From c4cb405cfa5e4651b8d96a5ee99ea56a09ebcf45 Mon Sep 17 00:00:00 2001 From: Tobias Neumann Date: Thu, 26 Jun 2025 14:12:50 +0200 Subject: [PATCH 1/2] fixed repos for open source simstack version --- docs/installation/index.rst | 26 ++++++++++++++++++-------- docs/installation/server.rst | 2 +- 2 files changed, 19 insertions(+), 9 deletions(-) diff --git a/docs/installation/index.rst b/docs/installation/index.rst index f09a36c..05aad25 100644 --- a/docs/installation/index.rst +++ b/docs/installation/index.rst @@ -21,7 +21,7 @@ After installing, make sure you have the **micromamba** or **conda** command ava .. code-block:: bash # Create a new environment for the simstack client: - micromamba create --name=simstack simstack -c https://mamba.nanomatch-distribution.de/mamba-repo -c conda-forge + micromamba create --name=simstack -c https://repo.prefix.dev/simstack simstack -c conda-forge # Activate the environment micromamba activate simstack # and run simstack: @@ -40,9 +40,9 @@ Finally, if you want to update an existing simstack install: .. code-block:: bash micromamba activate simstack - micromamba update simstack -c https://mamba.nanomatch-distribution.de/mamba-repo -c conda-forge + micromamba update simstack -c https://repo.prefix.dev/simstack simstack -c conda-forge # Or if you need a specific version, example 1.2.5: - micromamba install simstack=1.2.5 -c https://mamba.nanomatch-distribution.de/mamba-repo -c conda-forge + micromamba install simstack=1.2.5 -c https://repo.prefix.dev/simstack simstack -c conda-forge The client version requires passwordless via ``ssh`` access to communicate with the HPC. If you do not have passwordless via @@ -74,21 +74,22 @@ If you don't have the ``ssh`` keys, use the steps below to generate them. * Please choose the HPC where you want to have passwordless access. .. code-block:: bash - + ssh-copy-id @ * Test the connectivity of your passwordless ``ssh`` by running one of the commands below in the **Powershell** prompt. .. code-block:: bash - + ssh @ * After completing the above steps, run the below commands. .. code-block:: bash - cd simstack_linux - ./run_simstack.sh + micromamba activate simstack + # and run simstack: + simstack Installation on Windows @@ -118,7 +119,16 @@ If you don't have the ``ssh`` keys, use the steps below to generate them. type $env:USERPROFILE\.ssh\id_rsa.pub | ssh @ "cat >> .ssh/authorized_keys" - * After completing the above steps, double-click on ``run-simstack`` and be happy. + * The installation and execution works similar to Linux above: + + .. code-block:: bash + + # Create a new environment for the simstack client: + micromamba create --name=simstack -c https://repo.prefix.dev/simstack simstack -c conda-forge + # Activate the environment + micromamba activate simstack + # and run simstack: + simstack **Testing the connectivity** diff --git a/docs/installation/server.rst b/docs/installation/server.rst index 1609b0f..73f4d7b 100644 --- a/docs/installation/server.rst +++ b/docs/installation/server.rst @@ -22,7 +22,7 @@ After installing, make sure you have the **micromamba** command available in you .. code-block:: bash # Create a new environment for simstack client: - micromamba create --name=simstack_server_v6 simstackserver -c https://mamba.nanomatch-distribution.de/mamba-repo -c conda-forge + micromamba create --name=simstack_server_v6 simstackserver https://repo.prefix.dev/simstack simstackserver -c conda-forge # Activate the environment to see if it exists micromamba activate simstack_server_v6 From 8e14aeacc2835fbb28a07c5ff4b5898c7da6d6da Mon Sep 17 00:00:00 2001 From: Tobias Neumann Date: Thu, 26 Jun 2025 14:26:12 +0200 Subject: [PATCH 2/2] fixed missing -c --- docs/installation/server.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/installation/server.rst b/docs/installation/server.rst index 73f4d7b..71f33c1 100644 --- a/docs/installation/server.rst +++ b/docs/installation/server.rst @@ -22,7 +22,7 @@ After installing, make sure you have the **micromamba** command available in you .. code-block:: bash # Create a new environment for simstack client: - micromamba create --name=simstack_server_v6 simstackserver https://repo.prefix.dev/simstack simstackserver -c conda-forge + micromamba create --name=simstack_server_v6 simstackserver -c https://repo.prefix.dev/simstack simstackserver -c conda-forge # Activate the environment to see if it exists micromamba activate simstack_server_v6