[med-svn] [Git][med-team/busco][master] 2 commits: Fix install

Tue May 12 20:00:10 BST 2020


Andreas Tille pushed to branch master at Debian Med / busco


Commits:
27e98166 by Andreas Tille at 2020-05-12T20:56:52+02:00
Fix install

- - - - -
cffc0c41 by Andreas Tille at 2020-05-12T20:59:25+02:00
Add manpage

- - - - -


4 changed files:

- + debian/busco.1
- debian/control
- + debian/createmanpages
- + debian/manpages


Changes:

=====================================
debian/busco.1
=====================================
@@ -0,0 +1,84 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
+.TH BUSCO "1" "May 2020" "busco 4.0.6" "User Commands"
+.SH NAME
+busco \- benchmarking sets of universal single-copy orthologs
+.SH SYNOPSIS
+.B busco
+\fB\-i\fR [SEQUENCE_FILE] \fB\-l\fR [LINEAGE] \fB\-o\fR [OUTPUT_NAME] \fB\-m\fR [MODE] [OTHER OPTIONS]
+.SH DESCRIPTION
+Assessing genome assembly and annotation completeness with Benchmarking
+Universal Single-Copy Orthologs (BUSCO).
+.SH OPTIONS
+.TP
+\fB\-i\fR FASTA FILE, \fB\-\-in\fR FASTA FILE
+Input sequence file in FASTA format. Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set.
+.TP
+\fB\-c\fR N, \fB\-\-cpu\fR N
+Specify the number (N=integer) of threads/cores to use.
+.TP
+\fB\-o\fR OUTPUT, \fB\-\-out\fR OUTPUT
+Give your analysis run a recognisable short name. Output folders and files will be labelled with this name. WARNING: do not provide a path
+.TP
+\fB\-\-out_path\fR OUTPUT_PATH
+Optional location for results folder, excluding results folder name. Default is current working directory.
+.TP
+\fB\-e\fR N, \fB\-\-evalue\fR N
+E\-value cutoff for BLAST searches. Allowed formats, 0.001 or 1e\-03 (Default: 1e\-03)
+.TP
+\fB\-m\fR MODE, \fB\-\-mode\fR MODE
+Specify which BUSCO analysis mode to run.
+There are three valid modes:
+\- geno or genome, for genome assemblies (DNA)
+\- tran or transcriptome, for transcriptome assemblies (DNA)
+\- prot or proteins, for annotated gene sets (protein)
+.TP
+\fB\-l\fR LINEAGE, \fB\-\-lineage_dataset\fR LINEAGE
+Specify the name of the BUSCO lineage to be used.
+.TP
+\fB\-f\fR, \fB\-\-force\fR
+Force rewriting of existing files. Must be used when output files with the provided name already exist.
+.TP
+\fB\-\-limit\fR REGION_LIMIT
+How many candidate regions (contig or transcript) to consider per BUSCO (default: 3)
+.TP
+\fB\-\-long\fR
+Optimization mode Augustus self\-training (Default: Off) adds considerably to the run time, but can improve results for some non\-model organisms
+.TP
+\fB\-q\fR, \fB\-\-quiet\fR
+Disable the info logs, displays only errors
+.TP
+\fB\-\-augustus_parameters\fR AUGUSTUS_PARAMETERS
+Pass additional arguments to Augustus. All arguments should be contained within a single pair of quotation marks, separated by commas. E.g. '\-\-param1=1,\-\-param2=2'
+.TP
+\fB\-\-augustus_species\fR AUGUSTUS_SPECIES
+Specify a species for Augustus training.
+.TP
+\fB\-\-auto\-lineage\fR
+Run auto\-lineage to find optimum lineage path
+.TP
+\fB\-\-auto\-lineage\-prok\fR
+Run auto\-lineage just on non\-eukaryote trees to find optimum lineage path
+.TP
+\fB\-\-auto\-lineage\-euk\fR
+Run auto\-placement just on eukaryote tree to find optimum lineage path
+.TP
+\fB\-\-update\-data\fR
+Download and replace with last versions all lineages datasets and files necessary to their automated selection
+.TP
+\fB\-\-offline\fR
+To indicate that BUSCO cannot attempt to download files
+.TP
+\fB\-\-config\fR CONFIG_FILE
+Provide a config file
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+Show this version and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Show this help message and exit
+.TP
+\fB\-\-list\-datasets\fR
+Print the list of available BUSCO datasets
+.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/control
=====================================
@@ -13,8 +13,9 @@ Vcs-Git: https://salsa.debian.org/med-team/busco.git
 Homepage: https://gitlab.com/ezlab/busco
 
 Package: busco
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Architecture: all
+Depends: ${python3:Depends},
+         ${misc:Depends}
 Description: benchmarking sets of universal single-copy orthologs
  Assessing genome assembly and annotation completeness with Benchmarking
  Universal Single-Copy Orthologs (BUSCO).


=====================================
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 $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+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/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1



View it on GitLab: https://salsa.debian.org/med-team/busco/-/compare/569a2f6ee6004a530075ba4c0af1fe8605662f8a...cffc0c415a5022c8b36965fcbb6310bc5b2f3074

-- 
View it on GitLab: https://salsa.debian.org/med-team/busco/-/compare/569a2f6ee6004a530075ba4c0af1fe8605662f8a...cffc0c415a5022c8b36965fcbb6310bc5b2f3074
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