == 'Debian'
 
 - name: Metacentrum repo

From ec8912a0e6a09cc71a663cfded8c127c9bd5435f Mon Sep 17 00:00:00 2001
From: Martin Demko <325073@mail.muni.cz>
Date: Mon, 27 Apr 2026 13:56:31 +0200
Subject: [PATCH 03/10] optimizes conda settings

---
 dependency_resolvers_conf.xml | 2 --
 group_vars/pulsarservers.yml  | 5 +----
 2 files changed, 1 insertion(+), 6 deletions(-)
 delete mode 100644 dependency_resolvers_conf.xml

diff --git a/dependency_resolvers_conf.xml b/dependency_resolvers_conf.xml
deleted file mode 100644
index 29a9381..0000000
--- a/dependency_resolvers_conf.xml
+++ /dev/null
@@ -1,2 +0,0 @@
-<dependency_resolvers>
-</dependency_resolvers>
diff --git a/group_vars/pulsarservers.yml b/group_vars/pulsarservers.yml
index c4253e3..c83efea 100644
--- a/group_vars/pulsarservers.yml
+++ b/group_vars/pulsarservers.yml
@@ -1,6 +1,7 @@
 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
@@ -10,10 +11,6 @@ miniconda_version: 23.1.0
 miniconda_channels:
   - 'bioconda'
   - 'conda-forge'
-  - 'iuc'
-  - 'r'
-  - 'anaconda'
-  - 'defaults'
 csnt_dependency_resolvers: {}
 
 # only galaxyproject.pulsar role vars below

From 6e827577e8be36253171ce2d986bb5eeec0a60a9 Mon Sep 17 00:00:00 2001
From: Martin Demko <325073@mail.muni.cz>
Date: Mon, 27 Apr 2026 13:57:36 +0200
Subject: [PATCH 04/10] fixes my ssh connection

---
 ansible.cfg | 1 +
 1 file changed, 1 insertion(+)

diff --git a/ansible.cfg b/ansible.cfg
index 803e98f..a7e9653 100644
--- a/ansible.cfg
+++ b/ansible.cfg
@@ -22,3 +22,4 @@ always = True
 
 [ssh_connection]
 pipelining = true
+ssh_args = -o GSSAPIAuthentication=no -o GSSAPIDelegateCredentials=no

From 1c6a6c9bf1ca17c140610d4354e6b677bd2a5f27 Mon Sep 17 00:00:00 2001
From: Martin Demko <325073@mail.muni.cz>
Date: Mon, 27 Apr 2026 15:25:11 +0200
Subject: [PATCH 05/10] updates metacentrum repo key ID

---
 roles/metacentrum.krbnfs/tasks/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/roles/metacentrum.krbnfs/tasks/main.yml b/roles/metacentrum.krbnfs/tasks/main.yml
index 8db0889..8ff8b51 100644
--- a/roles/metacentrum.krbnfs/tasks/main.yml
+++ b/roles/metacentrum.krbnfs/tasks/main.yml
@@ -10,7 +10,7 @@
 - name: Metacentrum repo key
   apt_key:
     url: https://repo.metacentrum.cz/key.asc
-#    id: F11383F552848522E4EACA443573FD94A385CDB0
+    id: 3CCAEBFDC3398E762111FB2B403875C13E1F1A7D
   when: ansible_os_family == 'Debian'
 
 - name: Metacentrum repo

From f2d62905d0d0e158f4c5286569763102add108e7 Mon Sep 17 00:00:00 2001
From: Martin Demko <325073@mail.muni.cz>
Date: Mon, 27 Apr 2026 15:31:45 +0200
Subject: [PATCH 06/10] cleanup old code and comments

