[med-svn] [Git][med-team/prank][master] 6 commits: Team upload.
Charles Plessy (@plessy)
gitlab at salsa.debian.org
Fri Sep 5 02:08:54 BST 2025
Charles Plessy pushed to branch master at Debian Med / prank
Commits:
e9d2c9ba by Charles Plessy at 2025-09-05T09:57:03+09:00
Team upload.
* Team upload.
* Packaging update
- - - - -
299effb0 by Charles Plessy at 2025-09-05T09:57:03+09:00
Standards-Version: 4.7.2 (routine-update)
- - - - -
c23bab72 by Charles Plessy at 2025-09-05T09:57:18+09:00
debputy lint --auto-fix (routine-update)
- - - - -
5d501ecf by Charles Plessy at 2025-09-05T09:57:20+09:00
watch file standard 4 (routine-update)
- - - - -
7550aeae by Charles Plessy at 2025-09-05T09:58:29+09:00
routine-update: Ready to upload to unstable
- - - - -
640c65fa by Charles Plessy at 2025-09-05T10:07:18+09:00
Do not release yet.
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/watch
- − src/prank.1
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+prank (0.0.170427+dfsg-4) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Packaging update
+ * Standards-Version: 4.7.2 (routine-update)
+ * debputy lint --auto-fix (routine-update)
+ * watch file standard 4 (routine-update)
+
+ -- Charles Plessy <plessy at debian.org> Fri, 05 Sep 2025 09:57:21 +0900
+
prank (0.0.170427+dfsg-3) unstable; urgency=medium
* Standards-Version: 4.5.0 (routine-update)
=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Uploaders: Manuel Prinz <manuel at debian.org>,
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13)
-Standards-Version: 4.5.0
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/prank
Vcs-Git: https://salsa.debian.org/med-team/prank.git
Homepage: http://wasabiapp.org/software/prank/
=====================================
debian/copyright
=====================================
@@ -2,7 +2,7 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: prank-msa
Upstream-Contact: Ari Loytynoja <ari.loytynoja at helsinki.fi>
Source: http://wasabiapp.org/download/prank/
-Files-Excluded: .git
+Files-Excluded: .git/*
Files: *
Copyright: © 2005-2015 Ari Loytynoja <ari.loytynoja at gmail.com>
=====================================
debian/watch
=====================================
@@ -1,3 +1,3 @@
-version=3
+version=4
opts="uversionmangle=s/^/0.0./,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
http://wasabiapp.org/download/prank/ prank\.source\.(\d+)\.tgz
=====================================
src/prank.1 deleted
=====================================
@@ -1,230 +0,0 @@
-.\" Automatically generated by Pod::Man 2.28 (Pod::Simple 3.29)
-.\"
-.\" Standard preamble:
-.\" ========================================================================
-.de Sp \" Vertical space (when we can't use .PP)
-.if t .sp .5v
-.if n .sp
-..
-.de Vb \" Begin verbatim text
-.ft CW
-.nf
-.ne \\$1
-..
-.de Ve \" End verbatim text
-.ft R
-.fi
-..
-.\" Set up some character translations and predefined strings. \*(-- will
-.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
-.\" double quote, and \*(R" will give a right double quote. \*(C+ will
-.\" give a nicer C++. Capital omega is used to do unbreakable dashes and
-.\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff,
-.\" nothing in troff, for use with C<>.
-.tr \(*W-
-.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
-.ie n \{\
-. ds -- \(*W-
-. ds PI pi
-. if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
-. if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch
-. ds L" ""
-. ds R" ""
-. ds C` ""
-. ds C' ""
-'br\}
-.el\{\
-. ds -- \|\(em\|
-. ds PI \(*p
-. ds L" ``
-. ds R" ''
-. ds C`
-. ds C'
-'br\}
-.\"
-.\" Escape single quotes in literal strings from groff's Unicode transform.
-.ie \n(.g .ds Aq \(aq
-.el .ds Aq '
-.\"
-.\" If the F register is turned on, we'll generate index entries on stderr for
-.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
-.\" entries marked with X<> in POD. Of course, you'll have to process the
-.\" output yourself in some meaningful fashion.
-.\"
-.\" Avoid warning from groff about undefined register 'F'.
-.de IX
-..
-.nr rF 0
-.if \n(.g .if rF .nr rF 1
-.if (\n(rF:(\n(.g==0)) \{
-. if \nF \{
-. de IX
-. tm Index:\\$1\t\\n%\t"\\$2"
-..
