[med-svn] r17849 - trunk/packages/aevol/trunk/debian
David Parsons
dparsons-guest at moszumanska.debian.org
Tue Aug 26 09:32:44 UTC 2014
Author: dparsons-guest
Date: 2014-08-26 09:32:44 +0000 (Tue, 26 Aug 2014)
New Revision: 17849
Added:
trunk/packages/aevol/trunk/debian/aevol_misc_ancstats.1
trunk/packages/aevol/trunk/debian/aevol_misc_compute_pop_stats.1
trunk/packages/aevol/trunk/debian/aevol_misc_create_eps.1
trunk/packages/aevol/trunk/debian/aevol_misc_extract.1
trunk/packages/aevol/trunk/debian/aevol_misc_fixed_mutations.1
trunk/packages/aevol/trunk/debian/aevol_misc_gene_families.1
trunk/packages/aevol/trunk/debian/aevol_misc_lineage.1
trunk/packages/aevol/trunk/debian/aevol_misc_robustness.1
trunk/packages/aevol/trunk/debian/aevol_misc_view_generation.1
Removed:
trunk/packages/aevol/trunk/debian/aevol_run_X11.1
Modified:
trunk/packages/aevol/trunk/debian/aevol.manpages
trunk/packages/aevol/trunk/debian/aevol_create.1
trunk/packages/aevol/trunk/debian/aevol_modify.1
trunk/packages/aevol/trunk/debian/aevol_propagate.1
trunk/packages/aevol/trunk/debian/aevol_run.1
Log:
Added missing manpages and updated existing ones
Modified: trunk/packages/aevol/trunk/debian/aevol.manpages
===================================================================
--- trunk/packages/aevol/trunk/debian/aevol.manpages 2014-08-26 09:32:42 UTC (rev 17848)
+++ trunk/packages/aevol/trunk/debian/aevol.manpages 2014-08-26 09:32:44 UTC (rev 17849)
@@ -1,5 +1,13 @@
debian/aevol_create.1
debian/aevol_run.1
-debian/aevol_run_X11.1
debian/aevol_modify.1
debian/aevol_propagate.1
+debian/aevol_misc_ancstats.1
+debian/aevol_misc_compute_pop_stats.1
+debian/aevol_misc_create_eps.1
+debian/aevol_misc_extract.1
+debian/aevol_misc_fixed_mutations.1
+debian/aevol_misc_gene_families.1
+debian/aevol_misc_lineage.1
+debian/aevol_misc_robustness.1
+debian/aevol_misc_view_generation.1
Modified: trunk/packages/aevol/trunk/debian/aevol_create.1
===================================================================
--- trunk/packages/aevol/trunk/debian/aevol_create.1 2014-08-26 09:32:42 UTC (rev 17848)
+++ trunk/packages/aevol/trunk/debian/aevol_create.1 2014-08-26 09:32:44 UTC (rev 17849)
@@ -1,4 +1,5 @@
-.TH AEVOL "1" "January 2014" "aevol 4.3" "User Manual"
+/#test with man \-l <file>
+.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
.SH NAME
aevol \- an in silico experimental evolution platform
.SH SYNOPSIS
@@ -10,25 +11,40 @@
or
.B \-\-version
.br
-.B aevol_create [\-f
-.I param_file]
+.B aevol_create \fR[\fB\-v\fR] \fR[\fB\-f\fI PARAM_FILE\fR] \fR[\fB\-o\fI OUTDIR\fR] \fR[\fB\-c\fI CFILE\fR] \fR[\fB\-p\fI PFILE\fR]
.SH DESCRIPTION
.B Aevol
is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
.TP
.B aevol_create
-create an experiment with setup as specified in
+create an experiment with setup as specified in
.I param_file
.SH OPTIONS
