[med-svn] [Git][med-team/centrifuge][master] 4 commits: Fix watchfile to detect new versions on github
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Oct 12 07:45:48 BST 2021
Andreas Tille pushed to branch master at Debian Med / centrifuge
Commits:
be375c33 by Andreas Tille at 2021-10-12T07:43:52+02:00
Fix watchfile to detect new versions on github
- - - - -
88a3227c by Andreas Tille at 2021-10-12T07:44:19+02:00
routine-update: Standards-Version: 4.6.0
- - - - -
a827640f by Andreas Tille at 2021-10-12T08:43:46+02:00
Fix manpages
- - - - -
3fc0cffa by Andreas Tille at 2021-10-12T08:45:14+02:00
Upload to unstable
- - - - -
9 changed files:
- debian/changelog
- debian/control
- debian/createmanpages
- debian/mans/centrifuge-build.1
- debian/mans/centrifuge-compress.1
- debian/mans/centrifuge-download.1
- debian/mans/centrifuge-inspect.1
- debian/mans/centrifuge.1
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+centrifuge (1.0.3-9) unstable; urgency=medium
+
+ * Fix watchfile to detect new versions on github
+ * Standards-Version: 4.6.0 (routine-update)
+ * Fix manpages
+
+ -- Andreas Tille <tille at debian.org> Tue, 12 Oct 2021 08:43:55 +0200
+
centrifuge (1.0.3-8) unstable; urgency=medium
[ Helmut Grohne ]
=====================================
debian/control
=====================================
@@ -7,7 +7,7 @@ Build-Depends: debhelper-compat (= 13),
dh-python,
dh-sequence-python3,
jellyfish
-Standards-Version: 4.5.0
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/centrifuge
Vcs-Git: https://salsa.debian.org/med-team/centrifuge.git
Homepage: https://ccb.jhu.edu/software/centrifuge/
=====================================
debian/createmanpages
=====================================
@@ -11,31 +11,32 @@ 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
+ --version-string="$VERSION" /usr/bin/${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
+ --version-string="$VERSION" /usr/bin/${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
+ --version-string="$VERSION" /usr/bin/${progname} \
+ | sed 's/USAGE: perl centrifuge\\-compress.pl/centrifuge\-compress/' > $MANDIR/${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
+ --version-string="$VERSION" /usr/bin/${progname} > $MANDIR/${progname}.1
echo $AUTHOR >> $MANDIR/${progname}.1
progname=centrifuge-inspect
-help2man --no-info --no-discard-stderr --help-option=" -h" \
+help2man --no-info --discard-stderr --help-option=" -h" \
--name='inspecting the centrifuge index' \
- --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+ --version-string="$VERSION" /usr/bin/${progname} > $MANDIR/${progname}.1
echo $AUTHOR >> $MANDIR/${progname}.1
cat <<EOT
=====================================
debian/mans/centrifuge-build.1
=====================================
@@ -1,18 +1,86 @@
-.\" 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"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.48.1.
