# Cache conda packages for offline installation Installing conda packages on a computer without internet is somewhat challenging. One common approach is to `conda-pack` your environment, transfer the pack, then "unpack" it on the other computer - [link](https://hackmd.io/@pmitev/Python_Bianca#Using-conda). Here is an alternative way, perhaps easier, to achieve "clean" conda environment installation. Start with the computer on which you have already installed the environment or you can install it. 1. On **source** (your or other working computer with the same processor architecture as the target) ```bash # export the list of packages explicitly so you can download the files $(base) conda list -n my_env --explicit > packages.wget # Download the necessary packages $ mkdir -p pkgs && cd pkgs $ wget -i ../packages.wget ``` 2. Edit `packages.wget` to point to the local package copies. ```bash awk -F '/' '/^http/ {print "pkgs/"$NF; next} {print} ' packages.wget > my_env-local.yaml ``` The awk script above will convert the `http://...` lines in `packages.wget` to `pkgs/...` i.e. ```bash # From https://repo.anaconda.com/pkgs/main/linux-64/sqlite-3.39.3-h5082296_0.conda # to pkgs/sqlite-3.39.3-h5082296_0.conda ``` 3. Transfer the content of the `pkgs` folder to the **target** machine. 4. On the **target** machine - create and install the environment. ```bash # From the folder that contains `pkgs` $(base) conda create -n my_env --file my_env-local.yaml --offline ``` ## Contacts: - [Pavlin Mitev](https://katalog.uu.se/profile/?id=N3-1425) - [UPPMAX](https://www.uppmax.uu.se/) - [SNIC AE@UPPMAX - related documentation](/8sqXISVRRquPDSw9o1DizQ) ![](https://snic.se/digitalAssets/603/c_603880-l_1-k_image.png =122x38) ![](https://live.webb.uu.se/digitalAssets/207/c_207717-l_3-k_bg-city.png) ###### tags: `UPPMAX`, `SNIC`, `conda`, `bianca`, `offline`
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CAFE5 on Rackham@UPPMAX

https://github.com/hahnlab/CAFE5 wget https://github.com/hahnlab/CAFE5/archive/refs/tags/v5.0.tar.gz tar xvf 5.0.tar.gz # start clean module purge module load uppmax # These 4 lines are needed to compile (firts 2 to run)

3/2/2023
Running GenoPredPipe on Bianca

https://opain.github.io/GenoPred/ 1. Load the relevant modules module purge module load uppmax git module load bioinfo-tools GenoPredPipe/20221121-e3caf6b ::: danger Make sure you do not have other modules loaded or using your own conda installation. :::

1/20/2023
Linux Tools for Windows Users

[TOC] :hammer_and_wrench: --- Basic tools --- Over the years, Windows became more and more friendly with respect to interaction with Linux environment. Recent implementation of "Windows Subsystem for Linux - version 2" WSL2 is a significant step toward this direction and perhaps might be one of the best approach in the near feature. Despite that, there are tools that have became essential over the time and are more than enough for the purpose of effective interaction with Linux. :::success Advise: :pencil:

12/6/2022
Installing Python modules on Bianca - UPPMAX

Bianca is a research system dedicated for analyzing sensitive personal data from large-scale molecular experiments. Bianca is part of the SNIC-SENS project. Since Bianca is designed to handle sensitive personal data security is a key aspect of the configuration and features restricted access and lack of direct Internet access to and from the cluster. This make it particularly difficult to use common tools to maintain python modules or software installations. Here are some tips and advises on different way to approach the problem. User installs via pip pip documentation Download the necessary modules - docs.

10/27/2022
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