.TP
.B \-h, \-\-help
-print this help, then exit
+print help, then exit
.TP
.B \-V, \-\-version
print version number, then exit
-.TP
+.HP
.B \-f, \-\-file
-.I param_file
+.I PARAM_FILE
+.br
specify parameter file (default: param.in)
+.HP
+.B \-o, \-\-out
+.I OUTDIR
+.br
+specify output directory (default "./")
+.HP
+.B \-c, \-\-chromosome
+.I CFILE
+.br
+load chromosome from given text file instead of generating it
+.HP
+.B \-p, \-\-plasmid
+.I PFILE
+.br
+load plasmid from given text file instead of generating it (params must allow plasmids)
.SH "SEE ALSO"
.B aevol_run, aevol_modify, aevol_propagate
Copied: trunk/packages/aevol/trunk/debian/aevol_misc_ancstats.1 (from rev 17848, trunk/packages/aevol/trunk/debian/aevol_modify.1)
===================================================================
--- trunk/packages/aevol/trunk/debian/aevol_misc_ancstats.1 (rev 0)
+++ trunk/packages/aevol/trunk/debian/aevol_misc_ancstats.1 2014-08-26 09:32:44 UTC (rev 17849)
@@ -0,0 +1,34 @@
+/#test with man \-l <file>
+.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
+.SH NAME
+aevol \- an in silico experimental evolution platform
+.SH SYNOPSIS
+.B aevol_misc_ancstats \-h
+|
+.B \-\-help
+.br
+.B aevol_misc_ancstats \-V
+|
+.B \-\-version
+.br
+.B aevol_misc_ancstats \fB\-f\fI LINEAGE_FILE
+.SH DESCRIPTION
+.B Aevol
+is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
+.TP
+.B aevol_misc_ancstats
+issues statistics for the line of descent of a given individual.
+.SH OPTIONS
+.TP
+.B \-h, \-\-help
+print help, then exit
+.TP
+.B \-V, \-\-version
+print version number, then exit
+.HP
+.B \-f, \-\-file
+.I LINEAGE_FILE
+.br
+specify which lineage file to use. Lineage files are created by the ae_misc_lineage tool
+.SH "SEE ALSO"
+.B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run
Added: trunk/packages/aevol/trunk/debian/aevol_misc_compute_pop_stats.1
===================================================================
--- trunk/packages/aevol/trunk/debian/aevol_misc_compute_pop_stats.1 (rev 0)
+++ trunk/packages/aevol/trunk/debian/aevol_misc_compute_pop_stats.1 2014-08-26 09:32:44 UTC (rev 17849)
@@ -0,0 +1,49 @@
+/#test with man \-l <file>
+.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
+.SH NAME
+aevol \- an in silico experimental evolution platform
+.SH SYNOPSIS
+.B aevol_misc_compute_pop_stats \-h
+|
+.B \-\-help
+.br
+.B aevol_misc_compute_pop_stats \-V
+|
+.B \-\-version
+.br
+.B aevol_misc_compute_pop_stats \fR[\fB\-i\fI INDEX\fR | \fB\-r\fI RANK\fR] \fR[\fB\-b\fI GENER1\fR] \fB\-e\fI GENER2
+.SH DESCRIPTION
+.B Aevol
+is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
+.TP
+.B aevol_misc_compute_pop_stats
+issues population and replication statistics for each available backup from GENER1 to GENER2. These statistics are written in files global_pop_stats.out and stats/pop_stats/*.