---
 group_vars/pulsarservers.yml | 22 +---------------------
 pulsar.yml                   | 22 ----------------------
 2 files changed, 1 insertion(+), 43 deletions(-)

diff --git a/group_vars/pulsarservers.yml b/group_vars/pulsarservers.yml
index c83efea..0bd3cc6 100644
--- a/group_vars/pulsarservers.yml
+++ b/group_vars/pulsarservers.yml
@@ -63,29 +63,9 @@ 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.
+  ## 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 }}"
-#    resolvers:
-#      - type: conda
-#        auto_init: true
-#        auto_install: true
-#        ensure_channels: "{{ miniconda_channels|join(',') }}"
-#        exec: "{{ miniconda_exec }}"
-#        prefix: "{{ miniconda_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
   managers:
     _default_:
       type: queued_drmaa
diff --git a/pulsar.yml b/pulsar.yml
index 33eb8f3..88186b4 100644
--- a/pulsar.yml
+++ b/pulsar.yml
@@ -4,22 +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_exec: "{{ miniconda_prefix }}/bin/mamba"
-#    miniconda_version: 23.1.0
-#    miniconda_channels:
-#      - 'bioconda'
-#      - 'conda-forge'
-#      - 'iuc'
-#      - 'r'
-#      - 'anaconda'
-#      - 'defaults'
-
   pre_tasks:
     - group:
         name: "{{ pulsar.group }}"
@@ -50,12 +34,6 @@
       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: Create .drmaa folder in NFS home
       ansible.builtin.file:
         path: "{{ pulsar_network_homedir }}/.drmaa"

From bd017da9e5335d734e2a6d6cb24bb35f132dd8af Mon Sep 17 00:00:00 2001
From: Martin Demko <325073@mail.muni.cz>
Date: Mon, 27 Apr 2026 16:38:32 +0200
Subject: [PATCH 07/10] adds patch to pulsar source because of improved
 recursive rsync

---
 .../0.15.6/__init__.py.patch                  | 22 ++++++++
 .../0.15.6/down.py.patch                      | 10 ++++
 files/pulsar_repo.improved_rsync/0.15.6/patch | 51 +++++++++++++++++++
 .../0.15.6/ssh.py.patch                       | 19 +++++++
 pulsar.yml                                    |  6 +++
 5 files changed, 108 insertions(+)
 create mode 100644 files/pulsar_repo.improved_rsync/0.15.6/__init__.py.patch
 create mode 100644 files/pulsar_repo.improved_rsync/0.15.6/down.py.patch
 create mode 100644 files/pulsar_repo.improved_rsync/0.15.6/patch
 create mode 100644 files/pulsar_repo.improved_rsync/0.15.6/ssh.py.patch

diff --git a/files/pulsar_repo.improved_rsync/0.15.6/__init__.py.patch b/files/pulsar_repo.improved_rsync/0.15.6/__init__.py.patch
new file mode 100644
index 0000000..4632c0f
--- /dev/null
+++ b/files/pulsar_repo.improved_rsync/0.15.6/__init__.py.patch
@@ -0,0 +1,22 @@
+--- staging/__init__.py 2024-11-15 14:28:46.166714601 +0000
++++ staging/__init__.py.v2      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
diff --git a/files/pulsar_repo.improved_rsync/0.15.6/down.py.patch b/files/pulsar_repo.improved_rsync/0.15.6/down.py.patch
new file mode 100644
index 0000000..797b3ff
--- /dev/null
+++ b/files/pulsar_repo.improved_rsync/0.15.6/down.py.patch
@@ -0,0 +1,10 @@
+--- staging/down.py     2024-11-15 14:28:46.166714601 +0000
++++ staging/down.py.v2  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.
diff --git a/files/pulsar_repo.improved_rsync/0.15.6/patch b/files/pulsar_repo.improved_rsync/0.15.6/patch
new file mode 100644
index 0000000..c266c00
--- /dev/null
+++ b/files/pulsar_repo.improved_rsync/0.15.6/patch
@@ -0,0 +1,51 @@
+--- staging/down.py     2024-11-15 14:28:46.166714601 +0000
++++ staging/down.py.v2  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.
+--- staging/__init__.py 2024-11-15 14:28:46.166714601 +0000
++++ staging/__init__.py.v2      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
+--- transport/ssh.py    2024-11-15 14:28:46.166714601 +0000
++++ transport/ssh.py.patch  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,
diff --git a/files/pulsar_repo.improved_rsync/0.15.6/ssh.py.patch b/files/pulsar_repo.improved_rsync/0.15.6/ssh.py.patch
new file mode 100644
index 0000000..6c9c5d7
--- /dev/null
+++ b/files/pulsar_repo.improved_rsync/0.15.6/ssh.py.patch
@@ -0,0 +1,19 @@
+--- transport/ssh.py    2024-11-15 14:28:46.166714601 +0000
++++ transport/ssh.py.patch  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,
diff --git a/pulsar.yml b/pulsar.yml
index 88186b4..26d1cd5 100644
--- a/pulsar.yml
+++ b/pulsar.yml
@@ -34,6 +34,12 @@
       become_user: "{{ pulsar.user_name }}"
 
