[med-svn] [phyml] 01/02: Do not build phytime since it is not supported any more
Andreas Tille
tille at debian.org
Tue Jun 27 13:24:17 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository phyml.
commit d1686531247f8221765a19b889172b15ce151185
Author: Andreas Tille <tille at debian.org>
Date: Tue Jun 27 15:06:48 2017 +0200
Do not build phytime since it is not supported any more
---
debian/changelog | 1 +
debian/phytime.1 | 173 -------------------------------------------------------
debian/rules | 2 +
3 files changed, 3 insertions(+), 173 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 3d70393..8da3efd 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -5,6 +5,7 @@ phyml (3:3.3.20170530+dfsg-1) UNRELEASED; urgency=medium
* Standards-Version: 4.0.0 (no changes needed)
* Do not disable PIE
Closes: #865654
+ * Do not build phytime since it is not supported any more
-- Andreas Tille <tille at debian.org> Tue, 27 Jun 2017 13:20:47 +0200
diff --git a/debian/phytime.1 b/debian/phytime.1
deleted file mode 100644
index fd512aa..0000000
--- a/debian/phytime.1
+++ /dev/null
@@ -1,173 +0,0 @@
-.TH PHYTIME "1" "July 2013" "phytime " "User Commands"
-.SH NAME
-phytime \- Bayesian estimation of divergence times from large sequence alignments
-.SH DESCRIPTION
-Bayesian estimation of divergence times from molecular sequences relies
-on sophisticated Markov chain Monte Carlo techniques, and
-Metropolis-Hastings (MH) samplers have been successfully used in that
-context. This approach involves heavy computational burdens that can
-hinder the analysis of large phylogenomic data sets. Reliable estimation
-of divergence times can also be extremely time consuming, if not
-impossible, for sequence alignments that convey weak or conflicting
-phylogenetic signals, emphasizing the need for more efficient sampling
-methods. This article describes a new approach that estimates the
-posterior density of substitution rates and node times. The prior
-distribution of rates accounts for their potential autocorrelation along
-lineages, whereas priors on node ages are modeled with uniform
-densities. Also, the likelihood function is approximated by a
-multivariate normal density. The combination of these components leads
-to convenient mathematical simplifications, allowing the posterior
-distribution of rates and times to be estimated using a Gibbs sampling
-algorithm. The analysis of four real-world data sets shows that this
-sampler outperforms the standard MH approach and demonstrates the
-suitability of this new method for analyzing large and/or difficult data
-sets.
-.SH SYNOPSIS
-.B phytime
-[command args]
-.SH OPTIONS
-All the options below are optional except '\-i','\-u' and '\-\-calibration'.
-.PP
-Command options:
-.IP
-\-i (or \fB\-\-input\fR) seq_file_name
-.IP
-seq_file_name is the name of the nucleotide or amino\-acid sequence file in PHYLIP format.
-.PP
-
-.HP
-\fB\-d\fR (or \fB\-\-datatype\fR) data_type
-.IP
-data_type is 'nt' for nucleotide (default), 'aa' for amino\-acid sequences, or 'generic',
-(use NEXUS file format and the 'symbols' parameter here).
-.PP
-
-.HP
-\fB\-q\fR (or \fB\-\-sequential\fR)
-.PP
- Changes interleaved format (default) to sequential format.
-.PP
-
-.HP
-\fB\-m\fR (or \fB\-\-model\fR) model
-.IP
-model : substitution model name.
-\- Nucleotide\-based models : HKY85 (default) | JC69 | K80 | F81 | F84 | TN93 | GTR | custom (*)
-(*) : for the custom option, a string of six digits identifies the model. For instance, 000000
-.IP
-corresponds to F81 (or JC69 provided the distribution of nucleotide frequencies is uniform).
-012345 corresponds to GTR. This option can be used for encoding any model that is a nested within GTR.
-.IP
-\- Amino\-acid based models : LG (default) | WAG | JTT | MtREV | Dayhoff | DCMut | RtREV | CpREV | VT
-.TP
-Blosum62 | MtMam | MtArt | HIVw |
-HIVb | custom
-.PP
-
-.HP
-\fB\-\-aa_rate_file\fR filename
-.IP
-filename is the name of the file that provides the amino acid substitution rate matrix in PAML format.
