[med-svn] [iva] 01/01: Package builds and is lintian clean, but some tests still failing
Jorge Soares
jssoares-guest at moszumanska.debian.org
Sun Dec 7 14:14:11 UTC 2014
This is an automated email from the git hooks/post-receive script.
jssoares-guest pushed a commit to branch master
in repository iva.
commit 3f2af1ace4fdd15ddc83e3a04767fab722394b60
Author: Jorge Soares <j.s.soares at gmail.com>
Date: Sun Dec 7 14:08:30 2014 +0000
Package builds and is lintian clean, but some tests still failing
---
debian/man/iva.1 | 175 +++++++++++++++++++++++++
debian/man/iva_qc.1 | 109 +++++++++++++++
debian/man/iva_qc_make_db.1 | 48 +++++++
debian/patches/series | 2 +-
debian/patches/strip-dependencies-from-setuppy | 10 ++
debian/rules | 10 --
6 files changed, 343 insertions(+), 11 deletions(-)
diff --git a/debian/man/iva.1 b/debian/man/iva.1
new file mode 100644
index 0000000..ece955d
--- /dev/null
+++ b/debian/man/iva.1
@@ -0,0 +1,175 @@
+.\" 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
+conjuction 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
+conjuction 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 unecessary 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
new file mode 100644
index 0000000..0dec853
--- /dev/null
+++ b/debian/man/iva_qc.1
@@ -0,0 +1,109 @@
+.\" 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
new file mode 100644
index 0000000..1092a3a
--- /dev/null
+++ b/debian/man/iva_qc_make_db.1
@@ -0,0 +1,48 @@
+.\" 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/patches/series b/debian/patches/series
index 8d02f4a..a584f4d 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,2 @@
-delay-import-and-remove-dependencies
add-shebang-line-to-getMummerStats
+strip-dependencies-from-setuppy
diff --git a/debian/patches/strip-dependencies-from-setuppy b/debian/patches/strip-dependencies-from-setuppy
new file mode 100644
index 0000000..c1e81f4
--- /dev/null
+++ b/debian/patches/strip-dependencies-from-setuppy
@@ -0,0 +1,10 @@
+Description: Removing pypi dependencies from setup.py
+--- a/setup.py
++++ b/setup.py
+@@ -17,6 +17,5 @@
+ url='https://github.com/sanger-pathogens/iva',
+ scripts=glob.glob('scripts/*'),
+ test_suite='nose.collector',
+- install_requires=['nose >= 1.3', 'fastaq >= 1.6.0', 'networkx'],
+ license='GPLv3',
+ )
diff --git a/debian/rules b/debian/rules
index 386b3b7..0f40ddb 100755
--- a/debian/rules
+++ b/debian/rules
@@ -36,13 +36,3 @@ override_dh_auto_build:
override_dh_auto_test:
#PASS
-
-override_dh_auto_clean:
- dh_auto_clean
- rm -rf $(mandir)
-
-
-override_dh_installman:
- mkdir -p $(mandir)
- $(debfolder)/usage_to_man
- dh_installman --
--
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