cobot-tools: Biological data file formats and IO

[ bio, bsd3, library ] [ Propose Tags ]

Please see the README on GitHub at https://github.com/less-wrong/cobot-tools#readme


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Versions [faq] 0.1.0.1
Change log ChangeLog.md
Dependencies array (==0.5.*), base (>=4.7 && <5), cobot, containers (>=0.5.7.1 && <0.7), data-msgpack (>=0.0.9 && <0.1), deepseq (==1.4.*), lens (>=4.16 && <5.0), mtl (>=2.2.1 && <2.3.0), text [details]
License BSD-3-Clause
Copyright 2018-2019, Less Wrong Bio
Author Pavel Yakovlev, Bogdan Neterebskii, Alexander Sadovnikov
Maintainer pavel@yakovlev.me
Category Bio
Home page https://github.com/less-wrong/cobot-tools#readme
Bug tracker https://github.com/less-wrong/cobot-tools/issues
Source repo head: git clone https://github.com/less-wrong/cobot-tools
Uploaded by ozzzzz at Thu Nov 7 06:54:15 UTC 2019
Distributions NixOS:0.1.0.1
Downloads 30 total (30 in the last 30 days)
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Status Hackage Matrix CI
Docs not available [build log]
All reported builds failed as of 2019-11-07 [all 3 reports]

Modules

  • Bio
    • Tools
      • Sequence
        • Primers
          • Bio.Tools.Sequence.Primers.Constants
          • Bio.Tools.Sequence.Primers.Optimization
          • Bio.Tools.Sequence.Primers.Properties
          • Bio.Tools.Sequence.Primers.Types
        • ViennaRNA
          • Bio.Tools.Sequence.ViennaRNA.Cofold
          • Bio.Tools.Sequence.ViennaRNA.Fold
          • Internal
            • Bio.Tools.Sequence.ViennaRNA.Internal.Cofold
            • Bio.Tools.Sequence.ViennaRNA.Internal.Fold
            • Bio.Tools.Sequence.ViennaRNA.Internal.RNALike

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Readme for cobot-tools-0.1.0.1

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cobot-tools

Tools for computational biology

Software required to use cobot-tools

ViennaRNA

ViennaRNA is a library that already contains lots of useful algorithms that work with RNA sequences. We use it in order to make tools from cobot-tools better.

Installation guide for Linux can be found here.

Some issues occur when you try to install ViennaRNA for MacOS. If you want to avoid them, use the following guide.

Installation of ViennaRNA for MacOS

Installation of ViennaRNA for MacOS can be done in following steps:

  1. Download library. Here is the link for version 2.4.13.
  2. Unpack it.
  3. Go to the directory, where archive has been unpacked.
  4. Run command ./configure --without-perl --without-python.
  5. Remove field libRNA_la_LDFLAGS and flag -static from the file src/ViennaRNA/Makefile.am.
  6. Due to us having changed .am-file, it is needed to install following packages: autoconf and automake. In order to do it, run command: brew install autoconf automake.
  7. Run in the root of library command autoreconf.
  8. Compile library using command make -j8 (j8 - flag that allows us to compile code using 8 jobs).
  9. Run command make install.

Tools of cobot-tools

Sequence.Primer.Optimisation.designPrimer

Given 'DNA' sequence and position in that sequence designs forward primer for that sequence. Primer will start at the given position.