[med-svn] r20671 - in trunk/packages: . srst2 srst2/trunk srst2/trunk/debian srst2/trunk/debian/mans srst2/trunk/debian/source srst2/trunk/debian/upstream
Andreas Tille
tille at moszumanska.debian.org
Tue Dec 8 08:04:26 UTC 2015
Author: tille
Date: 2015-12-08 08:04:25 +0000 (Tue, 08 Dec 2015)
New Revision: 20671
Added:
trunk/packages/srst2/
trunk/packages/srst2/trunk/
trunk/packages/srst2/trunk/debian/
trunk/packages/srst2/trunk/debian/changelog
trunk/packages/srst2/trunk/debian/compat
trunk/packages/srst2/trunk/debian/control
trunk/packages/srst2/trunk/debian/copyright
trunk/packages/srst2/trunk/debian/docs
trunk/packages/srst2/trunk/debian/links
trunk/packages/srst2/trunk/debian/manpages
trunk/packages/srst2/trunk/debian/mans/
trunk/packages/srst2/trunk/debian/mans/getmlst.1
trunk/packages/srst2/trunk/debian/mans/scores_vs_expected.1
trunk/packages/srst2/trunk/debian/mans/slurm_srst2.1
trunk/packages/srst2/trunk/debian/mans/srst2.1
trunk/packages/srst2/trunk/debian/rules
trunk/packages/srst2/trunk/debian/source/
trunk/packages/srst2/trunk/debian/source/format
trunk/packages/srst2/trunk/debian/upstream/
trunk/packages/srst2/trunk/debian/upstream/metadata
trunk/packages/srst2/trunk/debian/watch
Log:
Inject initial packaging of srst2
Added: trunk/packages/srst2/trunk/debian/changelog
===================================================================
--- trunk/packages/srst2/trunk/debian/changelog (rev 0)
+++ trunk/packages/srst2/trunk/debian/changelog 2015-12-08 08:04:25 UTC (rev 20671)
@@ -0,0 +1,5 @@
+srst2 (0.1.6-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Mon, 07 Dec 2015 14:37:55 +0100
Added: trunk/packages/srst2/trunk/debian/compat
===================================================================
--- trunk/packages/srst2/trunk/debian/compat (rev 0)
+++ trunk/packages/srst2/trunk/debian/compat 2015-12-08 08:04:25 UTC (rev 20671)
@@ -0,0 +1 @@
+9
Added: trunk/packages/srst2/trunk/debian/control
===================================================================
--- trunk/packages/srst2/trunk/debian/control (rev 0)
+++ trunk/packages/srst2/trunk/debian/control 2015-12-08 08:04:25 UTC (rev 20671)
@@ -0,0 +1,26 @@
+Source: srst2
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ dh-python,
+ python-all,
+ python-setuptools,
+ python-markdown
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/srst2/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/srst2/trunk/
+Homepage: https://katholt.github.io/srst2/
+
+Package: srst2
+Architecture: any
+Depends: ${python:Depends},
+ ${misc:Depends},
+ bowtie2,
+ samtools,
+ python-scipy
+Description: Short Read Sequence Typing for Bacterial Pathogens
+ This program is designed to take Illumina sequence data, a MLST database
+ and/or a database of gene sequences (e.g. resistance genes, virulence
+ genes, etc) and report the presence of STs and/or reference genes.
Added: trunk/packages/srst2/trunk/debian/copyright
===================================================================
--- trunk/packages/srst2/trunk/debian/copyright (rev 0)
+++ trunk/packages/srst2/trunk/debian/copyright 2015-12-08 08:04:25 UTC (rev 20671)
@@ -0,0 +1,43 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: SRST2
+Upstream-Contact: Kathryn Holt <drkatholt at gmail.com>
+Source: https://github.com/katholt/srst2/
+
+Files: *
+Copyright: 2012-2015 Michael Inouye <minouye at unimelb.edu.au>, Harriet Dashnow <h.dashnow at gmail.com>,
+ Kathryn Holt <kholt at unimelb.edu.au>, Bernie Pope <bjpope at unimelb.edu.au>
+License: BSD-3-clause
+
+Files: debian/*
+Copyright: 2015 Andreas Tille <tille at debian.org>
+License: BSD-3-clause
+
+License: BSD-3-clause
+ Redistribution and use of this software in source and binary forms, with or
+ without modification, are permitted provided that the following conditions are
+ met:
+ .
+ * Redistributions of source code must retain the above
+ copyright notice, this list of conditions and the
+ following disclaimer.
+ .
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the
+ following disclaimer in the documentation and/or other
+ materials provided with the distribution.