+.SH OPTIONS
+.TP
+.B \-h, \-\-help
+print help, then exit
+.TP
+.B \-V, \-\-version
+print version number, then exit
+.HP
+.B \-i, \-\-index
+.I INDEX
+.br
+specify the index (ID in current generation) of the individual whose replication statistics should be outputted
+.HP
+.B \-r, \-\-rank
+.I RANK
+.br
+specify the rank of the individual whose replication statistics should be outputted
+.HP
+.B \-b, \-\-begin
+.I GENER
+.br
+specify the first generation for which the statistics should be computed
+.HP
+.B \-e, \-\-end
+.I GENER
+.br
+specify the last generation for which the statistics should be computed
+.SH "SEE ALSO"
+.B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run
Added: trunk/packages/aevol/trunk/debian/aevol_misc_create_eps.1
===================================================================
--- trunk/packages/aevol/trunk/debian/aevol_misc_create_eps.1 (rev 0)
+++ trunk/packages/aevol/trunk/debian/aevol_misc_create_eps.1 2014-08-26 09:32:44 UTC (rev 17849)
@@ -0,0 +1,44 @@
+/#test with man \-l <file>
+.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
+.SH NAME
+aevol \- an in silico experimental evolution platform
+.SH SYNOPSIS
+.B aevol_misc_create_eps \-h
+|
+.B \-\-help
+.br
+.B aevol_misc_create_eps \-V
+|
+.B \-\-version
+.br
+.B aevol_misc_create_eps \fR[\fB\-i\fI INDEX\fR | \fB\-r\fI RANK\fR] \fB\-g\fI GENER
+.SH DESCRIPTION
+.B Aevol
+is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
+.TP
+.B aevol_misc_create_eps
+produces several eps files describing an individual of this population
+.SH OPTIONS
+.TP
+.B \-h, \-\-help
+print help, then exit
+.TP
+.B \-V, \-\-version
+print version number, then exit
+.HP
+.B \-i, \-\-index
+.I INDEX
+.br
+specify the index (ID in current generation) of the individual
+.HP
+.B \-r, \-\-rank
+.I RANK
+.br
+specify the rank of the individual
+.HP
+.B \-g, \-\-gener
+.I GENER
+.br
+specify the generation of the individual
+.SH "SEE ALSO"
+.B aevol_create, aevol_modify, aevol_propagate, aevol_run
Added: trunk/packages/aevol/trunk/debian/aevol_misc_extract.1
===================================================================
--- trunk/packages/aevol/trunk/debian/aevol_misc_extract.1 (rev 0)
+++ trunk/packages/aevol/trunk/debian/aevol_misc_extract.1 2014-08-26 09:32:44 UTC (rev 17849)
@@ -0,0 +1,58 @@
+/#test with man \-l <file>
+.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
+.SH NAME
+aevol \- an in silico experimental evolution platform
+.SH SYNOPSIS
+.B aevol_misc_extract \-h
+|
+.B \-\-help
+.br
+.B aevol_misc_extract \-V
+|
+.B \-\-version
+.br
+.B aevol_misc_extract \fR[\fB\-r\fI GENER\fR | \fB\-p\fI POP_FILE\fR] \fR[\fB\-t\fI PHEN_FILE\fR] \fR[\fB\-s\fI SEQ_FILE\fR] \fR[\fB\-g\fI NUM_GU\fR] \fR[\fB\-b\fR]
+.SH DESCRIPTION
+.B Aevol
+is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
+.TP
+.B aevol_misc_extract
+extracts the genotype and/or data about the phenotype of individuals in the provided population and write them into text files easy to parse with e.g. matlab.
+.SH OPTIONS
+.TP
+.B \-h, \-\-help
+print help, then exit
+.TP
+.B \-V, \-\-version
+print version number, then exit
+.HP
+.B \-r
+.I GENER
+.br
+read generation GENER from a full aevol backup
+.HP
+.B \-p
+.I POP_FILE
+.br
+read the population saved in population file POP_FILE
+.HP
+.B \-t
+.I PHEN_FILE
+.br
+extract and save some infos about the phenotypes of the individuals to file PHEN_FILE
+.HP
+.B \-s
+.I SEQ_FILE
+.br
+extract and save the sequences of the individuals to file SEQ_FILE
+.HP
+.B \-g