-. if !\nF==2 \{
-. nr % 0
-. nr F 2
-. \}
-. \}
-.\}
-.rr rF
-.\" ========================================================================
-.\"
-.IX Title "PRANK 1"
-.TH PRANK 1 "2017-04-27" "v.121211" "The Probabilistic Alignment Kit"
-.\" For nroff, turn off justification. Always turn off hyphenation; it makes
-.\" way too many mistakes in technical documents.
-.if n .ad l
-.nh
-.SH "NAME"
-prank \- Computes probabilistic multiple sequence alignments
-.SH "SYNOPSIS"
-.IX Header "SYNOPSIS"
-\&\fBprank\fR \fIsequence_file\fR
-.PP
-\&\fBprank\fR [optional parameters] \-d=\fIsequence_file\fR [optional parameters]
-.SH "DESCRIPTION"
-.IX Header "DESCRIPTION"
-The Probabilistic Alignment Kit (\s-1PRANK\s0) is a probabilistic multiple alignment
-program for \s-1DNA,\s0 codon and amino-acid sequences. It's based on a novel algorithm
-that treats insertions correctly and avoids over-estimation of the number of
-deletion events.
-.PP
-In addition, \s-1PRANK\s0 borrows ideas from maximum likelihood methods used in
-phylogenetics and correctly takes into account the evolutionary distances
-between sequences. Lastly, \s-1PRANK\s0 allows for defining a potential structure for
-sequences to be aligned and then, simultaneously with the alignment, predicts
-the locations of structural units in the sequences.
-.SH "OPTIONS"
-.IX Header "OPTIONS"
-.SS "\s-1INPUT/OUTPUT PARAMETERS\s0"
-.IX Subsection "INPUT/OUTPUT PARAMETERS"
-.IP "\fB\-d=\f(BIsequence_file\fB\fR" 8
-.IX Item "-d=sequence_file"
-The input sequence file in \s-1FASTA\s0 format.
-.IP "\fB\-t=\f(BItree_file\fB\fR" 8
-.IX Item "-t=tree_file"
-The tree file to use. If unset, an appriximated \s-1NJ\s0 tree is generated.
-.IP "\fB\-o=\f(BIoutput_file\fB\fR" 8
-.IX Item "-o=output_file"
-Set the name of the output file. If unset, \fIoutput_file\fR is set to \fBoutput\fR.
-.IP "\fB\-f=\f(BIoutput_format\fB\fR" 8
-.IX Item "-f=output_format"
-Set the output format. \fIoutput_format\fR can be one of \fBfasta\fR (default),
-\&\fBphylipi\fR, \fBphylips\fR, \fBpaml\fR, or \fBnexus\fR.
-.IP "\fB\-m=\f(BImodel_file\fB\fR" 8
-.IX Item "-m=model_file"
-The model file to use. If unset, \fImodel_file\fR is set to \fB\s-1HKY2/WAG\s0\fR.
-.IP "\fB\-support\fR" 8
-.IX Item "-support"
-Compute posterior support.
-.IP "\fB\-showxml\fR" 8
-.IX Item "-showxml"
-Output alignment xml-file.
-.IP "\fB\-showtree\fR" 8
-.IX Item "-showtree"
-Output alignment guidetree.
-.IP "\fB\-showanc\fR" 8
-.IX Item "-showanc"
-Output ancestral sequences.
-.IP "\fB\-showall\fR" 8
-.IX Item "-showall"
-Output all of these.
-.IP "\fB\-noanchors\fR" 8
-.IX Item "-noanchors"
-Do not use Exonerate anchoring. (Exonerate to be installed separately.)
-.IP "\fB\-nomafft\fR" 8
-.IX Item "-nomafft"
-Do not use \s-1MAFFT\s0 for guide tree. (\s-1MAFFT\s0 to be installed separately.)
-.IP "\fB\-njtree\fR" 8
-.IX Item "-njtree"
-Estimate tree from an input alignment (and realign).
-.IP "\fB\-shortnames\fR" 8
-.IX Item "-shortnames"
-Truncate names at first space character.
-.IP "\fB\-quiet\fR" 8
-.IX Item "-quiet"
-Reduce output.
-.SS "\s-1ALIGNMENT MERGE\s0"
-.IX Subsection "ALIGNMENT MERGE"
-.IP "\fB\-d1=\f(BIalignment_file\fB\fR" 8
-.IX Item "-d1=alignment_file"
-The first input alignment file in \s-1FASTA\s0 format.