+ .
+ * Neither the name of the author nor the names of its
+ contributors may be used to endorse or promote products
+ derived from this software without specific prior
+ written permission of the author.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Added: trunk/packages/srst2/trunk/debian/docs
===================================================================
--- trunk/packages/srst2/trunk/debian/docs (rev 0)
+++ trunk/packages/srst2/trunk/debian/docs 2015-12-08 08:04:25 UTC (rev 20671)
@@ -0,0 +1,2 @@
+README.html
+example.txt
Added: trunk/packages/srst2/trunk/debian/links
===================================================================
--- trunk/packages/srst2/trunk/debian/links (rev 0)
+++ trunk/packages/srst2/trunk/debian/links 2015-12-08 08:04:25 UTC (rev 20671)
@@ -0,0 +1,4 @@
+usr/share/srst2/getmlst.py usr/bin/getmlst
+usr/share/srst2/scores_vs_expected.py usr/bin/scores_vs_expected
+usr/share/srst2/slurm_srst2.py usr/bin/slurm_srst2
+usr/share/srst2/srst2.py usr/bin/srst2
Added: trunk/packages/srst2/trunk/debian/manpages
===================================================================
--- trunk/packages/srst2/trunk/debian/manpages (rev 0)
+++ trunk/packages/srst2/trunk/debian/manpages 2015-12-08 08:04:25 UTC (rev 20671)
@@ -0,0 +1 @@
+debian/mans/*.1
Added: trunk/packages/srst2/trunk/debian/mans/getmlst.1
===================================================================
--- trunk/packages/srst2/trunk/debian/mans/getmlst.1 (rev 0)
+++ trunk/packages/srst2/trunk/debian/mans/getmlst.1 2015-12-08 08:04:25 UTC (rev 20671)
@@ -0,0 +1,43 @@
+.TH GETMLST "1" "December 2015" "getmlst 0.1.6" "User Commands"
+.SH NAME
+getmlst \- Download MLST datasets by speciesfrom pubmlst.org.
+.SH SYNOPSIS
+.B getmlst
+[\fB\-h\fR] [\fB\-\-repository_url\fR URL] \fB\-\-species\fR NAME
+[\fB\-\-force_scheme_name\fR]
+.SH DESCRIPTION
+Download MLST datasets from this site: http://pubmlst.org/data/ by
+parsing an xml file (http://pubmlst.org/data/dbases.xml).
+.P
+Data is downloaded for a species determined by the user:
+.IP
+- profiles (maps STs to allele numbers)
+.IP
+- numbered sequences for each locus in the scheme
+.P
+In addition, the alleles are concatenated together for use with SRST2.
+.P
+A log file is also generated in the working directory, detailing the
+time, date and location of all files downloaded, as well as the <retrieved>
+tag which tells us when the XML entry was last updated.
+.P
+If the species name input by the user matches multiple <species> in the
+xml file, the script simply reports the possible matches so the user can
+try again.
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-repository_url\fR URL
+URL for MLST repository XML index
+.TP
+\fB\-\-species\fR NAME
+The name of the species that you want to download
+(e.g. "Escherichia coli")
+.TP
+\fB\-\-force_scheme_name\fR
+Flage to force downloading of specific scheme name
+(e.g. "Clostridium difficile")
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
Added: trunk/packages/srst2/trunk/debian/mans/scores_vs_expected.1
===================================================================
--- trunk/packages/srst2/trunk/debian/mans/scores_vs_expected.1 (rev 0)
+++ trunk/packages/srst2/trunk/debian/mans/scores_vs_expected.1 2015-12-08 08:04:25 UTC (rev 20671)
@@ -0,0 +1,67 @@
+.TH SCORES_VS_EXPECTED "1" "December 2015" "scores_vs_expected 0.1.6" "User Commands"
+.SH NAME
+scores_vs_expected \- parse scores from SRST(v2)
+.SH OPTIONS
+.B scores_vs_expected
+[\fB\-h\fR] \fB\-\-scores\fR SCORES [SCORES ...] \fB\-\-output\fR OUTPUT
+[\fB\-\-mlst_delimiter\fR MLST_DELIMITER]
+[\fB\-\-known_alleles\fR KNOWN_ALLELES]
+[\fB\-\-known_STs\fR KNOWN_STS]
+[\fB\-\-ST_definitions\fR ST_DEFINITIONS] [\fB\-\-ignore_last\fR]
+[\fB\-\-min_coverage\fR MIN_COVERAGE]
+[\fB\-\-min_depth\fR MIN_DEPTH]
+[\fB\-\-min_edge_depth\fR MIN_EDGE_DEPTH]
+.SH DESCRIPTION
+SRST2 \- Short Read Sequence Typer (v2): Outputs score and gene summaries.