+.I num_gu
+.br
+only treat this genetic unit (by default: treat all genetic units)
+.HP
+.B \-b
+.br
+only treat the best individual
+.SH "SEE ALSO"
+.B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run
Added: trunk/packages/aevol/trunk/debian/aevol_misc_fixed_mutations.1
===================================================================
--- trunk/packages/aevol/trunk/debian/aevol_misc_fixed_mutations.1 (rev 0)
+++ trunk/packages/aevol/trunk/debian/aevol_misc_fixed_mutations.1 2014-08-26 09:32:44 UTC (rev 17849)
@@ -0,0 +1,34 @@
+/#test with man \-l <file>
+.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
+.SH NAME
+aevol \- an in silico experimental evolution platform
+.SH SYNOPSIS
+.B aevol_misc_fixed_mutations \-h
+|
+.B \-\-help
+.br
+.B aevol_misc_fixed_mutations \-V
+|
+.B \-\-version
+.br
+.B aevol_misc_fixed_mutations \fB\-f\fI LINEAGE_FILE
+.SH DESCRIPTION
+.B Aevol
+is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
+.TP
+.B aevol_misc_fixed_mutations
+issues the detailed list of mutations that occurred in the lineage of a given individual
+.SH OPTIONS
+.TP
+.B \-h, \-\-help
+print help, then exit
+.TP
+.B \-V, \-\-version
+print version number, then exit
+.HP
+.B \-f, \-\-file
+.I LINEAGE_FILE
+.br
+specify which lineage file to use. Lineage files are created by the ae_misc_lineage tool
+.SH "SEE ALSO"
+.B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run
Added: trunk/packages/aevol/trunk/debian/aevol_misc_gene_families.1
===================================================================
--- trunk/packages/aevol/trunk/debian/aevol_misc_gene_families.1 (rev 0)
+++ trunk/packages/aevol/trunk/debian/aevol_misc_gene_families.1 2014-08-26 09:32:44 UTC (rev 17849)
@@ -0,0 +1,34 @@
+/#test with man \-l <file>
+.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
+.SH NAME
+aevol \- an in silico experimental evolution platform
+.SH SYNOPSIS
+.B aevol_misc_gene_families \-h
+|
+.B \-\-help
+.br
+.B aevol_misc_gene_families \-V
+|
+.B \-\-version
+.br
+.B aevol_misc_gene_families \fB\-f\fI LINEAGE_FILE
+.SH DESCRIPTION
+.B Aevol
+is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
+.TP
+.B aevol_misc_gene_families
+issues the detailed history of each gene family on the lineage of a given individual
+.SH OPTIONS
+.TP
+.B \-h, \-\-help
+print help, then exit
+.TP
+.B \-V, \-\-version
+print version number, then exit
+.HP
+.B \-f, \-\-file
+.I LINEAGE_FILE
+.br
+specify which lineage file to use. Lineage files are created by the ae_misc_lineage tool
+.SH "SEE ALSO"
+.B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run
Added: trunk/packages/aevol/trunk/debian/aevol_misc_lineage.1
===================================================================
--- trunk/packages/aevol/trunk/debian/aevol_misc_lineage.1 (rev 0)
+++ trunk/packages/aevol/trunk/debian/aevol_misc_lineage.1 2014-08-26 09:32:44 UTC (rev 17849)
@@ -0,0 +1,49 @@
+/#test with man \-l <file>
+.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
+.SH NAME
+aevol \- an in silico experimental evolution platform
+.SH SYNOPSIS
+.B aevol_misc_lineage \-h
+|
+.B \-\-help
+.br
+.B aevol_misc_lineage \-V
+|
+.B \-\-version
+.br
+.B aevol_misc_lineage \fR[\fB\-i\fI INDEX\fR | \fB\-r\fI RANK\fR] \fR[\fB\-b\fI GENER1\fR] \fB\-e\fI GENER2
+.SH DESCRIPTION
+.B Aevol
+is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
+.TP
+.B aevol_misc_lineage
+allows for the reconstruction of the lineage of a given individual. Requires the tree to have been recorded during evolution.
