This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository iva.
commit b8e2a388b6463ba519dbfe73475a66e393820a9e Author: Sascha Steinbiss <[email protected]> Date: Wed May 4 10:09:55 2016 +0000 remove old manpage building facility --- debian/createmanpages | 16 ---- debian/man/iva.1 | 175 -------------------------------------------- debian/man/iva_qc.1 | 109 --------------------------- debian/man/iva_qc_make_db.1 | 48 ------------ debian/usage_to_man | 111 ---------------------------- 5 files changed, 459 deletions(-) diff --git a/debian/createmanpages b/debian/createmanpages deleted file mode 100755 index febcd91..0000000 --- a/debian/createmanpages +++ /dev/null @@ -1,16 +0,0 @@ -#!/bin/sh -MANDIR=debian -mkdir -p $MANDIR - -VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'` - -help2man --no-info --no-discard-stderr --help-option=" " \ - --name='<optional description of the program>' \ - --version-string="$VERSION" <programname> > $MANDIR/<programname>.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/man/iva.1 b/debian/man/iva.1 deleted file mode 100644 index 632f894..0000000 --- a/debian/man/iva.1 +++ /dev/null @@ -1,175 +0,0 @@ -.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4. -.TH IVA "1" "December 2014" "iva 0.10.0" "iva" -.SH NAME -iva \- run a de novo assembly -.SH DESCRIPTION -usage: iva [options] {\-f reads_fwd \fB\-r\fR reads_rev | \fB\-\-fr\fR reads} <output directory> -.SS "positional arguments:" -.TP -Output directory -Name of output directory (must not already exist) -.SS "optional arguments:" -.TP -\fB\-h\fR, \fB\-\-help\fR -show this help message and exit -.SS "Input and output:" -.TP -\fB\-f\fR filename[.gz], \fB\-\-reads_fwd\fR filename[.gz] -Name of forward reads fasta/q file. Must be used in -conjunction with \fB\-\-reads_rev\fR -.TP -\fB\-r\fR filename[.gz], \fB\-\-reads_rev\fR filename[.gz] -Name of reverse reads fasta/q file. Must be used in -conjunction with \fB\-\-reads_fwd\fR -.TP -\fB\-\-fr\fR filename[.gz] -Name of interleaved fasta/q file -.TP -\fB\-\-keep_files\fR -Keep intermediate files (could be many!). Default is -to delete all unnecessary files -.TP -\fB\-\-contigs\fR filename[.gz] -Fasta file of contigs to be extended. Incompatible -with \fB\-\-reference\fR -.TP -\fB\-\-reference\fR filename[.gz] -Fasta file of reference genome, or parts thereof. IVA -will try to assemble one contig per sequence in this -file. Incompatible with \fB\-\-contigs\fR -.TP -\fB\-v\fR, \fB\-\-verbose\fR -Be verbose by printing messages to stdout. Use up to -three times for increasing verbosity. -.SS "SMALT mapping options:" -.TP -\fB\-k\fR INT, \fB\-\-smalt_k\fR INT -kmer hash length in SMALT (the \fB\-k\fR option in smalt -index) [19] -.TP -\fB\-s\fR INT, \fB\-\-smalt_s\fR INT -kmer hash step size in SMALT (the \fB\-s\fR option in smalt -index) [11] -.TP -\fB\-y\fR FLOAT, \fB\-\-smalt_id\fR FLOAT -Minimum identity threshold for mapping to be reported -(the \fB\-y\fR option in smalt map) [0.5] -.SS "Contig options:" -.TP -\fB\-\-ctg_first_trim\fR INT -Number of bases to trim off the end of every contig -before extending for the first time [25] -.TP -\fB\-\-ctg_iter_trim\fR INT -During iterative extension, number of bases to trim -off the end of a contig when extension fails (then try -extending again) [10] -.TP -\fB\-\-ext_min_cov\fR INT -Minimum kmer depth needed to use that kmer to extend a -contig [5] -.TP -\fB\-\-ext_min_ratio\fR FLOAT -Sets N, where kmer for extension must be at least N -times more abundant than next most common kmer [2] -.TP -\fB\-\-ext_max_bases\fR INT -Maximum number of bases to try to extend on each -iteration [100] -.TP -\fB\-\-ext_min_clip\fR INT -Set minimum number of bases soft clipped off a read -for those bases to be used for extension [3] -.TP -\fB\-\-max_contigs\fR INT -Maximum number of contigs allowed in the assembly. No -more seeds generated if the cutoff is reached [50] -.SS "Seed generation options:" -.TP -\fB\-\-make_new_seeds\fR -When no more contigs can be extended, generate a new -seed. This is forced to be true when \fB\-\-contigs\fR is not -used -.TP -\fB\-\-seed_start_length\fR INT -When making a seed sequence, use the most common kmer -of this length. Default is to use the minimum of -(median read length, 95). Warning: it is not -recommended to set this higher than 95 -.TP -\fB\-\-seed_stop_length\fR INT -Stop extending seed using perfect matches from reads -when this length is reached. Future extensions are -then made by treating the seed as a contig -[0.9*max_insert] -.TP -\fB\-\-seed_min_kmer_cov\fR INT -Minimum kmer coverage of initial seed [25] -.TP -\fB\-\-seed_max_kmer_cov\fR INT -Maximum kmer coverage of initial seed [1000000] -.TP -\fB\-\-seed_ext_max_bases\fR INT -Maximum number of bases to try to extend on each -iteration [50] -.TP -\fB\-\-seed_overlap_length\fR INT -Number of overlapping bases needed between read and -seed to use that read to extend [seed_start_length] -.TP -\fB\-\-seed_ext_min_cov\fR INT -Minimum kmer depth needed to use that kmer to extend a -contig [5] -.TP -\fB\-\-seed_ext_min_ratio\fR FLOAT -Sets N, where kmer for extension must be at least N -times more abundant than next most common kmer [2] -.SS "Read trimming options:" -.TP -\fB\-\-trimmomatic\fR FILENAME -Provide location of trimmomatic.jar file to enable -read trimming. Required if \fB\-\-adapters\fR used -.TP -\fB\-\-trimmo_qual\fR STRING -Trimmomatic options used to quality trim reads -[LEADING:10 TRAILING:10 SLIDINGWINDOW:4:20] -.TP -\fB\-\-adapters\fR FILENAME -Fasta file of adapter sequences to be trimmed off -reads. -If used, must also use \fB\-\-trimmomatic\fR -/usr/local/lib/python3.4 -/dist\-packages/iva\-0.10.0\-py3.4.egg/iva/read_trim/adapters.fasta -.TP -\fB\-\-min_trimmed_length\fR INT -Minimum length of read after trimming [50] -.TP -\fB\-\-pcr_primers\fR FILENAME -FASTA file of primers. The first perfect match found -to a sequence in the primers file will be trimmed off -the start of each read. This is run after trimmomatic -(if \fB\-\-trimmomatic\fR used) -.SS "Other options:" -.TP -\fB\-i\fR INT, \fB\-\-max_insert\fR INT -Maximum insert size (includes read length). Reads with -inferred insert size more than the maximum will not be -used to extend contigs [500] -.TP -\fB\-t\fR INT, \fB\-\-threads\fR INT -Number of threads to use [1] -.TP -\fB\-\-strand_bias\fR FLOAT in [0,0.5] -Set strand bias cutoff of mapped reads when trimming -contig ends, in the interval [0,0.5]. A value of x -means that a base needs min(fwd_depth, rev_depth) / -total_depth <= x. [0.1] -.TP -\fB\-\-version\fR -show program's version number and exit -.SH "AUTHOR" -.sp -iva was originally written by Martin Hunt (mh12\@sanger.ac.uk) -.SH "COPYING" -.sp -Wellcome Trust Sanger Institute Copyright \(co 2013 Wellcome Trust Sanger Institute This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version\&. diff --git a/debian/man/iva_qc.1 b/debian/man/iva_qc.1 deleted file mode 100644 index 0dec853..0000000 --- a/debian/man/iva_qc.1 +++ /dev/null @@ -1,109 +0,0 @@ -.