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debian/changelog
View file @ d963713f
murasaki (1.68.6-7) unstable; urgency=medium
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.5
* Fix remaining spelling issues
* d/rules: Do not parse d/changelog
-- Andreas Tille <tille@debian.org> Sat, 14 Jul 2018 15:54:27 +0200
murasaki (1.68.6-6) unstable; urgency=medium
[ Gert Wollny ]
......
debian/control
View file @ d963713f
......@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
Uploaders: Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
Build-Depends: debhelper (>= 11~),
libboost-regex-dev,
libboost-iostreams-dev,
libboost-filesystem-dev,
......@@ -12,9 +12,9 @@ Build-Depends: debhelper (>= 9),
libcrypto++-dev,
libpstreams-dev,
libopenmpi-dev
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/murasaki.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/murasaki.git
Standards-Version: 4.1.5
Vcs-Browser: https://salsa.debian.org/med-team/murasaki
Vcs-Git: https://salsa.debian.org/med-team/murasaki.git
Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/
Package: murasaki
......
debian/patches/spelling.patch
View file @ d963713f
......@@ -4,6 +4,24 @@ Description: Spelling fixes
--- a/doc/murasaki.1
+++ b/doc/murasaki.1
@@ -338,7 +338,7 @@ Use gapped (true) or ungapped (false (de
.IP "\-\-scorebyminimumpair <B>" 4
.IX Item "--scorebyminimumpair <B>"
Do anchor scoring by minimum pair when appropriate
-(default). Alternative is arithmatic mean (seldom useful, but
+(default). Alternative is arithmetic mean (seldom useful, but
theoretically faster).
=item \-\-rifts|\-/ <D>
.Sp
@@ -360,7 +360,7 @@ Use gapped (true) or ungapped (false (de
.IP "\-\-scorebyminimumpair <B>" 4
.IX Item "--scorebyminimumpair <B>"
Do anchor scoring by minimum pair when appropriate
-(default). Alternative is arithmatic mean (seldom useful, but
+(default). Alternative is arithmetic mean (seldom useful, but
theoretically faster).
.SS "Output options"
.IX Subsection "Output options"
@@ -521,7 +521,7 @@ over the network (helpful for slow netwo
.IX Item "--mpidistro|-L <B>"
Toggles use of \s-1MPI\s0 to distribute sequence data over (if the sequence
......@@ -24,8 +42,53 @@ Description: Spelling fixes
.IP "If no: distribute storage evently. This more likely to achieve optimal run times, but might not utilize memory as efficiently." 4
.IX Item "If no: distribute storage evently. This more likely to achieve optimal run times, but might not utilize memory as efficiently."
.RE
@@ -628,7 +628,7 @@ this problem.
.SS ".anchors files"
.IX Subsection ".anchors files"
These files are 1 anchor per line, with a 3\-tuple per sequence. Each
-touple represents the start and stop coordinates and strand of the
+tuple represents the start and stop coordinates and strand of the
anchored interval on each sequence. The sequence order matches that of
the order in the .seqs file. The coordinates are structured such that
1 refers to the first base in the sequence, 2 to the second,
@@ -653,7 +653,7 @@ second sequence.
This is an antiquated file format, but used by \s-1GMV\s0 to calculate
statistics like TF-IDF scores, and has been kept around for that
reason. The .anchors.details file has the same format and information
-as the .anchors file, however after the anchor touples are two more
+as the .anchors file, however after the anchor tuples are two more
terms: a score, and a comma (,) delimited list of term and count pairs
(written \*(L"term:count\*(R"). The score and count data might be varied
depending on the \f(CW\*(C`\-\-histogram\*(C'\fR option choices.
@@ -699,7 +699,7 @@ by a blank line. A repeat record looks l
.PP
The first line (always prefixed \*(L"R:\*(R") shows the repeating seed itself
(where the . are the bases masked by the pattern). The subsequent
-lines show where these seeds occured in the input sequences (in the
+lines show where these seeds occurred in the input sequences (in the
first (0) and second (1) sequences). Note that if there are no hits in
a particular sequence, it doesn't include a blank line for that sequence. For example:
.PP
--- a/doc/murasaki.html
+++ b/doc/murasaki.html
@@ -326,7 +326,7 @@ parameter).</p>
<dd>
<p>Do anchor scoring by minimum pair when appropriate
-(default). Alternative is arithmatic mean (seldom useful, but
+(default). Alternative is arithmetic mean (seldom useful, but
theoretically faster).
