[med-svn] [Git][med-team/pftools][master] 6 commits: Remove man/* from debian/manpages
Nilesh Patra
gitlab at salsa.debian.org
Fri Dec 18 08:32:11 GMT 2020
Nilesh Patra pushed to branch master at Debian Med / pftools
Commits:
7d59f3fc by Nilesh Patra at 2020-12-18T07:38:29+00:00
Remove man/* from debian/manpages
This is so because the CMakeLists.txt in man/ already seems to install
manpages at the right place.
Hence re-copying man/* leads to error
- - - - -
265814a1 by Nilesh Patra at 2020-12-18T07:39:49+00:00
Remove duplicate manpage (already present in man/)
- - - - -
f11be1e5 by Nilesh Patra at 2020-12-18T07:42:12+00:00
dh_auto_clean Clean remaining stuff
- - - - -
1cb322c7 by Nilesh Patra at 2020-12-18T13:59:48+05:30
Remove useless files, move docs to correct place
- - - - -
647a6b41 by Nilesh Patra at 2020-12-18T14:00:08+05:30
Really fix perl interpreter path
- - - - -
8288094a by Nilesh Patra at 2020-12-18T14:01:28+05:30
Update changelog
- - - - -
6 changed files:
- debian/changelog
- debian/manpages
- debian/patches/fix_perl_interpreter.patch
- debian/patches/series
- − debian/pfsearch.1
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,8 +1,6 @@
pftools (3.2.6-1) UNRELEASED; urgency=medium
- [ Nilesh Patra ]
- * Fix gcc-10 FTBFS
-
+ * Team Upload.
[ Andreas Tille ]
* Fix watch file and homepage
* New upstream version
@@ -19,7 +17,14 @@ pftools (3.2.6-1) UNRELEASED; urgency=medium
* Force sequential execution of tests
* No need to replace [gh]top any more in examples
- -- Andreas Tille <tille at debian.org> Tue, 24 Nov 2020 21:17:21 +0100
+ [ Nilesh Patra ]
+ * Remove man/* from debian/manpages
+ * Remove duplicate manpage (already present in man/)
+ * dh_auto_clean Clean remaining stuff
+ * Remove useless files, move docs to correct place
+ * Really fix perl interpreter path
+
+ -- Nilesh Patra <npatra974 at gmail.com> Fri, 18 Dec 2020 14:00:23 +0530
pftools (3+dfsg-3) unstable; urgency=medium
=====================================
debian/manpages
=====================================
@@ -1,2 +1 @@
-# man/*
-debian/*.1
\ No newline at end of file
+debian/*.1
=====================================
debian/patches/fix_perl_interpreter.patch
=====================================
@@ -1,11 +1,11 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 24 Nov 2020 21:17:21 +0100
+Author: Andreas Tille <tille at debian.org>, Nilesh Patra <npatra974 at gmail.com>
+Last-Update: Fri, 18 Dec 2020 13:33:50 +0530
Description: Fix interpreter of perl script to fix build time test
--- a/src/Perl/sort_fasta.pl
+++ b/src/Perl/sort_fasta.pl
@@ -1,4 +1,4 @@
--#!/bin/env perl
+-#!/usr/bin/env perl
+#!/usr/bin/perl
use strict;
@@ -13,8 +13,64 @@ Description: Fix interpreter of perl script to fix build time test
--- a/src/Perl/make_iupac_cmp.pl
+++ b/src/Perl/make_iupac_cmp.pl
@@ -1,4 +1,4 @@
--#!/bin/env perl
+-#!/usr/bin/env perl
+#!/usr/bin/perl
use strict;
use Getopt::Std;
+--- a/src/Perl/compare_2_profiles.pl
++++ b/src/Perl/compare_2_profiles.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ # Perl embedded modules
+ use strict;
+--- a/src/Perl/ps_scan.pl
++++ b/src/Perl/ps_scan.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ # ps_scan - a PROSITE scanning program
+ #
+--- a/src/Perl/scramble_fasta.pl
++++ b/src/Perl/scramble_fasta.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ use strict;
+
+--- a/src/Perl/split_profile_file.pl
++++ b/src/Perl/split_profile_file.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ # Perl embedded modules
+ use strict;
+--- a/src/Perl/fasta_to_fastq.pl
++++ b/src/Perl/fasta_to_fastq.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+ #Copyright (c) 2010 LUQMAN HAKIM BIN ABDUL HADI (csilhah at nus.edu.sg)
+ #
+ #Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files
+--- a/tests/examples/test_pfsearchV3_iupac.pl.cmake
++++ b/tests/examples/test_pfsearchV3_iupac.pl.cmake
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ use strict;
+
+--- a/tests/examples/test_scan_search.pl.cmake
++++ b/tests/examples/test_scan_search.pl.cmake
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ use strict;
+
=====================================
debian/patches/series
=====================================
@@ -1,4 +1,4 @@
spelling.patch
-# fix_perl_interpreter.patch
0001-Harmonize-bin-env-path-Cleaning.patch
+fix_perl_interpreter.patch
destdir_for_examples.patch
=====================================
debian/pfsearch.1 deleted
=====================================
@@ -1,67 +0,0 @@
-.TH PFSEARCH "1" "March 2017" "pfsearch 3" "User Commands"
-.SH NAME
-pfsearch \- search protein and DNA generalized profiles (legacy)
-.SH SYNOPSIS
-.B pfsearch
-[ \fI\,-abCdfhlLmMkrsuvWxyz \/\fR] [ \fI\,profile-file | - \/\fR] [ \fI\,seq-library-file | - \/\fR] [ \fI\,parameters \/\fR]
-.SH DESCRIPTION
-Build protein and DNA generalized profiles and use them to scan and align sequences,
-and search databases.