+Reference fasta must have been in format cluster#__gene__allele
+.P
+Parses scores from SRST(v2) to produce a summary table of the top scoring allele for each locus/cluster for multiple samples.
+If a table of known/expected alleles are provided, this info is also included in the scores summary output.
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-scores\fR SCORES [SCORES ...]
+One or more .scores files produced by srst2.py
+.TP
+\fB\-\-output\fR OUTPUT
+Prefix for output tables summarising the top scoring
+allele for each gene with more detailed score
+information, and ST table.
+.TP
+\fB\-\-mlst_delimiter\fR MLST_DELIMITER
+Character that separates locus symbol from allele
+number (e.g. "\-")
+.TP
+\fB\-\-known_alleles\fR KNOWN_ALLELES
+File of known alleles for comparison (tab\-delimited)
+.TP
+\fB\-\-known_STs\fR KNOWN_STS
+File of known STs for comparison (tab\-delimited), must
+also provide ST definitions table (\fB\-\-mlst\fR)
+.TP
+\fB\-\-ST_definitions\fR ST_DEFINITIONS
+Table of ST definitions
+.TP
+\fB\-\-ignore_last\fR
+Ignore last column of ST profiles table (e.g.
+sometimes an additional column is added to indicate
+clonal complex, which is not part of the ST
+definition).
+.TP
+\fB\-\-min_coverage\fR MIN_COVERAGE
+Percent coverage cutoff for gene reporting (default
+90)
+.TP
+\fB\-\-min_depth\fR MIN_DEPTH
+Minimum mean depth to flag as dubious allele call
+(default 5)
+.TP
+\fB\-\-min_edge_depth\fR MIN_EDGE_DEPTH
+Minimum edge depth to flag as dubious allele call
+(default 2)
+.SH AUTHOR
+Harriet Dashnow (h.dashnow at gmail.com), Kathryn Holt (kholt at unimelb.edu.au)
+.P
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
Added: trunk/packages/srst2/trunk/debian/mans/slurm_srst2.1
===================================================================
--- trunk/packages/srst2/trunk/debian/mans/slurm_srst2.1 (rev 0)
+++ trunk/packages/srst2/trunk/debian/mans/slurm_srst2.1 2015-12-08 08:04:25 UTC (rev 20671)
@@ -0,0 +1,56 @@
+.TH SLURM_SRST2 "1" "December 2015" "slurm_srst2 0.1.6" "User Commands"
+.SH NAME
+slurm_srst2 \- running srst2 against multiple read sets
+.SH OPTIONS
+.B slurm_srst2
+[\fB\-h\fR] [\fB\-\-walltime\fR WALLTIME] [\fB\-\-memory\fR MEMORY]
+[\fB\-\-rundir\fR RUNDIR] \fB\-\-script\fR SCRIPT \fB\-\-output\fR OUTPUT
+[\fB\-\-input_se\fR INPUT_SE [INPUT_SE ...]]
+[\fB\-\-input_pe\fR INPUT_PE [INPUT_PE ...]] [\fB\-\-forward\fR FORWARD]
+[\fB\-\-reverse\fR REVERSE] [\fB\-\-other_args\fR OTHER_ARGS]
+.PP
+.SH DESCRIPTION
+Submit SRST2 jobs through SLURM (see srst(1))
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-walltime\fR WALLTIME
+wall time (default 0\-1:0 = 1 h)
+.TP
+\fB\-\-memory\fR MEMORY
+mem (default 4096 = 4gb)
+.TP
+\fB\-\-rundir\fR RUNDIR
+directory to run in (default current dir)
+.TP
+\fB\-\-script\fR SCRIPT
+path to srst2 (default srst2)
+.TP
+\fB\-\-output\fR OUTPUT
+identifier for outputs (will be combined with read set
+identifiers)
+.TP
+\fB\-\-input_se\fR INPUT_SE [INPUT_SE ...]
+Single end read file(s) for analysing (may be gzipped)
+.TP
+\fB\-\-input_pe\fR INPUT_PE [INPUT_PE ...]