=item --rifts|-/ &lt;D&gt;</p>
<p>Allow anchors to skip D sequences (default 0).</p>
@@ -357,7 +357,7 @@ parameter).</p>
<dd>
<p>Do anchor scoring by minimum pair when appropriate
-(default). Alternative is arithmatic mean (seldom useful, but
+(default). Alternative is arithmetic mean (seldom useful, but
theoretically faster).</p>
</dd>
</dl>
@@ -606,7 +606,7 @@ is too high.</p>
<dt><strong><a name="memorybalance_a_b" class="item">--memorybalance|-a &lt;B&gt;</a></strong></dt>
......@@ -35,8 +98,53 @@ Description: Spelling fixes
the amount of available ram.</strong></dt>
<dt><strong><a name="if_no_distribute_storage_evently_this_more_likely_to_achieve_optimal_run_times_but_might_not_utilize_memory_as_efficiently" class="item">If no: distribute storage evently. This more likely to achieve
@@ -697,7 +697,7 @@ this problem.</p>
</p>
<h2><a name="_anchors_files">.anchors files</a></h2>
<p>These files are 1 anchor per line, with a 3-tuple per sequence. Each
-touple represents the start and stop coordinates and strand of the
+tuple represents the start and stop coordinates and strand of the
anchored interval on each sequence. The sequence order matches that of
the order in the .seqs file. The coordinates are structured such that
1 refers to the first base in the sequence, 2 to the second,
@@ -719,7 +719,7 @@ second sequence.</p>
<p>This is an antiquated file format, but used by <em>GMV</em> to calculate
statistics like TF-IDF scores, and has been kept around for that
reason. The .anchors.details file has the same format and information
-as the .anchors file, however after the anchor touples are two more
+as the .anchors file, however after the anchor tuples are two more
terms: a score, and a comma (,) delimited list of term and count pairs
(written &quot;term:count&quot;). The score and count data might be varied
depending on the <a href="#histogram"><code>--histogram</code></a> option choices.</p>
@@ -764,7 +764,7 @@ by a blank line. A repeat record looks l
1: 2480929222 -1874514626 2543723555 -2550045172</pre>
<p>The first line (always prefixed &quot;R:&quot;) shows the repeating seed itself
(where the . are the bases masked by the pattern). The subsequent
-lines show where these seeds occured in the input sequences (in the
+lines show where these seeds occurred in the input sequences (in the
first (0) and second (1) sequences). Note that if there are no hits in
a particular sequence, it doesn't include a blank line for that sequence. For example:</p>
<pre>
--- a/doc/murasaki.pod
+++ b/doc/murasaki.pod
@@ -233,7 +233,7 @@ Use gapped (true) or ungapped (false (de
=item --scorebyminimumpair <B>
Do anchor scoring by minimum pair when appropriate
-(default). Alternative is arithmatic mean (seldom useful, but
+(default). Alternative is arithmetic mean (seldom useful, but
theoretically faster).
=item --rifts|-/ <D>
@@ -260,7 +260,7 @@ Use gapped (true) or ungapped (false (de
=item --scorebyminimumpair <B>
Do anchor scoring by minimum pair when appropriate
-(default). Alternative is arithmatic mean (seldom useful, but
+(default). Alternative is arithmetic mean (seldom useful, but
theoretically faster).
=back
@@ -486,7 +486,7 @@ Assign hashers to large memory nodes fir
=over
......@@ -46,8 +154,53 @@ Description: Spelling fixes
the amount of available ram.
=item If no: distribute storage evently. This more likely to achieve
@@ -577,7 +577,7 @@ this problem.
=head2 .anchors files
These files are 1 anchor per line, with a 3-tuple per sequence. Each
-touple represents the start and stop coordinates and strand of the
+tuple represents the start and stop coordinates and strand of the
anchored interval on each sequence. The sequence order matches that of
the order in the .seqs file. The coordinates are structured such that
1 refers to the first base in the sequence, 2 to the second,
@@ -601,7 +601,7 @@ second sequence.
This is an antiquated file format, but used by L<GMV> to calculate
statistics like TF-IDF scores, and has been kept around for that
reason. The .anchors.details file has the same format and information
-as the .anchors file, however after the anchor touples are two more
+as the .anchors file, however after the anchor tuples are two more
terms: a score, and a comma (,) delimited list of term and count pairs
(written "term:count"). The score and count data might be varied
depending on the C<--histogram> option choices.
@@ -648,7 +648,7 @@ by a blank line. A repeat record looks l
The first line (always prefixed "R:") shows the repeating seed itself
(where the . are the bases masked by the pattern). The subsequent
-lines show where these seeds occured in the input sequences (in the
+lines show where these seeds occurred in the input sequences (in the
first (0) and second (1) sequences). Note that if there are no hits in
a particular sequence, it doesn't include a blank line for that sequence. For example:
--- a/doc/murasaki.txt
+++ b/doc/murasaki.txt
@@ -200,7 +200,7 @@ OPTIONS
--scorebyminimumpair <B>
Do anchor scoring by minimum pair when appropriate (default).
