prun: Add documentation in markdown format

prun/pman.md

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+% PTYPE(1) | Mariux Tools Documentation
+
+NAME
+====
+
+**pman** - view manual pages installed in Mariux packages.
+
+SYNOPSIS
+========
+
+| **pman command**
+
+DESCRIPTION
+===========
+
+**ptype** uses the PATH set in the package wrapper and tries to find a manual page in the package directory.
+
+EXAMPLES
+========
+
+**display manpage found in /pkg/stellarium-0.21.0-0/share/man/man1**
+: pman stellarium
+
+
+BUGS
+====
+
+**pman** is very naive in looking up man pages, so your mileage may vary.
+
+See GitHub Issues: <https://github.molgen.mpg.de/mariux64/mxtools>
+
+SEE ALSO
+========
+
+**prun(1)**, **ptype(1)**, **man(1)**
+
+

prun/prun.md

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+% PRUN(1) Version n/a | Mariux Tools Documentation
+
+NAME
+====
+
+**prun** - Run Mariux packages (reads 'Package RUN').
+
+SYNOPSIS
+========
+
+| **prun package command** [COMMANDOPTION]...
+
+DESCRIPTION
+===========
+
+Runs applications, scripting languages, compilers, etc., from a dedicated directory.
+
+The main usage is to run software in a specific version, or to provide a given environment. See **EXAMPLES** below.
+
+There are some advantages over so called 'virtual environments' and the like. Packages are immutable, once installed they never change, thereby increasing the chances that an old program/script will also run in a few years. The packages also 
+use a standardized call procedure, independent of personal (un-)settings, thus an existing pipeline may be shared between different users.
+
+The whole 'magic' behind **prun** is, that it transparently sets the PATH variable and possibly LD_LIBRARY_PATH for the actual call without spoiling the default environment.
+
+EXAMPLES
+========
+
+
+**Run R-Studio with a brand new R version**
+
+: prun R-4.1.0-0 rstudio
+
+**Use an ancient python to run an unmaintained script**
+
+: prun python-2.7.13-2 /project/cruft/bin/old_script.py
+
+**Run nvidia nvcc from cuda-11.3 and list supported architectures**
+
+: prun cuda-11.3 nvcc --list-gpu-code
+
+**Start a plain shell with gcc-10.2 in the PATH**
+
+:  prun gcc-10.2.0-0 bash --norc
+
+**Or just show the manual page for gcc-10.2**
+
+:  prun gcc-10.2.0-0 man gcc
+
+**Create an own alias for a scripting language**
+
+: alias myperl='prun perl-5.18.2-0 perl'
+
+**Use prun in a script shebang**
+
+: `#! /usr/bin/prun perl-5.18.2-0 perl`
+
+**Alternatively using source**
+
+:  An alternative way to set a distinct environment is to source the profile from /pkg/FooBar-12.3.
+But beware, such a source command should **never** make it into the **\~/.bashrc** - in the worst case it may inhibit your login!
+(N.b. the alias method mentioned above is safe)
+
+\ 
+: source /pkg/gcc-10.2.0-0/profile
+
+
+FILES
+=====
+
+*/package/FOO* or */pkg/BAR*
+
+:   Mountpoint (top directory) for selected package.
+
+*/package/FOO/profile* or */pkg/BAR/profile*
+
+:   Contains settings for PATH, libraries, and possibly other stuff.
+
+*/usr/local/package/lib/\**
+
+:   Primary wrappers for individual packages.
+
+*/usr/local/package/admin/config*
+
+:   Definition of binaries provided and optional shortcuts.
+
+
+BUGS
+====
+
+See GitHub Issues: <https://github.molgen.mpg.de/mariux64/mxtools>
+
+AUTHORS
+=======
+
+D.Buczek, P.Marquardt, M.Tolzmann
+
+SEE ALSO
+========
+
+**ptype(1)**, **pman(1)**, **bash(1)**, **ld.so(8)**
+
+

prun/ptype.md

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+% PTYPE(1) | Mariux Tools Documentation
+
+NAME
+====
+
+**ptype** - small **type** like tool for Mariux packages.
+
+SYNOPSIS
+========
+
+| **ptype command**
+
+DESCRIPTION
+===========
+
+Similar to **type** or **which**. **ptype** gives information about a package binary. **type** would only tell something about the package wrapper, and not about the package where the real program is. 
+
+```
+
+  #> type snakemake
+  snakemake is /usr/local/package/bin/snakemake
+
+  #> ptype snakemake
+  snakemake is /pkg/python-3.8.9-1/bin/snakemake  ...
+               ... (/usr/local/package/lib/python.profile)
+
+
+```
+
+BUGS
+====
+
+**ptype** only handles true wrapper scripts from /usr/local/package/bin, not the aliases. I.e. **ptype R** works, **ptype R4** not.
+
+See GitHub Issues: <https://github.molgen.mpg.de/mariux64/mxtools>
+
+SEE ALSO
+========
+
+**prun(1)**, **pman(1)**
+
+