[med-svn] [iva] 01/07: remove old manpage building facility
Sascha Steinbiss
sascha at steinbiss.name
Wed May 4 10:19:12 UTC 2016
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 <sascha at steinbiss.name>
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);
-}
--
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