Running raxml for a folder of files

[Lilnet Cloud]

I have ~2000 files that I would like to run raxml for.

Is there a way to automate the running of all 2000 files on raxml on command line?

All my files have the same prefix:

file1.phy

file2.phy

file3.phy

..

[Alexandros Stamatakis]

no, this is much better handled via appropriate perl or python
scripts, I believe somebody on this list here asked that question before
and might have a solution,

alexis

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--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[Alexey Kozlov]

there is actually a script in RAxML github repository which seems to do exactly this:

https://github.com/stamatak/standard-RAxML/blob/master/usefulScripts/applyRAxML2AllFilesInDirectory.pl

at least based on its name :)

[Sergios-Orestis Kolokotronis]

Apurva wrote 3 wrappers a few years ago. Alexis posted them on http://sco.h-its.org/exelixis/web/software/raxml/index.html

• raxml_launch_serially.sh: A simple shell script that launches one job after the other awaiting for completion of each job.
  
• raxml_nexusPartConvert.pl: A Perl script that parses a partitioned alignment in Nexus format with charsets and produces a partition guide file to be fed to RAxML with -q. Preliminary - works with DNA or AA, but not the two together yet, so not suitable for mixed-molecule data. Unless the output gets redirected to a file with ">", it will appear on screen.
  
• raxml_wrapper.pl: A Perl script that reads a raxml.config file with common run parameters and executes a directory of Phylip alignment files in batch, then outputs the results in another directory. See the documentation with "perldoc ./raxml_wrapper.pl".
  

[Alexandros Stamatakis]

thanks alexey and sergio :-)

that's it,

alexis

On 29.10.2016 21:57, Sergios-Orestis Kolokotronis wrote:
> Apurva wrote 3 wrappers a few years ago. Alexis posted them
> on http://sco.h-its.org/exelixis/web/software/raxml/index.html
>

> * raxml_launch_serially.sh
> <http://sco.h-its.org/exelixis/resource/download/software/raxml_launch_serially.sh>:

> A simple shell script that launches one job after the other awaiting
> for completion of each job.

> * raxml_nexusPartConvert.pl:
> <http://sco.h-its.org/exelixis/resource/download/software/raxml_nexusPartConvert.pl> A

> Perl script that parses a partitioned alignment in Nexus format with
> charsets and produces a partition guide file to be fed to RAxML with
> -q. Preliminary - works with DNA or AA, but not the two together
> yet, so not suitable for mixed-molecule data. Unless the output gets
> redirected to a file with ">", it will appear on screen.

> * raxml_wrapper.pl
> <http://sco.h-its.org/exelixis/resource/download/software/raxml_wrapper.pl>:

> A Perl script that reads a raxml.config file with common run
> parameters and executes a directory of Phylip alignment files in
> batch, then outputs the results in another directory. See the
> documentation with "perldoc ./raxml_wrapper.pl".
>
>
> On Saturday, October 29, 2016 at 12:09:06 AM UTC-4, Lilnet Cloud wrote:
>
> I have ~2000 files that I would like to run raxml for.
> Is there a way to automate the running of all 2000 files on raxml on
> command line?
>
> All my files have the same prefix:
> file1.phy
> file2.phy
> file3.phy
> ..
>

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