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commit fb6f3b14fce05d916e7db9fcdbf4571e5861648f Author: Andreas Tille <[email protected]> Date: Sat Jan 6 11:52:45 2018 +0100 Add manpages --- debian/bin/centrifuge-sort-nt | 1 - debian/createmanpages | 46 +++++++++++++++++++++++++++++++++ debian/manpages | 1 + debian/mans/centrifuge-build.1 | 18 +++++++++++++ debian/mans/centrifuge-compress.1 | 8 ++++++ debian/mans/centrifuge-download.1 | 53 +++++++++++++++++++++++++++++++++++++++ debian/mans/centrifuge-inspect.1 | 18 +++++++++++++ debian/mans/centrifuge.1 | 10 ++++++++ 8 files changed, 154 insertions(+), 1 deletion(-) diff --git a/debian/bin/centrifuge-sort-nt b/debian/bin/centrifuge-sort-nt deleted file mode 120000 index 397b56e..0000000 --- a/debian/bin/centrifuge-sort-nt +++ /dev/null @@ -1 +0,0 @@ -centrifuge \ No newline at end of file diff --git a/debian/createmanpages b/debian/createmanpages new file mode 100755 index 0000000..ade8494 --- /dev/null +++ b/debian/createmanpages @@ -0,0 +1,46 @@ +#!/bin/sh +MANDIR=debian/mans +mkdir -p $MANDIR + +VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'` + +AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and +can be used for any other usage of the program. +" + +progname=centrifuge +help2man --no-info --no-discard-stderr --help-option=" -h" \ + --name='rapid and memory-efficient system for classification of DNA sequences' \ + --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 +echo $AUTHOR >> $MANDIR/${progname}.1 + +progname=centrifuge-build +help2man --no-info --no-discard-stderr --help-option=" -h" \ + --name='building index on all complete bacterial and viral genomes' \ + --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 +echo $AUTHOR >> $MANDIR/${progname}.1 + +progname=centrifuge-compress +help2man --no-info --no-discard-stderr --help-option=" " \ + --name='genome compression in the database construction' \ + --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 +echo $AUTHOR >> $MANDIR/${progname}.1 + +progname=centrifuge-download +help2man --no-info --no-discard-stderr --help-option=" " \ + --name='centrifuge helper to download databases' \ + --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 +echo $AUTHOR >> $MANDIR/${progname}.1 + +progname=centrifuge-inspect +help2man --no-info --no-discard-stderr --help-option=" -h" \ + --name='inspecting the centrifuge index' \ + --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 +echo $AUTHOR >> $MANDIR/${progname}.1 + +cat <<EOT +Please enhance the help2man output. +The following web page might be helpful in doing so: + http://liw.fi/manpages/ +EOT + diff --git a/debian/manpages b/debian/manpages new file mode 100644 index 0000000..63ab24a --- /dev/null +++ b/debian/manpages @@ -0,0 +1 @@ +debian/mans/* diff --git a/debian/mans/centrifuge-build.1 b/debian/mans/centrifuge-build.1 new file mode 100644 index 0000000..9bb0067 --- /dev/null +++ b/debian/mans/centrifuge-build.1 @@ -0,0 +1,18 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5. +.TH CENTRIFUGE-BUILD "1" "December 2017" "centrifuge-build 1.0.3~beta" "User Commands" +.SH NAME +centrifuge-build \- building index on all complete bacterial and viral genomes +.SH DESCRIPTION +.SS "Traceback (most recent call last):" +.IP +File "./centrifuge\-build", line 79, in <module> +.IP +main() +.IP +File "./centrifuge\-build", line 76, in main +.IP +os.execv(build_bin_spec, argv) +.PP +OSError: [Errno 2] No such file or directory +.SH AUTHOR +This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. diff --git a/debian/mans/centrifuge-compress.1 b/debian/mans/centrifuge-compress.1 new file mode 100644 index 0000000..61af33b --- /dev/null +++ b/debian/mans/centrifuge-compress.1 @@ -0,0 +1,8 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5. +.TH