start:software:topical:lifesciences [MogonWiki]

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====== Software for LifeScience Data Analyis ======

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<callout type="tip" icon="true">
This page is always "under construction". It will hardly ever display a comprehensive/complete list: 
  * We install many new tools upon request and it is hard to keep track documenting them all.
  * Software compiled / installed locally by projects is not supported by the HPC team and cannot be displayed here.
 Links which are displayed in red, do not exist, yet. Any contribution or suggestion is welcome.
</callout>
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<callout type="info" title="A Note on Limitations" icon="true">
  * Benchmarks displayed on these pages are only benchmarks with respect to speed. The values are valid only for the given parameters and may greatly vary for deviating parameters or input. (You may indicate deviating experiences to us.)
  * We strive to improve the beauty and information content of this page. However, the conducted science is up to you as a user - whether or not a particular program invocation (the arguments supplied) actually make sense for your scientific question is up to you to decide.
</callout>
<callout type="info" title="News" icon="true">
News on software in bioinformatics and related stuff is distributed via a [[https://lists.uni-mainz.de/sympa/review/bioinf-news|mailing list]] (low traffic). You can subscribe, too. You may also distribute and share information using this list. 
</callout>
<callout type="info" title="Contributing" icon="true">
Yes, please! Please get in touch with us, if you want to benchmark or contribute wrapper scripts. We created some [[https://gitlab.rlp.net/hpc-jgu-lifescience|repositories]] and would be delighted to you to the list of contributors. Also, contributions to this wiki (reports, suggestions, error notes) are welcome!
</callout>

===== Installed Life Science Software =====

Life science software is installed on Mogon I and II in the ''bio'' [[:start:software:installation_remarks|module category]]((This is true with a few exceptions, e.g. AutoDock.)). 

To list the available tools, you can type:

<code bash>
module av bio/ |& cut -f2 -d '/' | uniq
</code>

A subsequent 
<code bash>
module av|& grep <tool of interest>
</code>
, where ''tool of interest'' is copy-pasted from the output above, will show the respective versions for that software.

You can ask for updates on a particular software or to install previously not supported software [[https://hpc.uni-mainz.de/high-performance-computing/service-angebot/softwareinstallation/|via our webpage]].

<callout type="info" icon="true">
If an installed tool is not listed on this page, respectively its underlying links, you may contribute this (its a wiki!) or ask for further documentation.
</callout>
==== Overview ====
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  * {{fa>file-code-o?fw&color=#000}} [[:start:software:topical:lifesciences:r_bio|R and BioConductor]]
  * {{fa>file-code-o?fw&color=#000}} [[:start:software:topical:lifesciences:ngs|NGS & Co.]]
  * {{fa>file-code-o?fw&color=#000}} [[:start:software:topical:lifesciences:evol_soft|Evolutionary & Phylogenetics Software Tools]]
  * {{fa>file-code-o?fw&color=#000}}[[:start:software:topical:lifesciences:development|Development]]
</list-group>
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  * {{fa>file-code-o?fw&color=#000}} [[:start:software:topical:lifesciences:molecular_docking|Molecular Docking Tools]]
  * {{fa>file-code-o?fw&color=#000}} [[:start:software:topical:lifesciences:molecular_dynamics|Molecular Dynamics Simulations]]
  * {{fa>file-code-o?fw&color=#000}} [[:start:software:topical:lifesciences:single_particle_analysis|Single Particle Processing / Analysis]]
</list-group>
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<panel type="default" title="What Else?">

This wiki does not cover your topic / favorite software? Please let us know.

  - We can install [[https://hpc.uni-mainz.de/high-performance-computing/service-angebot/softwareinstallation/|your software]], which frequently is better than to install software yourself((With the exception of abandonware, crappy software, scripts which can be installed with ''pip'', ''cran'', etc..)), because:
    * we install software in an optimized fashion
    * if installed as a module, we made the commitment to support the software, if there are issues with the module, the batch system or I/O((but, of course, not with respect to bugs within the software))
  - Writing wrapper scripts for otherwise non-performant applications can take time. We still encourage to approach us and ask us, before being stuck in a project.

<callout type="info" icon="true">
Any contribution (a script, an idea, a reported issue, feature request, documentation, test data, own benchmark, etc.) is welcome! Particularly, section links labeled with "*" require attention((Missing links wait to be filled with content - a re-structuring might also occur.)).

  * [[:start:training_and_outreach:faq#may_i_contribute_to_this_wiki|Here is info on how to contribute to documentation]].
  * If you have written a piece of software (e.g. a script for a particular workflow) you would like to share, please [[hpc@uni-mainz.de|do not hesitate to approach us]].
</callout>

<callout type="info" title="Tired of" icon="true">
... [[https://en.wikipedia.org/wiki/Software_as_a_service|Software as a Service]]?
  * You have the option to collaborate on specific setups or if a specific tool needs to be written.
  * Any feedback will help.
</callout>
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