- Alternative is arithmatic mean (seldom useful, but theoretically
+ Alternative is arithmetic mean (seldom useful, but theoretically
faster). =item --rifts|-/ <D>
Allow anchors to skip D sequences (default 0).
@@ -221,7 +221,7 @@ OPTIONS
--scorebyminimumpair <B>
Do anchor scoring by minimum pair when appropriate (default).
- Alternative is arithmatic mean (seldom useful, but theoretically
+ Alternative is arithmetic mean (seldom useful, but theoretically
faster).
Output options
@@ -372,7 +372,7 @@ OPTIONS
--memorybalance|-a <B>
......@@ -57,6 +210,33 @@ Description: Spelling fixes
amount of available ram.
If no: distribute storage evently. This more likely to achieve
optimal run times, but might not utilize memory as efficiently.
@@ -428,7 +428,7 @@ FILE FORMATS
.anchors files
These files are 1 anchor per line, with a 3-tuple per sequence. Each
- touple represents the start and stop coordinates and strand of the
+ tuple represents the start and stop coordinates and strand of the
anchored interval on each sequence. The sequence order matches that of
the order in the .seqs file. The coordinates are structured such that 1
refers to the first base in the sequence, 2 to the second, etc. Negative
@@ -450,7 +450,7 @@ FILE FORMATS
This is an antiquated file format, but used by GMV to calculate
statistics like TF-IDF scores, and has been kept around for that reason.
The .anchors.details file has the same format and information as the
- .anchors file, however after the anchor touples are two more terms: a
+ .anchors file, however after the anchor tuples are two more terms: a
score, and a comma (,) delimited list of term and count pairs (written
"term:count"). The score and count data might be varied depending on the
"--histogram" option choices.
@@ -493,7 +493,7 @@ FILE FORMATS
The first line (always prefixed "R:") shows the repeating seed itself
(where the . are the bases masked by the pattern). The subsequent lines
- show where these seeds occured in the input sequences (in the first (0)
+ show where these seeds occurred in the input sequences (in the first (0)
and second (1) sequences). Note that if there are no hits in a
particular sequence, it doesn't include a blank line for that sequence.
For example:
--- a/src/murasaki.cc
+++ b/src/murasaki.cc
@@ -303,7 +303,7 @@ void MurasakiRuntime::prep(){
......@@ -90,3 +270,14 @@ Description: Spelling fixes
but they do affect the visible range, and thus causes some scrunching.
"--showall=scale" manually sets to the X and Y ranges to the range of the
data (so 1's are visibly different from 0's).
--- a/simpal.pl
+++ b/simpal.pl
@@ -272,7 +272,7 @@ simpal.pl [options] <ref seq> <target se
maxLoop -- specifies max separation for the ends of the palindromes
maxDistance -- specifies the maximum difference in palindrome length
when comparing palindromes
-tolerance -- max permissable misses in palindromes between sequences
+tolerance -- max permissible misses in palindromes between sequences
Setting either to -1 means no limit
debian/rules
View file @ d963713f
......@@ -3,11 +3,12 @@
# Copyright 2015 Andreas Tille
# GPL
DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
DEBMEDBIN := debian/$(DEBPKGNAME)-common/usr/lib/debian-med/bin
MANDIR := debian/$(DEBPKGNAME)/usr/share/man/man1
CMANDIR := debian/$(DEBPKGNAME)-common/usr/share/man/man1
MMANDIR := debian/$(DEBPKGNAME)-mpi/usr/share/man/man1
include /usr/share/dpkg/default.mk
DEBMEDBIN := debian/$(DEB_SOURCE)-common/usr/lib/debian-med/bin
MANDIR := debian/$(DEB_SOURCE)/usr/share/man/man1
CMANDIR := debian/$(DEB_SOURCE)-common/usr/share/man/man1
MMANDIR := debian/$(DEB_SOURCE)-mpi/usr/share/man/man1
# export DEB_BUILD_MAINT_OPTIONS = hardening=+all
# leads to linking failure:
......@@ -44,8 +45,8 @@ override_dh_link:
override_dh_install-arch:
dh_install -a
# using wildcards in install files is practical but it duplicates some files
find debian/$(DEBPKGNAME)/usr -name "*-mpi" -delete
find debian/$(DEB_SOURCE)/usr -name "*-mpi" -delete
override_dh_fixperms-indep:
dh_fixperms -i
chmod a+x debian/$(DEBPKGNAME)-common/usr/share/perl5/murasaki/config.pl
chmod a+x debian/$(DEB_SOURCE)-common/usr/share/perl5/murasaki/config.pl