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 You're receiving this email because of your account on salsa.debian.org.
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