[med-svn] [Git][med-team/seer][master] 9 commits: d/watch: repair github changes; move to git mode.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Nov 6 14:01:12 GMT 2022
Étienne Mollier pushed to branch master at Debian Med / seer
Commits:
ae9cd59f by Étienne Mollier at 2022-11-06T14:05:14+01:00
d/watch: repair github changes; move to git mode.
- - - - -
bf7c6238 by Étienne Mollier at 2022-11-06T14:06:58+01:00
initialize changelog.
- - - - -
832a30dd by Étienne Mollier at 2022-11-06T14:07:23+01:00
routine-update: Standards-Version: 4.6.1
- - - - -
ec284270 by Étienne Mollier at 2022-11-06T14:09:27+01:00
routine-update: Ready to upload to unstable
- - - - -
a50528ac by Étienne Mollier at 2022-11-06T14:23:06+01:00
typos.patch: add; fix typos caught by lintian.
- - - - -
d1a2fc18 by Étienne Mollier at 2022-11-06T14:52:39+01:00
d/m/blastn_to_phandango.1: new manual page.
- - - - -
99169866 by Étienne Mollier at 2022-11-06T14:57:18+01:00
d/control: add myself to uploaders.
- - - - -
b72f726f by Étienne Mollier at 2022-11-06T14:59:29+01:00
d/copyright: refresh debian/ copyright years.
- - - - -
09022c4a by Étienne Mollier at 2022-11-06T15:00:39+01:00
update changelog.
- - - - -
7 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/mans/blastn_to_phandango.1
- debian/patches/series
- + debian/patches/typos.patch
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+seer (1.1.4-7) unstable; urgency=medium
+
+ * d/watch: repair github changes; move to git mode.
+ * Standards-Version: 4.6.1 (routine-update)
+ * typos.patch: add; fix typos caught by lintian.
+ * d/m/blastn_to_phandango.1: new manual page.
+ * d/control: add myself to uploaders.
+ * d/copyright: refresh debian/ copyright years.
+
+ -- Étienne Mollier <emollier at debian.org> Sun, 06 Nov 2022 15:00:11 +0100
+
seer (1.1.4-6) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -1,6 +1,7 @@
Source: seer
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Étienne Mollier <emollier at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
@@ -11,7 +12,7 @@ Build-Depends: debhelper-compat (= 13),
libgzstream-dev,
libboost-dev,
libboost-program-options-dev
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/seer
Vcs-Git: https://salsa.debian.org/med-team/seer.git
Homepage: https://github.com/johnlees/seer
=====================================
debian/copyright
=====================================
@@ -8,7 +8,10 @@ Copyright: 2015-2016 John Lees <john at johnlees.me>
License: GPL-2+
Files: debian/*
-Copyright: 2016 Andreas Tille <tille at debian.org>
+Copyright: 2016-2020 Andreas Tille <tille at debian.org>
+ 2019 Steffen Möller <moeller at debian.org>
+ 2021 Nilesh Patra <nilesh at debian.org>
+ 2021-2022 Étienne Mollier <emollier at debian.org>
License: GPL-2+
License: GPL-2+
=====================================
debian/mans/blastn_to_phandango.1
=====================================
@@ -0,0 +1,28 @@
+.TH BLASTN_TO_PHANDANGO "1" "November 2022" "Seer 1.1.4" "User Commands"
+.SH NAME
+blastn_to_phandango \- create a plot file for visualisation in phandango
+.SH SYNOPSYS
+.B blastn_to_phandango
+.RB [ -h ]
+.B -b
+.I <blast_file>
+.B -a
+.I <fastlmm_kmers>
+.R >
+.I phandango.plot
+.SH DESCRIPTION
+.PP
+Creates a plot file for visualisation in phandango.
+.SH OPTIONS
+.TP
+\fB-b\fR , \fB--blast\fR
+blast results (required)
+.TP
+\fB-a\fR, \fB--assoc\fR
+fastlmm results (required)
+.TP
+\fB-h\fR, \fB--help\fR
+displays help message
+.SH AUTHOR
+This manpage was written by Étienne Mollier for the Debian distribution.
+It can be used for any other usage of the program.
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
fix_lib_location.patch
hardening.patch
gcc11.patch
+typos.patch
=====================================
debian/patches/typos.patch
=====================================
@@ -0,0 +1,28 @@
+Description: fix typos caught by lintian.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: https://github.com/johnlees/seer/pull/79
+Last-Update: 2022-11-06
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- seer.orig/src/kmdsCmdLine.cpp
++++ seer/src/kmdsCmdLine.cpp
+@@ -38,7 +38,7 @@
+ ("no_filtering", "turn off all filtering and do not output new kmer file")
+ ("max_length", po::value<long int>()->default_value(max_length_default), "maximum kmer length")
+ ("maf", po::value<double>()->default_value(maf_default), "minimum kmer frequency")
+- ("min_words", po::value<int>(), "minimum kmer occurences. Overrides --maf");
++ ("min_words", po::value<int>(), "minimum kmer occurrences. Overrides --maf");
+
+ po::options_description other("Other options");
+ other.add_options()
+--- seer.orig/src/seerCmdLine.cpp
++++ seer/src/seerCmdLine.cpp
+@@ -42,7 +42,7 @@
+ ("no_filtering", "turn off all filtering and perform tests on all kmers input")
+ ("max_length", po::value<long int>()->default_value(max_length_default), "maximum kmer length")
+ ("maf", po::value<double>()->default_value(maf_default), "minimum kmer frequency")
+- ("min_words", po::value<int>(), "minimum kmer occurences. Overrides --maf")
++ ("min_words", po::value<int>(), "minimum kmer occurrences. Overrides --maf")
+ ("chisq", po::value<std::string>()->default_value(chisq_default), "p-value threshold for initial chi squared test. Set to 1 to show all")
+ ("pval", po::value<std::string>()->default_value(pval_default), "p-value threshold for final logistic test. Set to 1 to show all");
+
=====================================
debian/watch
=====================================
@@ -1,3 +1,4 @@
version=4
-
-https://github.com/johnlees/seer/releases .*/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+opts="mode=git,dversionmangle=auto" \
+https://github.com/johnlees/seer.git \
+refs/tags/v(\d[\d.-]+)
View it on GitLab: https://salsa.debian.org/med-team/seer/-/compare/4acb4ebeb3e952ca6f6f5b68243ae05231d005da...09022c4abed2560e5a2bf6bf6021e4277fb6049b
--
View it on GitLab: https://salsa.debian.org/med-team/seer/-/compare/4acb4ebeb3e952ca6f6f5b68243ae05231d005da...09022c4abed2560e5a2bf6bf6021e4277fb6049b
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