-.SH OPTIONS
-.HP
-\fB\-a\fR: report optimal alignment for all sequences.
-.HP
-\fB\-b\fR: search complementary strand of DNA sequences.
-.HP
-\fB\-f\fR: input sequence file is in FASTA format.
-.HP
-\fB\-h\fR: print usage help text.
-.HP
-\fB\-l\fR: indicate highest cut\-off level (number).
-.HP
-\fB\-L\fR: indicate highest cut\-off level (text).
-.HP
-\fB\-m\fR: report individual matches for circular profiles.
-.HP
-\fB\-r\fR: use raw score.
-.HP
-\fB\-u\fR: force profile disjointness to UNIQUE.
-.HP
-\fB\-C\fR<value>:
-.IP
-cut\-off value. An integer value forces \fB\-r\fR. Same as parameter C.
-.HP
-\fB\-M\fR<value>:
-.IP
-set the normalization mode to use for the score computation.
-Overrides the profile PRIORITY parameter.
-.IP
-output modifiers:
-.HP
-\fB\-d\fR: impose length limit on sequence description.
-.HP
-\fB\-k\fR: output using the xPSA header (using keyword=value pairs).
-.HP
-\fB\-s\fR: list sequences of the matched regions.
-.HP
-\fB\-v\fR: suppress warnings on stderr.
-.HP
-\fB\-x\fR: list alignments in PSA format.
-.HP
-\fB\-y\fR: list alignments in human readable form.
-.HP
-\fB\-z\fR: indicate profile start and stop positions.
-.HP
-\fB\-W\fR<value>:
-.IP
-specifies the output width. Same as parameter W.
-.IP
-valid (but deprecated) parameters are:
-.TP
-[C=cut\-off\-value]
-use option \fB\-C\fR instead
-.TP
-[W=output\-width]
-use option \fB\-W\fR instead
-.SH AUTHOR
-This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
=====================================
debian/rules
=====================================
@@ -21,6 +21,8 @@ override_dh_installman:
dh_installman
mv debian/$(DEB_SOURCE)/usr/share/man/man1/gtop.1 debian/$(DEB_SOURCE)/usr/share/man/man1/pfgtop.1
mv debian/$(DEB_SOURCE)/usr/share/man/man1/htop.1 debian/$(DEB_SOURCE)/usr/share/man/man1/pfhtop.1
+ mv debian/$(DEB_SOURCE)/usr/share/doc/*.pdf debian/$(DEB_SOURCE)/usr/share/doc/${DEB_SOURCE}/
+ rm -f debian/$(DEB_SOURCE)/usr/share/doc/*.txt debian/${DEB_SOURCE}/usr/ChangeLog debian/${DEB_SOURCE}/usr/README* debian/${DEB_SOURCE}/usr/LICENSE
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
@@ -34,3 +36,7 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
grep -v '^DT *' test.out > test.compare ; \
diff -u test.compare test.build || true
endif
+
+override_dh_auto_clean:
+ dh_auto_clean
+ rm -rf data/test.*
View it on GitLab: https://salsa.debian.org/med-team/pftools/-/compare/926e3a358ffb268aa8f5c6b41fd75d8e5fdb32d3...8288094a7701ca3cac4393eabb47807ce35f9532
--
View it on GitLab: https://salsa.debian.org/med-team/pftools/-/compare/926e3a358ffb268aa8f5c6b41fd75d8e5fdb32d3...8288094a7701ca3cac4393eabb47807ce35f9532
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20201218/288ab954/attachment-0001.html>
More information about the debian-med-commit
mailing list