[med-svn] [Git][med-team/murasaki][master] 6 commits: debhelper 11
Andreas Tille
gitlab at salsa.debian.org
Sat Jul 14 15:01:56 BST 2018
Andreas Tille pushed to branch master at Debian Med / murasaki
Commits:
e5bac3e1 by Andreas Tille at 2018-07-14T09:23:08+02:00
debhelper 11
- - - - -
649aedbc by Andreas Tille at 2018-07-14T09:23:11+02:00
Point Vcs fields to salsa.debian.org
- - - - -
197362d6 by Andreas Tille at 2018-07-14T09:23:11+02:00
Standards-Version: 4.1.5
- - - - -
5dfa90a0 by Andreas Tille at 2018-07-14T15:48:15+02:00
Fix remaining spelling issues
- - - - -
3f04adbf by Andreas Tille at 2018-07-14T15:54:21+02:00
Do not parse d/changelog
- - - - -
d963713f by Andreas Tille at 2018-07-14T15:58:53+02:00
Upload to unstable
- - - - -
5 changed files:
- debian/changelog
- debian/compat
- debian/control
- debian/patches/spelling.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,13 @@
+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 at debian.org> Sat, 14 Jul 2018 15:54:27 +0200
+
murasaki (1.68.6-6) unstable; urgency=medium
[ Gert Wollny ]
=====================================
debian/compat
=====================================
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+11
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at 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
=====================================
--- a/debian/patches/spelling.patch
+++ b/debian/patches/spelling.patch
@@ -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|-/ <D></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 <B></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 "term:count"). 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 "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:</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
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -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
View it on GitLab: https://salsa.debian.org/med-team/murasaki/compare/f70f15204db1582601977c87b7e24630248b8367...d963713feafb191ef4e34b254ef15b59bf10b0e6
--
View it on GitLab: https://salsa.debian.org/med-team/murasaki/compare/f70f15204db1582601977c87b7e24630248b8367...d963713feafb191ef4e34b254ef15b59bf10b0e6
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