CENTRIFUGE-COMPRESS "1" "December 2017" "centrifuge-compress 1.0.3~beta" "User Commands" +.SH NAME +centrifuge-compress \- genome compression in the database construction +.SH DESCRIPTION +USAGE: perl centrifuge\-compress.pl path_to_download_files path_to_taxnonomy [\-map header_to_taxid_map \fB\-o\fR compressed \fB\-noCompress\fR \fB\-t\fR 1 \fB\-maxG\fR 50000000 \fB\-noDustmasker]\fR +.SH AUTHOR +This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. diff --git a/debian/mans/centrifuge-download.1 b/debian/mans/centrifuge-download.1 new file mode 100644 index 0000000..b398afc --- /dev/null +++ b/debian/mans/centrifuge-download.1 @@ -0,0 +1,53 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5. +.TH CENTRIFUGE-DOWNLOAD "1" "December 2017" "centrifuge-download 1.0.3~beta" "User Commands" +.SH NAME +centrifuge-download \- centrifuge helper to download databases +.SH DESCRIPTION +centrifuge\-download [<options>] <database> +.PP +ARGUMENT +.TP +<database> +One of refseq, genbank, contaminants or taxonomy: +.TP +\- use refseq or genbank for genomic sequences, +\- contaminants gets contaminant sequences from UniVec and EmVec, +\- taxonomy for taxonomy mappings. +.PP +COMMON OPTIONS +.TP +\fB\-o\fR <directory> +Folder to which the files are downloaded. Default: '.'. +.TP +\fB\-P\fR <# of threads> +Number of processes when downloading (uses xargs). Default: '1' +.SS "WHEN USING database refseq OR genbank:" +.TP +\fB\-d\fR <domain> +What domain to download. One or more of bacteria, viral, archaea, fungi, protozoa, invertebrate, plant, vertebrate_mammalian, vertebrate_other (comma separated). +.TP +\fB\-a\fR <assembly level> +Only download genomes with the specified assembly level. Default: 'Complete Genome'. +.TP +\fB\-c\fR <refseq category> +Only download genomes in the specified refseq category. Default: any. +.TP +\fB\-t\fR <taxids> +Only download the specified taxonomy IDs, comma separated. Default: any. +.TP +\fB\-r\fR +Download RNA sequences, too. +.TP +\fB\-u\fR +Filter unplaced sequences. +.TP +\fB\-m\fR +Mask low\-complexity regions using dustmasker. Default: off. +.TP +\fB\-l\fR +Modify header to include taxonomy ID. Default: off. +.TP +\fB\-g\fR +Download GI map. +.SH AUTHOR +This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. diff --git a/debian/mans/centrifuge-inspect.1 b/debian/mans/centrifuge-inspect.1 new file mode 100644 index 0000000..541112f --- /dev/null +++ b/debian/mans/centrifuge-inspect.1 @@ -0,0 +1,18 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5. +.TH CENTRIFUGE-INSPECT "1" "December 2017" "centrifuge-inspect 1.0.3~beta" "User Commands" +.SH NAME +centrifuge-inspect \- inspecting the centrifuge index +.SH DESCRIPTION +.SS "Traceback (most recent call last):" +.IP +File "./centrifuge\-inspect", line 55, in <module> +.IP +main() +.IP +File "./centrifuge\-inspect", line 51, in main +.IP +os.execv(inspect_bin_spec, arguments) +.PP +OSError: [Errno 2] No such file or directory +.SH AUTHOR +This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. diff --git a/debian/mans/centrifuge.1 b/debian/mans/centrifuge.1 new file mode 100644 index 0000000..7086bb8 --- /dev/null +++ b/debian/mans/centrifuge.1 @@ -0,0 +1,10 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5. +.TH CENTRIFUGE "1" "December 2017" "centrifuge 1.0.3~beta" "User Commands" +.SH NAME +centrifuge \- rapid and memory-efficient system for classification of DNA sequences +.SH DESCRIPTION +(ERR): Expected centrifuge to be in same directory with centrifuge\-class: +/home/andreas/debian\-maintain/alioth/debian\-med_git/0_prospective/centrifuge/ +Exiting now ... +.SH AUTHOR +This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/centrifuge.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
