[med-svn] [Git][med-team/cat-bat][master] 4 commits: Fix installation, add Depends

Mon May 18 16:14:57 BST 2020


Andreas Tille pushed to branch master at Debian Med / cat-bat


Commits:
99e0ce5b by Andreas Tille at 2020-05-18T16:52:35+02:00
Fix installation, add Depends

- - - - -
97476fe0 by Andreas Tille at 2020-05-18T16:57:52+02:00
Add manpage

- - - - -
a0ae69ff by Andreas Tille at 2020-05-18T17:08:35+02:00
Upload to new

- - - - -
d88bd680 by Andreas Tille at 2020-05-18T17:11:45+02:00
Fix typo in interpreter line

- - - - -


9 changed files:

- + debian/CAT.1
- debian/changelog
- debian/control
- + debian/createmanpages
- debian/install
- + debian/links
- + debian/manpages
- + debian/patches/fix_interpreter.patch
- + debian/patches/series


Changes:

=====================================
debian/CAT.1
=====================================
@@ -0,0 +1,39 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
+.TH CAT "1" "May 2020" "CAT 5.0.4" "User Commands"
+.SH NAME
+CAT \- tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
+.SH SYNOPSIS
+.B CAT
+(prepare | contigs | bin | bins | add_names | summarise) [\-v / \fB\-\-version]\fR [\-h / \fB\-\-help]\fR
+.SH DESCRIPTION
+Run Contig Annotation Tool (CAT) or Bin Annotation Tool (BAT).
+.SH OPTIONS
+.SS "Required choice:"
+.TP
+prepare
+Download database files and construct databases.
+.TP
+contigs
+Run CAT.
+.TP
+bin
+Run BAT on a single bin.
+.TP
+bins
+Run BAT on a set of bins.
+.TP
+add_names
+Add taxonomic names to CAT or BAT output files.
+.TP
+summarise
+Summarise a named CAT or BAT classification file.
+.SS "Optional arguments:"
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+Print version information and exit.
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Show this help message and exit.
+.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/changelog
=====================================
@@ -1,5 +1,5 @@
-cat-bat (5.0.4-1) UNRELEASED; urgency=medium
+cat-bat (5.0.4-1) unstable; urgency=medium
 
-  * Initial release (Closes: #<bug>)
+  * Initial release (Closes: #960937)
 
- -- Andreas Tille <tille at debian.org>  Mon, 18 May 2020 16:30:46 +0200
+ -- Andreas Tille <tille at debian.org>  Mon, 18 May 2020 17:05:20 +0200


=====================================
debian/control
=====================================
@@ -14,8 +14,10 @@ Homepage: https://github.com/dutilh/CAT
 Package: cat-bat
 Architecture: any
 Depends: ${python3:Depends},
-         ${misc:Depends}
-Description: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
+         ${misc:Depends},
+         diamond-aligner,
+         prodigal
+Description: taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
  Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines
  for the taxonomic classification of long DNA sequences and metagenome
  assembled genomes (MAGs/bins) of both known and (highly) unknown
@@ -24,4 +26,4 @@ Description: tool for taxonomic classification of contigs and metagenome-assembl
  predicted ORFs against the nr protein database, and voting-based
  classification of the entire contig / MAG based on classification of the
  individual ORFs. CAT and BAT can be run from intermediate steps if files
- are formated appropriately
+ are formatted appropriately.


=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,28 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=CAT
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT


=====================================
debian/install
=====================================
@@ -1,2 +1 @@
-CAT_pack/*.py	usr/share/cat-bat
-CAT_pack/CAT	usr/bin
+CAT_pack/*	usr/share/cat-bat


=====================================
debian/links
=====================================
@@ -0,0 +1,2 @@
+usr/share/cat-bat/CAT	usr/bin/CAT
+


=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1


=====================================
debian/patches/fix_interpreter.patch
=====================================
@@ -0,0 +1,12 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 18 May 2020 17:05:20 +0200
+Description: Fix typo in interpreter line
+
+--- a/CAT_pack/check.py
++++ b/CAT_pack/check.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env/ python3
++#!/usr/bin/env python3
+ 
+ import datetime
+ import decimal


=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+fix_interpreter.patch



View it on GitLab: https://salsa.debian.org/med-team/cat-bat/-/compare/76c2f9e92b5ac75ef4089b5d193cfde11dc724b1...d88bd6803ccabda697f75d0ab33e2cc2b4fb510c

-- 
View it on GitLab: https://salsa.debian.org/med-team/cat-bat/-/compare/76c2f9e92b5ac75ef4089b5d193cfde11dc724b1...d88bd6803ccabda697f75d0ab33e2cc2b4fb510c
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