+.TH CENTRIFUGE-BUILD "1" "October 2021" "centrifuge-build 1.0.3" "User Commands"
.SH NAME
centrifuge-build \- building index on all complete bacterial and viral genomes
+.SH SYNOPSIS
+.B centrifuge-build
+[\fI\,options\/\fR]\fI\,* --conversion-table <table file> --taxonomy-tree <taxonomy tree file> <reference_in> <cf_index_base>\/\fR
.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
+Centrifuge version 1.0.3\-beta by Daehwan Kim (infphilo at gmail.com, http://www.ccb.jhu.edu/people/infphilo)
+.TP
+reference_in
+comma\-separated list of files with ref sequences
+.TP
+centrifuge_index_base
+write cf data to files with this dir/basename
+.SH OPTIONS
+.TP
+\fB\-c\fR
+reference sequences given on cmd line (as
+<reference_in>)
+.TP
+\fB\-\-large\-index\fR
+force generated index to be 'large', even if ref
+has fewer than 4 billion nucleotides
+.TP
+\fB\-a\fR/\-\-noauto
+disable automatic \fB\-p\fR/\-\-bmax/\-\-dcv memory\-fitting
+.TP
+\fB\-\-bmax\fR <int>
+max bucket sz for blockwise suffix\-array builder
+.TP
+\fB\-\-bmaxdivn\fR <int>
+max bucket sz as divisor of ref len (default: 4)
+.TP
+\fB\-\-dcv\fR <int>
+diff\-cover period for blockwise (default: 1024)
+.TP
+\fB\-\-nodc\fR
+disable diff\-cover (algorithm becomes quadratic)
+.TP
+\fB\-r\fR/\-\-noref
+don't build .3/.4.bt2 (packed reference) portion
+.TP
+\fB\-3\fR/\-\-justref
+just build .3/.4.bt2 (packed reference) portion
+.TP
+\fB\-o\fR/\-\-offrate <int>
+SA is sampled every 2^offRate BWT chars (default: 5)
+.TP
+\fB\-t\fR/\-\-ftabchars <int>
+# of chars consumed in initial lookup (default: 10)
+.TP
+\fB\-\-conversion\-table\fR <file name>
+a table that converts any id to a taxonomy id
+.TP
+\fB\-\-taxonomy\-tree\fR
+<file name> taxonomy tree
+.TP
+\fB\-\-name\-table\fR
+<file name> names corresponding to taxonomic IDs
+.TP
+\fB\-\-size\-table\fR
+<file name> table of contig (or genome) sizes
+.TP
+\fB\-\-seed\fR <int>
+seed for random number generator
+.TP
+\fB\-q\fR/\-\-quiet
+verbose output (for debugging)
+.TP
+\fB\-p\fR/\-\-threads <int>
+number of alignment threads to launch (1)
+.TP
+\fB\-\-kmer\-count\fR <int>
+k size for counting the number of distinct k\-mer
+.TP
+\fB\-h\fR/\-\-help
+print detailed description of tool and its options
+.TP
+\fB\-\-usage\fR
+print this usage message
+.TP
+\fB\-\-version\fR
+print version information and quit
.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/mans/centrifuge-compress.1
=====================================
@@ -1,8 +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"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.48.1.
+.TH CENTRIFUGE-COMPRESS "1" "October 2021" "centrifuge-compress 1.0.3" "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
+centrifuge-compress 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.
=====================================
debian/mans/centrifuge-download.1
=====================================
@@ -1,5 +1,5 @@
-.\" 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"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.48.1.
+.TH CENTRIFUGE-DOWNLOAD "1" "October 2021" "centrifuge-download 1.0.3" "User Commands"
.SH NAME
centrifuge-download \- centrifuge helper to download databases
.SH DESCRIPTION
@@ -27,7 +27,7 @@ Number of processes when downloading (uses xargs). Default: '1'
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'.
+Only download genomes with the specified assembly level. Default: 'Complete Genome'. Use 'Any' for any assembly level.
.TP
\fB\-c\fR <refseq category>
Only download genomes in the specified refseq category. Default: any.
=====================================
debian/mans/centrifuge-inspect.1
=====================================
@@ -1,18 +1,55 @@
-.\" 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"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.48.1.
+.TH CENTRIFUGE-INSPECT "1" "October 2021" "centrifuge-inspect 1.0.3" "User Commands"
.SH NAME
centrifuge-inspect \- inspecting the centrifuge index
+.SH SYNOPSIS
+.B centrifuge-inspect
+[\fI\,options\/\fR]\fI\,* <cf_base>\/\fR
.SH DESCRIPTION
-.SS "Traceback (most recent call last):"
+Centrifuge version 1.0.3\-beta by Daehwan Kim (infphilo at gmail.com, http://www.ccb.jhu.edu/people/infphilo)
+.TP
+<cf_base>
+cf filename minus trailing .1.cf/.2.cf/.3.cf
.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
+By default, prints FASTA records of the indexed nucleotide sequences to
+standard out. With \fB\-n\fR, just prints names. With \fB\-s\fR, just prints a summary of
+the index parameters and sequences. With \fB\-e\fR, preserves colors if applicable.
