[med-svn] [Git][med-team/bcalm][master] Add manpages
Shayan Doust
gitlab at salsa.debian.org
Mon Sep 23 23:18:27 BST 2019
Shayan Doust pushed to branch master at Debian Med / bcalm
Commits:
d339a979 by Shayan Doust at 2019-09-23T07:29:32Z
Add manpages
- - - - -
3 changed files:
- + debian/createmanpages
- + debian/manpages
- + debian/mans/bcalm.1
Changes:
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,26 @@
+#!/bin/sh
+MANDIR=debian/mans
+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\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+progname=bcalm
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name="$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/mans/*.1
=====================================
debian/mans/bcalm.1
=====================================
@@ -0,0 +1,139 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.
+.TH BCALM "1" "September 2019" "bcalm 2.2.1" "User Commands"
+.SH NAME
+bcalm \- de Bruijn compaction in low memory
+.SH DESCRIPTION
+Bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data.
+.PP
+[bcalm_1 options]
+.TP
+\fB\-nb\-cores\fR (1 arg) :
+number of cores [default '0']
+.TP
+\fB\-verbose\fR
+(1 arg) : verbosity level [default '1']
+.TP
+\fB\-version\fR
+(0 arg) : version
+.TP
+\fB\-help\fR
+(0 arg) : help
+.IP
+[graph options]
+.TP
+\fB\-no\-mphf\fR
+(0 arg) : don't construct the MPHF
+.IP
+[kmer count options]
+.TP
+\fB\-in\fR
+(1 arg) : reads file [default '']
+.TP
+\fB\-kmer\-size\fR
+(1 arg) : size of a kmer [default '31']
+.TP
+\fB\-abundance\-min\fR
+(1 arg) : min abundance threshold for solid kmers [default '2']
+.TP
+\fB\-abundance\-max\fR
+(1 arg) : max abundance threshold for solid kmers [default '2147483647']
+.TP
+\fB\-solidity\-custom\fR
+(1 arg) : when solidity\-kind is custom, specifies list of files where kmer must be present [default '']
+.TP
+\fB\-max\-memory\fR
+(1 arg) : max memory (in MBytes) [default '5000']
+.TP
+\fB\-max\-disk\fR
+(1 arg) : max disk (in MBytes) [default '0']
+.TP
+\fB\-out\fR
+(1 arg) : output file [default '']
+.TP
+\fB\-out\-dir\fR
+(1 arg) : output directory [default '.']
+.TP
+\fB\-out\-tmp\fR
+(1 arg) : output directory for temporary files [default '.']
+.TP
+\fB\-out\-compress\fR
+(1 arg) : h5 compression level (0:none, 9:best) [default '0']
+.TP
+\fB\-storage\-type\fR
+(1 arg) : storage type of kmer counts ('hdf5' or 'file') [default 'hdf5']
+.TP
+\fB\-histo2D\fR
+(1 arg) : compute the 2D histogram (with first file = genome, remaining files = reads) [default '0']
+.TP
+\fB\-histo\fR
+(1 arg) : output the kmer abundance histogram [default '0']
+.IP
+[kmer count, advanced performance tweaks options]
+.TP
+\fB\-minimizer\-type\fR
+(1 arg) : minimizer type (0=lexi, 1=freq) [default '1']
+.TP
+\fB\-minimizer\-size\fR
+(1 arg) : size of a minimizer [default '10']
+.TP
+\fB\-repartition\-type\fR (1 arg) :
+minimizer repartition (0=unordered, 1=ordered) [default '1']
+.IP
+[bloom options]
+.TP
+\fB\-bloom\fR
+(1 arg) : bloom type ('basic', 'cache', 'neighbor') [default 'neighbor']
+.TP
+\fB\-debloom\fR
+(1 arg) : debloom type ('none', 'original' or 'cascading') [default 'cascading']
+.TP
+\fB\-debloom\-impl\fR (1 arg) :
+debloom impl ('basic', 'minimizer') [default 'minimizer']
+.IP
+[branching options]
+.TP
+\fB\-branching\-nodes\fR (1 arg) :
+branching type ('none' or 'stored') [default 'stored']
+.TP
+\fB\-topology\-stats\fR
+(1 arg) : topological information level (0 for none) [default '0']
+.IP
+[general options]
+.TP
+\fB\-config\-only\fR
+(0 arg) : dump config only
+.TP
+\fB\-nb\-cores\fR
+(1 arg) : number of cores [default '0']
+.TP
+\fB\-verbose\fR
+(1 arg) : verbosity level [default '1']
+.TP
+\fB\-integer\-precision\fR (1 arg) :
+integers precision (0 for optimized value) [default '0']
+.TP
+[debug
+options]
+.TP
+\fB\-redo\-bcalm\fR
+(0 arg) : debug function, redo the bcalm algo
+.TP
+\fB\-skip\-bcalm\fR
+(0 arg) : same, but skip bcalm
+.TP
+\fB\-redo\-bglue\fR
+(0 arg) : same, but redo bglue
+.TP
+\fB\-skip\-bglue\fR
+(0 arg) : same, but skip bglue
+.TP
+\fB\-redo\-links\fR
+(0 arg) : same, but redo links
+.TP
+\fB\-skip\-links\fR
+(0 arg) : same, but skip links
+.TP
+\fB\-nb\-glue\-partitions\fR (1 arg) :
+number of glue partitions (automatically calculated by default) [default '0']
+.SH AUTHOR
+This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.
View it on GitLab: https://salsa.debian.org/med-team/bcalm/commit/d339a979afa82e7ad60398a7d143f24e7411de47
--
View it on GitLab: https://salsa.debian.org/med-team/bcalm/commit/d339a979afa82e7ad60398a7d143f24e7411de47
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