phylip shellscript

Hassan Badrane hbadrane at pasteur.fr
Wed Jun 28 04:24:05 EST 1995


Jeremy Packer <jclp100 at mole.bio.cam.ac.uk> wrote:
>
> Does anyone have experience of running phylip progs. in batch on UNIX
> machines? ie does anyone have a shellscript that works?!
> 
> Jeremy

hi Jeremy,

We have at the pasteur institute two machines "mendel" and "darwin". the shellscript
you search for must look like the one done by Tekaia for "mendel". follow is all the 
help file : (hope this reelly help)

                Use of Phylip Programs in bg and at modes
                        on mendel and darwin

  How to use the phylip programs in the background
        example with the dnaml program
  /usr/gensrc/phylip/dnaml.x < file.param > /dev/null  2>&1 &   on mendel
  /usr/gensoft/phylip/bin/dnaml.x <file.param > /dev/null  2>&1 on darwin

  How to use the phylip programs (example dnaml) in the at mode

  at now + 1 minutes atdnaml
where atdnaml is the following script :
#!/bin/sh
USER = tekaia at pasteur.fr  (for example, put your adress here not mine)
/usr/gensrc/clustalv/clustalv   < file.param > /dev/null
mail -s "dnaml terminated"  $USER  << FIN
 dnaml job terminated at : `date`.
FIN

 The user might execute the script at another time as for example :

 at midnight atdnaml or at 20:00 Sunday atdnaml etc,...


 On darwin, change the pathname : /usr/gensrc/phylip/dnaml.x by
/usr/gensoft/phylip/bin/dnaml.x
and execute the command as follows :

at `date +%H%M` atdnaml  (the now cariable is not available on convex).


 How to use the phylip programs (example of dnaml) in the batch mode :

At the unix prompt type the following commands :

batch << EOF
/usr/gensrc/clustalv/clustalv   < file.param > /dev/null
mail -s "dnaml terminated"  tekaia at pasteur.fr  << FIN
 dnaml job terminated at : `date`.
FIN
EOF


 The user might execute the previous script in batch mode as follows :

 batch atdnaml

On darwin : change the pathname as previously indicated and type
qsub instead of batch.

-------------
Phylip programs :

In an interactive use of the phylip programs, you are presented with a menu
to modify default values or to accept them as indicated.
If you want to modify a parameter you need to indicate the
one you want to change, alternative values will be presented. You may
change one parameter at once, the menu will presented again and you may
change another parameter, etc...
When you finish changing parameters you type Y to accept the presented
values. The program begin then its execution.

 To run the same program in the backgroud, you create a file (file.param)
 each line of which contains the number of parameter you want to change,
 as explaned previously.

Example :
 Use of dnaml in the backgroud :

  dnaml < file.param > /dev/null  2>&1 &

(infile is the input file and outfile is the
outpufile as is usual in the phylip programs)

where :
- The last "&" corresponds to backgroud run of the program
- "2>&1" standard output and standard error output redirected to /dev/null
(the text which is written on the screen will be redirected to /dev/null )
- /dev/null : is a unix null file name;
- file.param : the file containing the paramters, the user feeds the
  program with

 For the phylip programs the file.param might be very simple, and reduced
to the one line "y" which corresponds to the "yes" respons if the user
accpets the default values presented by the programs. We consider here
a more co;plicated example to show how to construct a file.param file.
 In the following example dnaml is applied to infile (as usual), where the user
The corresponding file.param contains the following values :
j
111
3
o
5
y
-------
  These are what the user writes in the interactive use as indicated
in the following text :

dnaml interactive use
---------------------------
Script started on Tue Jun 22 17:31:08 1993
bash$ dnaml


 [2J [HNucleic acid sequence Maximum Likelihood method, version 3.41

Settings for this run:
  U                 Search for best tree?  Yes
  T        Transition/transversion ratio:  2.0
  F       Use empirical base frequencies?  Yes
  C   One category of substitution rates?  Yes
  G                Global rearrangements?  No
  J   Randomize input order of sequences?  No. Use input order
  O                        Outgroup root?  No, use as outgroup species  1
  M           Analyze multiple data sets?  No
  I          Input sequences interleaved?  Yes
  0   Terminal type (IBM PC, VT52, ANSI)?  ANSI
  1    Print out the data at start of run  No
  2  Print indications of progress of run  Yes
  3                        Print out tree  Yes
  4       Write out trees onto tree file?  Yes

Are these settings correct? (type Y or the letter for one to change)
j                  <--------------------
Random number seed (must be odd)?
111                <-------------------

 [2J [HNucleic acid sequence Maximum Likelihood method, version 3.41

Settings for this run:
  U                 Search for best tree?  Yes
  T        Transition/transversion ratio:  2.0
  F       Use empirical base frequencies?  Yes
  C   One category of substitution rates?  Yes
  G                Global rearrangements?  No
  J   Randomize input order of sequences?  Yes (random number seed =     111)
  O                        Outgroup root?  No, use as outgroup species  1
  M           Analyze multiple data sets?  No
  I          Input sequences interleaved?  Yes
  0   Terminal type (IBM PC, VT52, ANSI)?  ANSI
  1    Print out the data at start of run  No
  2  Print indications of progress of run  Yes
  3                        Print out tree  Yes
  4       Write out trees onto tree file?  Yes

Number of times to Jumble?
3

 [2J [HNucleic acid sequence Maximum Likelihood method, version 3.41

Settings for this run:
  U                 Search for best tree?  Yes
  T        Transition/transversion ratio:  2.0
  F       Use empirical base frequencies?  Yes
  C   One category of substitution rates?  Yes
  G                Global rearrangements?  No
  J   Randomize input order of sequences?  Yes (random number seed =     111)
  O                        Outgroup root?  No, use as outgroup species  1
  M           Analyze multiple data sets?  No
  I          Input sequences interleaved?  Yes
  0   Terminal type (IBM PC, VT52, ANSI)?  ANSI
  1    Print out the data at start of run  No
  2  Print indications of progress of run  Yes
  3                        Print out tree  Yes
  4       Write out trees onto tree file?  Yes

Are these settings correct? (type Y or the letter for one to change)
o                        <------------------
Type number of the outgroup:
5                        <-----------------

 [2J [HNucleic acid sequence Maximum Likelihood method, version 3.41

Settings for this run:
  U                 Search for best tree?  Yes
  T        Transition/transversion ratio:  2.0
  F       Use empirical base frequencies?  Yes
  C   One category of substitution rates?  Yes
  G                Global rearrangements?  No
  J   Randomize input order of sequences?  Yes (random number seed =     111)
  O                        Outgroup root?  Yes, at sequence number  5
  M           Analyze multiple data sets?  No
  I          Input sequences interleaved?  Yes
  0   Terminal type (IBM PC, VT52, ANSI)?  ANSI
  1    Print out the data at start of run  No
  2  Print indications of progress of run  Yes
  3                        Print out tree  Yes
  4       Write out trees onto tree file?  Yes

Are these settings correct? (type Y or the letter for one to change)
y                             <--------------------

Adding species:
   Orang
   Bovine
   Mouse
   Gibbon
   Human
   Chimp
   Gorilla


Output written to output file

Tree also written onto file

You have mail in /usr/spool/mail/tekaia
bash$ exit
exit

script done on Tue Jun 22 17:33:26 1993

script done on Tue Jun 22 17:33:26 1993

----------------------- End of script of interactive file




   IP 18/06/93

Fredj Tekaia
tekaia at pasteur.fr

Last modified 16/08/93
FT






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