+.SH OPTIONS
+.TP
+\fB\-\-large\-index\fR
+force inspection of the 'large' index, even if a
+\&'small' one is present.
+.TP
+\fB\-a\fR/\-\-across <int>
+Number of characters across in FASTA output (default: 60)
+.TP
+\fB\-n\fR/\-\-names
+Print reference sequence names only
+.TP
+\fB\-s\fR/\-\-summary
+Print summary incl. ref names, lengths, index properties
+.TP
+\fB\-e\fR/\-\-bt2\-ref
+Reconstruct reference from .cf (slow, preserves colors)
+.HP
+\fB\-\-conversion\-table\fR Print conversion table
+.TP
+\fB\-\-taxonomy\-tree\fR
+Print taxonomy tree
+.TP
+\fB\-\-name\-table\fR
+Print names corresponding to taxonomic IDs
+.TP
+\fB\-\-size\-table\fR
+Print the lengths of the sequences belonging to the same taxonomic ID
+.TP
+\fB\-v\fR/\-\-verbose
+Verbose output (for debugging)
+.TP
+\fB\-h\fR/\-\-help
+print detailed description of tool and its options
+.TP
+\fB\-\-help\fR
+print this usage message
.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/mans/centrifuge.1
=====================================
@@ -1,10 +1,151 @@
-.\" 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"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.48.1.
+.TH CENTRIFUGE "1" "October 2021" "centrifuge 1.0.3" "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 ...
+Centrifuge version 1.0.3\-beta by the Centrifuge developer team (centrifuge.metagenomics at gmail.com)
+Usage:
+.IP
+centrifuge [options]* \fB\-x\fR <cf\-idx> {\-1 <m1> \fB\-2\fR <m2> | \fB\-U\fR <r>} [\-S <filename>] [\-\-report\-file <report>]
+.TP
+<cf\-idx>
+Index filename prefix (minus trailing .X.cf).
+.TP
+<m1>
+Files with #1 mates, paired with files in <m2>.
+Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
+.TP
+<m2>
+Files with #2 mates, paired with files in <m1>.
+Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
+.TP
+<r>
+Files with unpaired reads.
+Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
+.TP
+<filename>
+File for classification output (default: stdout)
+.TP
+<report>
+File for tabular report output (default: centrifuge_report.tsv)
+.IP
+<m1>, <m2>, <r> can be comma\-separated lists (no whitespace) and can be
+specified many times. E.g. '\-U file1.fq,file2.fq \fB\-U\fR file3.fq'.
+.PP
+Options (defaults in parentheses):
+.IP
+Input:
+.TP
+\fB\-q\fR
+query input files are FASTQ .fq/.fastq (default)
+.TP
+\fB\-\-qseq\fR
+query input files are in Illumina's qseq format
+.TP
+\fB\-f\fR
+query input files are (multi\-)FASTA .fa/.mfa
+.TP
+\fB\-r\fR
+query input files are raw one\-sequence\-per\-line
+.TP
+\fB\-c\fR
+<m1>, <m2>, <r> are sequences themselves, not files
+.TP
+\fB\-s\fR/\-\-skip <int>
+skip the first <int> reads/pairs in the input (none)
+.TP
+\fB\-u\fR/\-\-upto <int>
+stop after first <int> reads/pairs (no limit)
+.TP
+\fB\-5\fR/\-\-trim5 <int>
+trim <int> bases from 5'/left end of reads (0)
+.TP
+\fB\-3\fR/\-\-trim3 <int>
+trim <int> bases from 3'/right end of reads (0)
+.TP
+\fB\-\-phred33\fR
+qualities are Phred+33 (default)
+.TP
+\fB\-\-phred64\fR
+qualities are Phred+64
+.TP
+\fB\-\-int\-quals\fR
+qualities encoded as space\-delimited integers
+.TP
+\fB\-\-ignore\-quals\fR
+treat all quality values as 30 on Phred scale (off)