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4. -.TH IVA_QC "1" "December 2014" "iva_qc 0.10.0" "iva_qc" -.SH NAME -iva_qc \- compares an assembly against a reference -.SH DESCRIPTION -usage: iva_qc [options] {(\fB\-f\fR <reads_1.fq> \fB\-r\fR <reads_2.fq>) | \fB\-\-fr\fR reads.fq} {(\fB\-\-embl_dir\fR | \fB\-\-ref_db\fR) <directory>} <assembly.fasta> <prefix of output files> -.SS "positional arguments:" -.TP -assembly.fasta -Name of assembly fasta file to be compared to -reference -.TP -prefix of output files -Prefix to use for name of all output files -.SS "optional arguments:" -.TP -\fB\-h\fR, \fB\-\-help\fR -show this help message and exit -.SS "Reference options (REQUIRED: either --embl_dir or --ref_db):" -.TP -\fB\-\-embl_dir\fR Directory -Directory of reference EMBL files. If not used, must -use \fB\-\-ref_db\fR -.TP -\fB\-\-ref_db\fR Directory -Directory of database made by iva_qc_make_db. If not -used, must use \fB\-\-embl_dir\fR -.SS "Reads options (REQUIRED: either --fr, or (-f and -r)):" -.TP -\fB\-f\fR filename[.gz], \fB\-\-reads_fwd\fR filename[.gz] -Name of forwards reads fasta or fastq file. Must be -used with \fB\-\-reads_rev\fR -.TP -\fB\-r\fR filename[.gz], \fB\-\-reads_rev\fR filename[.gz] -Name of reverse reads fasta or fastq file. Must be -used with \fB\-\-reads_rev\fR -.TP -\fB\-\-fr\fR filename[.gz] -Name of interleaved fasta/q file -.SS "MUMmer options:" -.TP -\fB\-\-cds_min_hit_length\fR INT -Minimum hit length when running nucmer of CDS -sequences against contigs [30] -.TP -\fB\-\-cds_min_hit_id\fR FLOAT -Minimum hit percent identity when running nucmer of -CDS sequences against contigs [80] -.TP -\fB\-\-ctg_min_hit_length\fR INT -Minimum hit length when running nucmer of contigs -against reference [100] -.TP -\fB\-\-ctg_min_hit_id\fR FLOAT -Minimum hit percent identity when running nucmer of -contigs against reference [80] -.SS "SMALT mapping options:" -.TP -\fB\-k\fR INT, \fB\-\-smalt_k\fR INT -kmer hash length in SMALT (the \fB\-k\fR option in smalt -index) [15] -.TP -\fB\-s\fR INT, \fB\-\-smalt_s\fR INT -kmer hash step size in SMALT (the \fB\-s\fR option in smalt -index) [3] -.TP -\fB\-y\fR FLOAT, \fB\-\-smalt_id\fR FLOAT -Minimum identity threshold for mapping to be reported -(the \fB\-y\fR option in smalt map) [0.5] -.SS "External tools:" -.TP -\fB\-\-gage_minid\fR INT in [0,100] -Minimum percent identity used when GAGE runs nucmer -[80] -.TP -\fB\-\-kraken_preload\fR -Use the \fB\-\-preload\fR option when running kraken -.TP -\fB\-\-ratt_config\fR filename -Specify your own RATT config file -/usr/local/lib/python3.4/distpackages/iva\-0.10.0\-py3.4.egg/iva/ratt/ratt.config -.SS "Other options:" -.TP -\fB\-\-ctg_layout_plot_title\fR STRING -Title to use in contig layout plot [IVA QC contig -layout and read depth] -.TP -\fB\-\-min_ref_cov\fR INT -Minimum read coverage of the reference, on each -strand, to count as OK coverage [5] -.TP -\fB\-\-noclean\fR -Do not clean temporary files -.TP -\fB\-\-threads\fR INT -Number of threads to use [1] -.TP -\fB\-\-version\fR -show program's version number and exit -.PP -You must supply reads in one of two ways: 1) both \fB\-\-reads_fwd\fR and \fB\-\-reads_rev\fR; -or 2) \fB\-\-fr\fR. Also, you must either supply a reference with \fB\-\-embl_dir\fR, or -choose one automatically from a database with \fB\-\-ref_db\fR. -.SH "AUTHOR" -.sp -iva_qc was originally written by Martin Hunt (mh12\@sanger.ac.uk) -.SH "COPYING" -.sp -Wellcome Trust Sanger Institute Copyright \(co 2013 Wellcome Trust Sanger Institute This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version\&. diff --git a/debian/man/iva_qc_make_db.1 b/debian/man/iva_qc_make_db.1 deleted file mode 100644 index 1092a3a..0000000 --- a/debian/man/iva_qc_make_db.1 +++ /dev/null @@ -1,48 +0,0 @@ -.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4. -.TH IVA_QC_MAKE_DB "1" "December 2014" "iva_qc_make_db 0.10.0" "iva_qc_make_db" -.SH NAME -iva_qc_make_db \- makes a database for use as input to iva_qc -.SH DESCRIPTION -usage: iva_qc_make_db [options] <output directory> -.SS "positional arguments:" -.TP -Directory_name -Name of output directory -.SS "optional arguments:" -.TP -\fB\-h\fR, \fB\-\-help\fR -show this help message and exit -.TP -\fB\-\-add_to_ref\fR Filename -Filename of Genbank IDs or GI numbers to be added to -database. Format is: whitespace