-.IP "\fB\-d2=\f(BIalignment_file\fB\fR" 8
-.IX Item "-d2=alignment_file"
-The second input alignment file in \s-1FASTA\s0 format.
-.IP "\fB\-t1=\f(BItree_file\fB\fR" 8
-.IX Item "-t1=tree_file"
-The tree file for the first alignment. If unset, an appriximated \s-1NJ\s0 tree is generated.
-.IP "\fB\-t2=\f(BItree_file\fB\fR" 8
-.IX Item "-t2=tree_file"
-The tree file for the second alignment. If unset, an appriximated \s-1NJ\s0 tree is generated.
-.SS "\s-1MODEL PARAMETERS\s0"
-.IX Subsection "MODEL PARAMETERS"
-.IP "\fB\-F\fR, \fB+F\fR" 8
-.IX Item "-F, +F"
-Force insertions to be always skipped.
-.IP "\fB\-gaprate=\f(BI#\fB\fR" 8
-.IX Item "-gaprate=#"
-Set the gap opening rate. The default is \fB0.025\fR for \s-1DNA\s0 and \fB0.005\fR for
-proteins.
-.IP "\fB\-gapext=\f(BI#\fB\fR" 8
-.IX Item "-gapext=#"
-Set the gap extension probability. The default is \fB0.75\fR for \s-1DNA\s0 and \fB0.5\fR for
-proteins.
-.IP "\fB\-codon\fR" 8
-.IX Item "-codon"
-Use empirical codon model for coding \s-1DNA.\s0
-.IP "\fB\-DNA\fR, \fB\-protein\fR" 8
-.IX Item "-DNA, -protein"
-Use \s-1DNA\s0 or protein model, respectively. Disables auto-detection of model.
-.IP "\fB\-termgap\fR" 8
-.IX Item "-termgap"
-Penalise terminal gaps normally.
-.IP "\fB\-nomissing\fR" 8
-.IX Item "-nomissing"
-No missing data. Use \fB\-F\fR for terminal gaps.
-.IP "\fB\-keep\fR" 8
-.IX Item "-keep"
-Do not remove gaps from pre-aligned sequences.
-.SS "\s-1OTHER PARAMETERS\s0"
-.IX Subsection "OTHER PARAMETERS"
-.IP "\fB\-iterate=#\fR" 8
-.IX Item "-iterate=#"
-Rounds of re-alignment iteration; by default, iterate five times and keep the best result.
-.IP "\fB\-once\fR" 8
-.IX Item "-once"
-Run only once. Same as \-iterate=1.
-.IP "\fB\-prunetree\fR" 8
-.IX Item "-prunetree"
-Prune guide tree branches with no sequence data.
-.IP "\fB\-prunedata\fR" 8
-.IX Item "-prunedata"
-Prune sequence data with no guide tree leaves.
-.IP "\fB\-uselogs\fR" 8
-.IX Item "-uselogs"
-Slower but should work for a greater number of sequences.
-.IP "\fB\-translate\fR" 8
-.IX Item "-translate"
-Translate input data to protein sequences.
-.IP "\fB\-mttranslate\fR" 8
-.IX Item "-mttranslate"
-Translate input data to protein sequencess using mt table.
-.IP "\fB\-convert\fR" 8
-.IX Item "-convert"
-Do not align, just convert to a different format.
-.IP "\fB\-dna=\f(BIdna_sequence_file\fB\fR" 8
-.IX Item "-dna=dna_sequence_file"
-\&\s-1DNA\s0 sequence file for backtranslation of protein alignment.
-.IP "\fB\-help\fR" 8
-.IX Item "-help"
-Show an extended help page with more options.
-.IP "\fB\-version\fR" 8
-.IX Item "-version"
-Show version and check for updates.
-.SH "AUTHORS"
-.IX Header "AUTHORS"
-\&\fBprank\fR was written by Ari Loytynoja.
-.PP
-This manual page was originally written by Manuel Prinz <manuel at debian.org> for
-the Debian project (and may be used by others).
View it on GitLab: https://salsa.debian.org/med-team/prank/-/compare/028109aa4e3d58151b33db8ef0ed1c9e7a0db544...640c65fa93051ada897947b574541d1743ce00aa
--
View it on GitLab: https://salsa.debian.org/med-team/prank/-/compare/028109aa4e3d58151b33db8ef0ed1c9e7a0db544...640c65fa93051ada897947b574541d1743ce00aa
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