+.SH OPTIONS
+.TP
+.B \-h, \-\-help
+print help, then exit
+.TP
+.B \-V, \-\-version
+print version number, then exit
+.HP
+.B \-i, \-\-index
+.I INDEX
+.br
+specify the index (ID in current generation) of the individual whose lineage is to be reconstructed
+.HP
+.B \-r, \-\-rank
+.I RANK
+.br
+specify the rank of the individual whose lineage is to be reconstructed
+.HP
+.B \-b, \-\-begin
+.I GENER
+.br
+specify the generation up to which the lineage is to be reconstructed
+.HP
+.B \-e, \-\-end
+.I GENER
+.br
+specify the generation of the individual whose lineage is to be reconstructed
+.SH "SEE ALSO"
+.B aevol_create, aevol_modify, aevol_propagate, aevol_run
Added: trunk/packages/aevol/trunk/debian/aevol_misc_robustness.1
===================================================================
--- trunk/packages/aevol/trunk/debian/aevol_misc_robustness.1 (rev 0)
+++ trunk/packages/aevol/trunk/debian/aevol_misc_robustness.1 2014-08-26 09:32:44 UTC (rev 17849)
@@ -0,0 +1,51 @@
+/#test with man \-l <file>
+.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
+.SH NAME
+aevol \- an in silico experimental evolution platform
+.SH SYNOPSIS
+.B aevol_misc_robustness \-h
+|
+.B \-\-help
+.br
+.B aevol_misc_robustness \-V
+|
+.B \-\-version
+.br
+.B aevol_misc_robustness \fR\fB\-g\fI GENER\fR [\fB\-n\fI NBCHILDREN] \fR[\fB\-i\fI INDEX\fR | \fB\-r\fI RANK\fR]
+.SH DESCRIPTION
+.B Aevol
+is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
+.TP
+.B aevol_misc_robustness
+computes the replication statistics of all the individuals of a given generation, like the proportion of neutral, beneficial, deleterious offsprings. This is done by simulating NBCHILDREN replications for each individual (1000 replications by default), with its mutation, rearrangement and transfer rates. Depending on those rates and genome size, there can be several mutations per replication. Those global statistics are written in stat/robustness_GENER.out, with one line per individual in the specified generation. The program also outputs detailed statistics for one of the individuals (the best one by default). The detailed statistics for this individual are written in stats/replication_GENER.out, with one line per simulated child of this particular individual.
+
+.SH OPTIONS
+.TP
+.B \-h, \-\-help
+print help, then exit
+.TP
+.B \-V, \-\-version
+print version number, then exit
+.HP
+.B \-g, \-\-gener
+.I GENER
+.br
+specify the generation number for which the robustness statistics are desired
+.HP
+.B \-n, \-\-nb\-children
+.I NBCHILDREN
+.br
+specify the number of reproductions to simulate for each individual
+.HP
+.B \-i, \-\-index
+.I INDEX
+.br
+specify the index (ID in current generation) of the individual for whom detailed reproduction statistics are desired
+.HP
+.B \-r, \-\-rank
+.I RANK
+.br
+specify the rank of the individual for whom detailed reproduction statistics are desired
+
+.SH "SEE ALSO"
+.B aevol_create, aevol_modify, aevol_propagate, aevol_run, aevol_misc_view_generation, aevol_misc_create_eps
Copied: trunk/packages/aevol/trunk/debian/aevol_misc_view_generation.1 (from rev 17848, trunk/packages/aevol/trunk/debian/aevol_modify.1)
===================================================================
--- trunk/packages/aevol/trunk/debian/aevol_misc_view_generation.1 (rev 0)
+++ trunk/packages/aevol/trunk/debian/aevol_misc_view_generation.1 2014-08-26 09:32:44 UTC (rev 17849)
@@ -0,0 +1,34 @@
+/#test with man \-l <file>
+.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
+.SH NAME
+aevol \- an in silico experimental evolution platform
+.SH SYNOPSIS
+.B aevol_misc_view_generation \-h
+|
+.B \-\-help
+.br
+.B aevol_misc_view_generation \-V
+|
+.B \-\-version
+.br
+.B aevol_misc_view_generation \fB\-g\fI GENER
+.SH DESCRIPTION
+.B Aevol
+is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
+.TP
+.B aevol_misc_view_generation
+allows one to visualize a generation using the exact same graphical outputs used in aevol_run.
