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        "description": "Ctshed - Container Toolshed\n===========================\n![Travis (.org)](https://img.shields.io/travis/kkarolis/ctshed.svg)\n![Coveralls github](https://img.shields.io/coveralls/github/kkarolis/ctshed.svg)\n![PyPI - Python Version](https://img.shields.io/pypi/pyversions/ctshed.svg)\n![PyPI](https://img.shields.io/pypi/v/ctshed.svg)\n![GitHub](https://img.shields.io/github/license/kkarolis/ctshed.svg)\n[![Project Status: Concept \u2013 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)\n\n\nContainer Toolshed. A CLI tool manager for creating container centric\nnamespaces with specific tools installed. This could possibly help to easier\nmanage cli tools for users (multiple tool versions, no screw-up with os level\npackage executables)\n\nExample\n-------\n\n```sh\n# a single tool executable, debian:stable implicit source\nctshed install --packages=curl --cmd=curl mycurl\n# downloads the P04156.fasta file and saves it in the current directory\nctshed-mycurl -LO https://www.uniprot.org/uniprot/P04156.fasta\n\n# a tool namespace \nctshed install --source=biocontainers/blast:2.2.31 myblast\nctshed-myblast curl -LO https://www.uniprot.org/uniprot/P04156.fasta\nctshed-myblast curl -LO ftp://ftp.ncbi.nih.gov/refseq/D_rerio/mRNA_Prot/zebrafish.1.protein.faa.gz\nctshed-myblast gunzip zebrafish.1.protein.faa.gz\nctshed-myblast makeblastdb -in zebrafish.1.protein.faa -dbtype prot\nctshed-myblast blastp -query P04156.fasta -db zebrafish.1.protein.faa -out results.txt\n```\n\nInstallation\n------------\n```sh\npip install ctshed\n```\n\nThe tool places binaries to `~/bin` directory blindly without checking if it\nexists or if theres a nameclash. Make sure `~/bin` exists in your path. E.g.\nplace something like this in `~/.bash_rc`:\n\n```sh\n#~/.bash_rc file\nexport PATH=\"$HOME/bin:$PATH\"\n```\n\nThe tool depends on `docker` binary existing on the host system. You have to\ninstall 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/)\n\n\nFeatures\n--------\n\n* Create a docker based tool namespace\n* Create an executable with specific tool installation\n\n\nPrinciples of working\n---------------------\n\n1. An image is created during the install step and some name is automatically given to it.\n2. An executable is created in executable directory of the users workspace.\n3. Executable contains a container run command with stdin/stdout/stderr\n   attached and /home directory mounted.\n\nTesting\n-------\n\n```sh\npython -m unittest discover tests\n```\n\nLimitations\n-----------\n\nThere are limitations with using container as a wrapper for command line.\n* Configuration might not be picked up by the tool.\n* Input/Output works correctly only under /home directory\n* Security, because /home is mounted\n* More will come. \n\n\n",
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