+.TP
+\fB\-\-nofw\fR
+do not align forward (original) version of read (off)
+.TP
+\fB\-\-norc\fR
+do not align reverse\-complement version of read (off)
+.SS "Classification:"
+.TP
+\fB\-\-min\-hitlen\fR <int>
+minimum length of partial hits (default 22, must be greater than 15)
+.TP
+\fB\-\-min\-totallen\fR <int>
+minimum summed length of partial hits per read (default 0)
+.HP
+\fB\-\-host\-taxids\fR <taxids> comma\-separated list of taxonomic IDs that will be preferred in classification
+.HP
+\fB\-\-exclude\-taxids\fR <taxids> comma\-separated list of taxonomic IDs that will be excluded in classification
+.IP
+Output:
+.TP
+\fB\-\-out\-fmt\fR <str>
+define output format, either 'tab' or 'sam' (tab)
+.TP
+\fB\-\-tab\-fmt\-cols\fR <str>
+columns in tabular format, comma separated
+default: readID,seqID,taxID,score,2ndBestScore,hitLength,queryLength,numMatches
+.TP
+\fB\-t\fR/\-\-time
+print wall\-clock time taken by search phases
+.TP
+\fB\-\-un\fR <path>
+write unpaired reads that didn't align to <path>
+.TP
+\fB\-\-al\fR <path>
+write unpaired reads that aligned at least once to <path>
+.TP
+\fB\-\-un\-conc\fR <path>
+write pairs that didn't align concordantly to <path>
+.TP
+\fB\-\-al\-conc\fR <path>
+write pairs that aligned concordantly at least once to <path>
+.IP
+(Note: for \fB\-\-un\fR, \fB\-\-al\fR, \fB\-\-un\-conc\fR, or \fB\-\-al\-conc\fR, add '\-gz' to the option name, e.g.
+\fB\-\-un\-gz\fR <path>, to gzip compress output, or add '\-bz2' to bzip2 compress output.)
+\fB\-\-quiet\fR print nothing to stderr except serious errors
+\fB\-\-met\-file\fR <path> send metrics to file at <path> (off)
+\fB\-\-met\-stderr\fR send metrics to stderr (off)
+\fB\-\-met\fR <int> report internal counters & metrics every <int> secs (1)
+.IP
+Performance:
+.HP
+\fB\-o\fR/\-\-offrate <int> override offrate of index; must be >= index's offrate
+.HP
+\fB\-p\fR/\-\-threads <int> number of alignment threads to launch (1)
+.TP
+\fB\-\-mm\fR
+use memory\-mapped I/O for index; many instances can share
+.IP
+Other:
+.TP
+\fB\-\-qc\-filter\fR
+filter out reads that are bad according to QSEQ filter
+.TP
+\fB\-\-seed\fR <int>
+seed for random number generator (0)
+.HP
+\fB\-\-non\-deterministic\fR seed rand. gen. arbitrarily instead of using read attributes
+.TP
+\fB\-\-version\fR
+print version information and quit
+.TP
+\fB\-h\fR/\-\-help
+print this usage message
.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/watch
=====================================
@@ -1,3 +1,3 @@
version=4
-https://github.com//infphilo/centrifuge/releases .*/archive/v?(\d[.\d]+)@ARCHIVE_EXT@
+https://github.com//infphilo/centrifuge/releases .*/v?(\d[.\d]+)@ARCHIVE_EXT@
View it on GitLab: https://salsa.debian.org/med-team/centrifuge/-/compare/4c6b9dd49d6b3cf34faa5245c05449dcfd75b877...3fc0cffa987f45271a2fe78c0c75fb64b4c9f533
--
View it on GitLab: https://salsa.debian.org/med-team/centrifuge/-/compare/4c6b9dd49d6b3cf34faa5245c05449dcfd75b877...3fc0cffa987f45271a2fe78c0c75fb64b4c9f533
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20211012/cae443e5/attachment-0001.htm>
More information about the debian-med-commit
mailing list