+.SH OPTIONS
+.TP
+.B \-h, \-\-help
+print help, then exit
+.TP
+.B \-V, \-\-version
+print version number, then exit
+.HP
+.B \-g, \-\-gener
+.I GENER
+.br
+specify generation to visualize (default 0)
+.SH "SEE ALSO"
+.B aevol_create, aevol_modify, aevol_propagate, aevol_run
Modified: trunk/packages/aevol/trunk/debian/aevol_modify.1
===================================================================
--- trunk/packages/aevol/trunk/debian/aevol_modify.1 2014-08-26 09:32:42 UTC (rev 17848)
+++ trunk/packages/aevol/trunk/debian/aevol_modify.1 2014-08-26 09:32:44 UTC (rev 17849)
@@ -1,4 +1,5 @@
-.TH AEVOL "1" "January 2014" "aevol 4.3" "User Manual"
+/#test with man \-l <file>
+.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
.SH NAME
aevol \- an in silico experimental evolution platform
.SH SYNOPSIS
@@ -10,24 +11,24 @@
or
.B \-\-version
.br
-.B aevol_modify \fR[\fB\-g\fI GENERATION\fR] \fR[\fB\-f\fI param_file\fR]
+.B aevol_modify \-g\fI GENER \fR[\fB\-f\fI param_file\fR]
.SH DESCRIPTION
.B Aevol
is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
.TP
.B aevol_modify
-modify an experiment as specified in
+modify an experiment as specified in
.I param_file
.SH OPTIONS
.TP
.B \-h, \-\-help
-print this help, then exit
+print help, then exit
.TP
.B \-V, \-\-version
print version number, then exit
.HP
.B \-g, \-\-gener
-.I GENERATION
+.I GENER
.br
specify generation number
.HP
Modified: trunk/packages/aevol/trunk/debian/aevol_propagate.1
===================================================================
--- trunk/packages/aevol/trunk/debian/aevol_propagate.1 2014-08-26 09:32:42 UTC (rev 17848)
+++ trunk/packages/aevol/trunk/debian/aevol_propagate.1 2014-08-26 09:32:44 UTC (rev 17849)
@@ -1,4 +1,5 @@
-.TH AEVOL "1" "January 2014" "aevol 4.3" "User Manual"
+/#test with man \-l <file>
+.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
.SH NAME
aevol \- an in silico experimental evolution platform
.SH SYNOPSIS
@@ -10,37 +11,70 @@
or
.B \-\-version
.br
-.B aevol_propagate \fR[\fB\-g\fI GENERATION\fR] \fR[\fB\-i\fI in_dir\fR] \fR[\fB\-o\fI out_dir\fR] \fR[\fB\-v\fR]
+.B aevol_propagate \fR[\fB\-v\fR] \fR[\fB\-g\fI GENER\fR] \fR[\fB\-i\fI INDIR\fR] \fR[\fB\-o\fI OUTDIR\fR] \fR[\fB\-S\fI GENERALSEED\fR]
+.br
+.B aevol_propagate \fR[\fB\-v\fR] \fR[\fB\-g\fI GENER\fR] \fR[\fB\-i\fI INDIR\fR] \fR[\fB\-o\fI OUTDIR\fR] \fR[\fB\-s\fI SELSEED\fR] \fR[\fB\-m\fI MUTSEED\fR] \fR[\fB\-t\fI STOCHSEED\fR] \fR[\fB\-e\fI ENVVARSEED\fR] \fR[\fB\-n\fI ENVNOISESEED\fR]
.SH DESCRIPTION
.B Aevol
is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
.TP
.B aevol_propagate
-create a fresh copy of the experiment
+creates a fresh copy of the experiment as it was at the given generation. The generation number of the copy will be reset to 0. If you use aevol_propagate repeatedly to initialize several simulations, you should specify a different seed for each simulation, otherwise all simulations will yield exactly the same results. You can use the option \-S to do so. In this case, the random drawings will be different for all random processes enabled in your simulations (mutations, stochastic gene expression, selection, migration, environmental variation, environmental noise). Alternatively, to change the random drawings for specific random processes only, do not use \-S but the options \-m, \-s, \-t, \-e, \-n (see below).
.SH OPTIONS
.TP
.B \-h, \-\-help
-print this help, then exit
+print help, then exit
.TP
.B \-V, \-\-version
print version number, then exit
+.TP
+.B \-v, \-\-verbose
+be verbose
.HP
.B \-g, \-\-gener
-.I GENERATION
+.I GENER
.br
specify generation number
+(default: that contained in file last_gener.txt, if any)
.HP
.B \-i, \-\-in
-.I in_dir
+.I INDIR
.br
specify input directory (default ".")