   post_tasks:
+    #DEMON: Not finished yet!!!
+    - name: Apply recursive rsync changes in pulsar package
+      ansible.posix.patch:
+        src: "files/pulsar_repo.improved_rsync/{{ pulsar_package_version }}/patch"
+        basedir: /opt/pulsar/venv/lib/python3.11/site-packages/pulsar/client
+
     - name: Create .drmaa folder in NFS home
       ansible.builtin.file:
         path: "{{ pulsar_network_homedir }}/.drmaa"

From a6e884876853145f9ea95b5e12416fa67ca02fe4 Mon Sep 17 00:00:00 2001
From: martindemko <325073@mail.muni.cz>
Date: Mon, 27 Apr 2026 22:05:35 +0200
Subject: [PATCH 08/10] adds patching of pulsar in one task

---
 .../0.15.6/__init__.py.patch                  | 22 -------------------
 .../0.15.6/down.py.patch                      | 10 ---------
 .../0.15.6/ssh.py.patch                       | 19 ----------------
 .../0.15.6/recursive_rsync.patch}             | 14 +++++++-----
 group_vars/pulsarservers.yml                  |  1 +
 pulsar.yml                                    |  7 +++---
 6 files changed, 13 insertions(+), 60 deletions(-)
 delete mode 100644 files/pulsar_repo.improved_rsync/0.15.6/__init__.py.patch
 delete mode 100644 files/pulsar_repo.improved_rsync/0.15.6/down.py.patch
 delete mode 100644 files/pulsar_repo.improved_rsync/0.15.6/ssh.py.patch
 rename files/{pulsar_repo.improved_rsync/0.15.6/patch => pulsar_repo/0.15.6/recursive_rsync.patch} (82%)

diff --git a/files/pulsar_repo.improved_rsync/0.15.6/__init__.py.patch b/files/pulsar_repo.improved_rsync/0.15.6/__init__.py.patch
deleted file mode 100644
index 4632c0f..0000000
--- a/files/pulsar_repo.improved_rsync/0.15.6/__init__.py.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- staging/__init__.py 2024-11-15 14:28:46.166714601 +0000
-+++ staging/__init__.py.v2      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
diff --git a/files/pulsar_repo.improved_rsync/0.15.6/down.py.patch b/files/pulsar_repo.improved_rsync/0.15.6/down.py.patch
deleted file mode 100644
index 797b3ff..0000000
--- a/files/pulsar_repo.improved_rsync/0.15.6/down.py.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- staging/down.py     2024-11-15 14:28:46.166714601 +0000
-+++ staging/down.py.v2  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.
diff --git a/files/pulsar_repo.improved_rsync/0.15.6/ssh.py.patch b/files/pulsar_repo.improved_rsync/0.15.6/ssh.py.patch
deleted file mode 100644
index 6c9c5d7..0000000
--- a/files/pulsar_repo.improved_rsync/0.15.6/ssh.py.patch
+++ /dev/null
@@ -1,19 +0,0 @@
---- transport/ssh.py    2024-11-15 14:28:46.166714601 +0000
-+++ transport/ssh.py.patch  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,
diff --git a/files/pulsar_repo.improved_rsync/0.15.6/patch b/files/pulsar_repo/0.15.6/recursive_rsync.patch
similarity index 82%
rename from files/pulsar_repo.improved_rsync/0.15.6/patch
rename to files/pulsar_repo/0.15.6/recursive_rsync.patch
index c266c00..a83f003 100644
--- a/files/pulsar_repo.improved_rsync/0.15.6/patch
+++ b/files/pulsar_repo/0.15.6/recursive_rsync.patch
@@ -1,5 +1,5 @@
---- staging/down.py     2024-11-15 14:28:46.166714601 +0000
-+++ staging/down.py.v2  2026-04-27 14:18:40.826792741 +0000
+--- 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)
@@ -8,8 +8,9 @@
 +            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.
---- staging/__init__.py 2024-11-15 14:28:46.166714601 +0000
-+++ staging/__init__.py.v2      2026-04-27 14:12:38.332467975 +0000
+
+--- 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)
@@ -30,8 +31,9 @@
 +        edir = dict()
 +        edir[local_path(name)] = name
 +        return edir
---- transport/ssh.py    2024-11-15 14:28:46.166714601 +0000
-+++ transport/ssh.py.patch  2026-04-27 14:05:24.769565794 +0000
+
+--- 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 = [
diff --git a/group_vars/pulsarservers.yml b/group_vars/pulsarservers.yml
index 0bd3cc6..d7a22b9 100644
--- a/group_vars/pulsarservers.yml
+++ b/group_vars/pulsarservers.yml
@@ -24,6 +24,7 @@ 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
diff --git a/pulsar.yml b/pulsar.yml
index 26d1cd5..cfe5995 100644
--- a/pulsar.yml
+++ b/pulsar.yml
@@ -34,11 +34,12 @@
       become_user: "{{ pulsar.user_name }}"
 