separated list of GI -numbers on each line. One line defines one genome -(e.g. flu is 8 segements, so put 8 GI numbers on one -line for one flu reference) -.TP -\fB\-\-skip_viruses\fR -Do not run kraken\-build \fB\-\-download\-library\fR viruses -when building the database. If this option used, then -\fB\-\-add_to_ref\fR must also be used -.TP -\fB\-\-threads\fR INT -Number of threads to use [1] -.TP -\fB\-\-minimizer_len\fR INT -Number to pass to kraken\-build minimizer_len option -[13] -.TP -\fB\-\-max_db_size\fR INT -Number to pass to kraken\-build max_db_size option [3] -.TP -\fB\-\-verbose\fR -Be verbose -.TP -\fB\-\-version\fR -show program's version number and exit -.SH "AUTHOR" -.sp -iva_qc_make_db was originally written by Martin Hunt (mh12\@sanger.ac.uk) -.SH "COPYING" -.sp -Wellcome Trust Sanger Institute Copyright \(co 2013 Wellcome Trust Sanger Institute This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version\&. diff --git a/debian/usage_to_man b/debian/usage_to_man deleted file mode 100755 index a60a7b4..0000000 --- a/debian/usage_to_man +++ /dev/null @@ -1,111 +0,0 @@ -#!/usr/bin/perl -use strict; -use warnings; - -#Converts Fastaq python scripts usage into man pages. -#The man pages are placed in the man folder of the main Fastaq directory - -createManPages(); - -sub createManPages { - - my $source= 'scripts'; - my $destination= 'debian/man'; - my $app_name = 'iva'; - my $descriptions = shortDescription(); - - unless ( -d $destination ) { - system(mkdir $destination); - } - - my @files; - - push(@files,`ls $source/iva*`); - - if ( scalar @files > 0 ) { - - print "Creating manpages\n"; - for my $file ( @files ) { - $file =~ s/\n$//; - - my $filename = $file; - $filename =~ s/$source\///; - - my $uc_filename = uc($filename); - my $man_file = $filename; - - $man_file = $destination . '/' . $man_file . '.1'; - - open (my $man_fh, ">", $man_file); - - my $grep_string = $filename . ': error: too few arguments'; - - my $cmd = "help2man -m $filename -n $filename --no-discard-stderr $file | sed 's/usage://gi'"; - my @output; - push(@output, `$cmd`); - - for my $line (@output) { - $line =~ s/\n$//; - - } - - for (my $i = 0; $i < scalar @output; $i++) { - my $output_line = $output[$i]; - - if ($output_line =~ m/^\.TH/) { - $output_line =~ s/\s+/ /g; - $output_line =~ s/(\.TH) ("\d+") ("[a-zA-Z0-9_ ]*") ("[a-zA-Z0-9_<>\[\]\/\.\(\), ]*") ("[a-zA-Z0-9_]*")/$1 $uc_filename $2 $3 "$app_name" "Fastaq executables"/; - } - - $output_line =~ s/ \\- $filename/$filename \- $descriptions->{$filename}/; - - if ( $output_line =~ m/^.PP/ && $output[$i + 1] =~ m/^$filename\:/ ) { - $output_line = $output[$i + 1] = ''; - } - - if ($output_line =~ m/^\.SH "SEE ALSO"/) { - last; - } - print $man_fh "$output_line\n"; - } - - writeAuthorAndCopyright($man_fh,$filename); - close($man_fh); - } - print "Manpage creation complete\n"; - } -} - -sub writeAuthorAndCopyright { - - my ($man_fh,$filename) = @_; - - my $author_blurb = <<END_OF_AUTHOR_BLURB; -.SH "AUTHOR" -.sp -$filename was originally written by Martin Hunt (mh12\@sanger.ac.uk) -END_OF_AUTHOR_BLURB - - print $man_fh "$author_blurb\n"; - - my $copyright_blurb = <<'END_OF_C_BLURB'; -.SH "COPYING" -.sp -Wellcome Trust Sanger Institute Copyright \(co 2013 Wellcome Trust Sanger Institute This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version\&. -END_OF_C_BLURB - - print $man_fh "$copyright_blurb\n"; - -} - - -sub shortDescription { - - my %descriptions = ( - iva => 'makes an interleaved file of read pairs', - iva_qc => 'splits a multi fasta/q file into separate files', - iva_qc_make_db => 'counts the number of sequences in a fasta/q file', - ); - - return(\%descriptions); -} -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/iva.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