.HP
.B \-o, \-\-out
-.I in_dir
+.I OUTDIR
.br
specify output directory (default "./output")
-.TP
-.B \-v, \-\-verbose
-be verbose
+.HP
+.B \-S, \-\-general\-seed
+.I GENERALSEED
+.br
+specify an integer to be used as a seed for random numbers. If you use aevol_propagate repeatedly to initialize several simulations, you should specify a different seed for each simulation, otherwise all simulations will yield exactly the same results. If you specify this general seed, random drawings will be different for all random processes enabled in your simulations (mutations, stochastic gene expression, selection, migration, environmental variation, environmental noise). To change the random drawings for a specific random process only, do not use \-S but the options below.
+.HP
+.B \-s, \-\-sel\-seed
+.I SELSEED
+.br
+specify an integer as a seed for random numbers needed for selection and migration (if spatial structure is enabled).
+.HP
+.B \-m, \-\-mut\-seed
+.I MUTSEED
+.br
+specify an integer as a seed for random numbers needed for mutations.
+.HP
+.B \-t, \-\-stoch\-seed
+.I STOCHSEED
+.br
+specify an integer as a seed for random numbers needed for stochastic gene expression.
+.HP
+.B \-e, \-\-env\-var\-seed
+.I ENVVARSEED
+.br
+specify an integer as a seed for random numbers needed for environmental variation.
+.HP
+.B \-n, \-\-env\-noise\-seed
+.I ENVNOISESEED
+.br
+specify an integer as a seed for random numbers needed for environmental noise.
.SH "SEE ALSO"
.B aevol_create, aevol_run, aevol_modify
Modified: trunk/packages/aevol/trunk/debian/aevol_run.1
===================================================================
--- trunk/packages/aevol/trunk/debian/aevol_run.1 2014-08-26 09:32:42 UTC (rev 17848)
+++ trunk/packages/aevol/trunk/debian/aevol_run.1 2014-08-26 09:32:44 UTC (rev 17849)
@@ -1,39 +1,40 @@
-.TH AEVOL "1" "January 2014" "aevol 4.3" "User Manual"
+/#test with man \-l <file>
+.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
.SH NAME
aevol \- an in silico experimental evolution platform
.SH SYNOPSIS
-.B aevol_run_X11 \-h
+.B aevol_run \-h
|
.B \-\-help
.br
-.B aevol_run_X11 \-V
+.B aevol_run \-V
|
.B \-\-version
.br
-.B aevol_run_X11 \fR[\fB\-r\fI GENERATION\fR] \fR[\fB\-n\fI NB_GENER\fR] \fR[\fB\-tvwx\fR]
+.B aevol_run \fR[\fB\-r\fI GENER\fR] \fR[\fB\-n\fI NB_GENER\fR] \fR[\fB\-tvwx\fR]
.SH DESCRIPTION
.B Aevol
is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
.TP
-.B aevol_run, aevol_run_X11
+.B aevol_run
run an aevol simulation.
.SH OPTIONS
.TP
.B \-h, \-\-help
-print this help, then exit
+print help, then exit
.TP
.B \-V, \-\-version
print version number, then exit
.HP
+.B \-r, \-\-resume
+.I GENER
+.br
+specify generation to resume simulation at (default 0)
+.HP
.B \-n, \-\-nbgener
.I NB_GENER
.br
-number of generations to be run
-.HP
-.B \-r, \-\-resume
-.I GENERATION
-.br
-resume simulation at given generation
+specify number of generations to be run (default 1000)
.TP
.B \-t, \-\-text
use text files instead of binary files when possible
Deleted: trunk/packages/aevol/trunk/debian/aevol_run_X11.1
===================================================================
--- trunk/packages/aevol/trunk/debian/aevol_run_X11.1 2014-08-26 09:32:42 UTC (rev 17848)
+++ trunk/packages/aevol/trunk/debian/aevol_run_X11.1 2014-08-26 09:32:44 UTC (rev 17849)
@@ -1 +0,0 @@
-link aevol_run.1
\ No newline at end of file
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