   post_tasks:
-    #DEMON: Not finished yet!!!
     - name: Apply recursive rsync changes in pulsar package
       ansible.posix.patch:
-        src: "files/pulsar_repo.improved_rsync/{{ pulsar_package_version }}/patch"
-        basedir: /opt/pulsar/venv/lib/python3.11/site-packages/pulsar/client
+        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:

From 2f71c997b03f643bed499052d30873e34212d422 Mon Sep 17 00:00:00 2001
From: martindemko <325073@mail.muni.cz>
Date: Mon, 27 Apr 2026 23:16:47 +0200
Subject: [PATCH 09/10] improves conda channels for RE2

---
 host_vars/pulsar-re2.grid.cesnet.cz/vars.yml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/host_vars/pulsar-re2.grid.cesnet.cz/vars.yml b/host_vars/pulsar-re2.grid.cesnet.cz/vars.yml
index 907556a..4ab40c5 100644
--- a/host_vars/pulsar-re2.grid.cesnet.cz/vars.yml
+++ b/host_vars/pulsar-re2.grid.cesnet.cz/vars.yml
@@ -8,13 +8,9 @@ pulsar:
   nfs_prefix: pulsar-re
 
 miniconda_channels: 
-  - 'conda-forge'
   - 'bioconda'
-  - 'iuc'
-  - 'r'
-  - 'anaconda'
+  - 'conda-forge'
   - 'petrnovak'
-  - 'defaults'
 miniconda_prefix: "/storage/{{ pulsar.nfs_home }}/home/{{ pulsar.user_name }}/anaconda3"
 miniconda_exec: "{{ miniconda_prefix }}/bin/mamba"
 

From eae9b256dfbb6ca16c077989024790c4954f8eaf Mon Sep 17 00:00:00 2001
From: martindemko <325073@mail.muni.cz>
Date: Wed, 29 Apr 2026 00:39:00 +0200
Subject: [PATCH 10/10] adds restart task after change

---
 pulsar.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/pulsar.yml b/pulsar.yml
index cfe5995..6b6d00c 100644
--- a/pulsar.yml
+++ b/pulsar.yml
@@ -40,6 +40,11 @@
         basedir: "{{ pulsar_package_change_dir }}"
         backup: true
         strip: 1
+    - name: Restart pulsar service after change
+      ansible.builtin.systemd:
+        state: restarted
+        name: "{{ pulsar_systemd_service_name }}"
+      become: yes
 
     - name: Create .drmaa folder in NFS home
       ansible.builtin.file: