Metadata-Version: 2.1
Name: ctshed
Version: 0.1.1
Summary: A Docker based CLI Tools manager.
Home-page: https://github.com/kkarolis/ctshed
License: UNKNOWN
Description: Ctshed - Container Toolshed
        ===========================
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        [![Project Status: Concept – Minimal or no implementation has been done yet, or the repository is only intended to be a limited example, demo, or proof-of-concept.](https://www.repostatus.org/badges/latest/concept.svg)](https://www.repostatus.org/#concept)
        
        
        Container Toolshed. A CLI tool manager for creating container centric
        namespaces with specific tools installed. This could possibly help to easier
        manage cli tools for users (multiple tool versions, no screw-up with os level
        package executables)
        
        Example
        -------
        
        ```sh
        # a single tool executable, debian:stable implicit source
        ctshed install --packages=curl --cmd=curl mycurl
        # downloads the P04156.fasta file and saves it in the current directory
        ctshed-mycurl -LO https://www.uniprot.org/uniprot/P04156.fasta
        
        # a tool namespace 
        ctshed install --source=biocontainers/blast:2.2.31 myblast
        ctshed-myblast curl -LO https://www.uniprot.org/uniprot/P04156.fasta
        ctshed-myblast curl -LO ftp://ftp.ncbi.nih.gov/refseq/D_rerio/mRNA_Prot/zebrafish.1.protein.faa.gz
        ctshed-myblast gunzip zebrafish.1.protein.faa.gz
        ctshed-myblast makeblastdb -in zebrafish.1.protein.faa -dbtype prot
        ctshed-myblast blastp -query P04156.fasta -db zebrafish.1.protein.faa -out results.txt
        ```
        
        Installation
        ------------
        ```sh
        pip install ctshed
        ```
        
        The tool places binaries to `~/bin` directory blindly without checking if it
        exists or if theres a nameclash. Make sure `~/bin` exists in your path. E.g.
        place something like this in `~/.bash_rc`:
        
        ```sh
        #~/.bash_rc file
        export PATH="$HOME/bin:$PATH"
        ```
        
        The tool depends on `docker` binary existing on the host system. You have to
        install it if you don't have it. Installation of docker on `ubuntu` systems is described [docker-ce/ubuntu](https://docs.docker.com/install/linux/docker-ce/ubuntu/)
        
        
        Features
        --------
        
        * Create a docker based tool namespace
        * Create an executable with specific tool installation
        
        
        Principles of working
        ---------------------
        
        1. An image is created during the install step and some name is automatically given to it.
        2. An executable is created in executable directory of the users workspace.
        3. Executable contains a container run command with stdin/stdout/stderr
           attached and /home directory mounted.
        
        Testing
        -------
        
        ```sh
        python -m unittest discover tests
        ```
        
        Limitations
        -----------
        
        There are limitations with using container as a wrapper for command line.
        * Configuration might not be picked up by the tool.
        * Input/Output works correctly only under /home directory
        * Security, because /home is mounted
        * More will come. 
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.7
Description-Content-Type: text/markdown