-It is compulsory to use this option when analysing amino acid sequences with the `custom' model.
-.PP
-
-.HP
-\fB\-\-calibration\fR filename
-.IP
-filename is the name of the calibration file that provides a priori defined boundaries for node ages.
-Please read the manual for more information about the format of this file.
-.PP
-
-.HP
-\fB\-t\fR (or \fB\-\-ts\fR/tv) ts/tv_ratio
-.IP
-ts/tv_ratio : transition/transversion ratio. DNA sequences only.
-Can be a fixed positive value (ex:4.0) or e to get the maximum likelihood estimate.
-.PP
-
-.HP
-\fB\-v\fR (or \fB\-\-pinv\fR) prop_invar
-.IP
-prop_invar : proportion of invariable sites.
-Can be a fixed value in the [0,1] range or e to get the maximum likelihood estimate.
-.PP
-
-.HP
-\fB\-c\fR (or \fB\-\-nclasses\fR) nb_subst_cat
-.IP
-nb_subst_cat : number of relative substitution rate categories. Default : nb_subst_cat=4.
-Must be a positive integer.
-.PP
-
-.HP
-\fB\-a\fR (or \fB\-\-alpha\fR) gamma
-.IP
-gamma : distribution of the gamma distribution shape parameter.
-Can be a fixed positive value or e to get the maximum likelihood estimate.
-.PP
-
-.HP
-\fB\-u\fR (or \fB\-\-inputtree\fR) user_tree_file
-.IP
-user_tree_file : starting tree filename. The tree must be in Newick format.
-.PP
-
-.HP
-\fB\-\-r_seed\fR num
-.IP
-num is the seed used to initiate the random number generator.
-Must be an integer.
-.PP
-
-.HP
-\fB\-\-run_id\fR ID_string
-.IP
-Append the string ID_string at the end of each PhyML output file.
-This option may be useful when running simulations involving PhyML.
-.PP
-
-.HP
-\fB\-\-quiet\fR
-.IP
-No interactive question (for running in batch mode) and quiet output.
-.PP
-
-.HP
-\fB\-\-no_memory_check\fR
-.IP
-No interactive question for memory usage (for running in batch mode). Normal output otherwise.
-.PP
-
-.HP
-\fB\-\-chain_len\fR num
-.IP
-num is the number of generations or runs of the Markov Chain Monte Carlo. Set to 1E+6 by default.
-Must be an integer.
-.PP
-
-.HP
-\fB\-\-sample_freq\fR num
-.IP
-The chain is sampled every num generations. Set to 1E+3 by default.
-Must be an integer.
-.PP
-
-.HP
-\fB\-\-no_data\fR
-.IP
-Use this option to sample from the priors only (rather from the posterior joint density
-of the model parameters).
-.PP
-
-.HP
-\fB\-\-fastlk\fR
-.IP
-Use the multivariate normal approximation to the likelihood and speed up calculations
-.SH SEE ALSO
-.PP
- 'Bayesian estimation of divergence times from large sequence alignments.'
- Stephane Guindon,
- Molecular Biology and Evolution 27(8):1768\-81, 2010.
-.PP
- Please cite this paper if you use this software in your publications.
-
diff --git a/debian/rules b/debian/rules
index ec6e68b..e2cdf36 100755
--- a/debian/rules
+++ b/debian/rules
@@ -40,9 +40,11 @@ endif
# move phyml binary to temporary dir inside debian/
# mkdir -p $(CURDIR)/debian/bin
mv src/phyml-mpi $(CURDIR)/debian/bin/phyml-mpi
+ifeq ($(BUILDPHYTIME), 'yes')
$(MAKE) distclean
dh_auto_configure -- --enable-phytime
dh_auto_build -- LDFLAGS="$(LDFLAGS)" CPPFLAGS="-DPHYREX $(CPPFLAGS)"
+endif
mv phyml-manual.pdf doc
override_dh_auto_install:
--
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