+Paired end read files for analysing (may be gzipped)
+.TP
+\fB\-\-forward\fR FORWARD
+Designator for forward reads (only used if NOT in
+MiSeq format sample_S1_L001_R1_001.fastq.gz; otherwise
+default is _1, i.e. expect forward reads as
+sample_1.fastq.gz)
+.TP
+\fB\-\-reverse\fR REVERSE
+Designator for reverse reads (only used if NOT in
+MiSeq format sample_S1_L001_R2_001.fastq.gz; otherwise
+default is _2, i.e. expect forward reads as
+sample_2.fastq.gz)
+.TP
+\fB\-\-other_args\fR OTHER_ARGS
+string containing all other arguments to pass to srst2
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
Added: trunk/packages/srst2/trunk/debian/mans/srst2.1
===================================================================
--- trunk/packages/srst2/trunk/debian/mans/srst2.1 (rev 0)
+++ trunk/packages/srst2/trunk/debian/mans/srst2.1 2015-12-08 08:04:25 UTC (rev 20671)
@@ -0,0 +1,159 @@
+.TH SRST2 "1" "December 2015" "srst2 0.1.6" "User Commands"
+.SH NAME
+srst2 \- Short Read Sequence Typer
+.SH SYNOPSIS
+.B srst2
+[\fB\-h\fR] [\fB\-\-version\fR] [\fB\-\-input_se\fR INPUT_SE [INPUT_SE ...]]
+[\fB\-\-input_pe\fR INPUT_PE [INPUT_PE ...]] [\fB\-\-merge_paired\fR]
+[\fB\-\-forward\fR FORWARD] [\fB\-\-reverse\fR REVERSE] [\fB\-\-read_type\fR {q,qseq,f}]
+[\fB\-\-mlst_db\fR MLST_DB] [\fB\-\-mlst_delimiter\fR MLST_DELIMITER]
+[\fB\-\-mlst_definitions\fR MLST_DEFINITIONS]
+[\fB\-\-mlst_max_mismatch\fR MLST_MAX_MISMATCH]
+[\fB\-\-gene_db\fR GENE_DB [GENE_DB ...]] [\fB\-\-no_gene_details\fR]
+[\fB\-\-gene_max_mismatch\fR GENE_MAX_MISMATCH]
+[\fB\-\-min_coverage\fR MIN_COVERAGE] [\fB\-\-max_divergence\fR MAX_DIVERGENCE]
+[\fB\-\-min_depth\fR MIN_DEPTH] [\fB\-\-min_edge_depth\fR MIN_EDGE_DEPTH]
+[\fB\-\-prob_err\fR PROB_ERR] [\fB\-\-stop_after\fR STOP_AFTER] [\fB\-\-other\fR OTHER]
+[\fB\-\-mapq\fR MAPQ] [\fB\-\-baseq\fR BASEQ] [\fB\-\-samtools_args\fR SAMTOOLS_ARGS]
+\fB\-\-output\fR OUTPUT [\fB\-\-log\fR] [\fB\-\-save_scores\fR] [\fB\-\-report_new_consensus\fR]
+[\fB\-\-report_all_consensus\fR] [\fB\-\-use_existing_pileup\fR]
+[\fB\-\-use_existing_scores\fR] [\fB\-\-keep_interim_alignment\fR]
+[\fB\-\-prev_output\fR PREV_OUTPUT [PREV_OUTPUT ...]]
+.SH DESCRIPTION
+SRST2 \- Short Read Sequence Typer (v2)
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-\-input_se\fR INPUT_SE [INPUT_SE ...]
+Single end read file(s) for analysing (may be gzipped)
+.TP
+\fB\-\-input_pe\fR INPUT_PE [INPUT_PE ...]
+Paired end read files for analysing (may be gzipped)
+.TP
+\fB\-\-merge_paired\fR
+Switch on if all the input read sets belong to a
+single sample, and you want to merge their data to get
+a single result
+.TP
+\fB\-\-forward\fR FORWARD
+Designator for forward reads (only used if NOT in
+MiSeq format sample_S1_L001_R1_001.fastq.gz; otherwise
+default is _1, i.e. expect forward reads as
+sample_1.fastq.gz)
+.TP
+\fB\-\-reverse\fR REVERSE
+Designator for reverse reads (only used if NOT in
+MiSeq format sample_S1_L001_R2_001.fastq.gz; otherwise
+default is _2, i.e. expect forward reads as
+sample_2.fastq.gz
+.TP
+\fB\-\-read_type\fR {q,qseq,f}
+Read file type (for bowtie2; default is q=fastq; other
+options: qseq=solexa, f=fasta).
+.TP
+\fB\-\-mlst_db\fR MLST_DB
+Fasta file of MLST alleles (optional)
+.TP
+\fB\-\-mlst_delimiter\fR MLST_DELIMITER
+Character(s) separating gene name from allele number
+in MLST database (default "\-", as in arcc\-1)
+.TP
+\fB\-\-mlst_definitions\fR MLST_DEFINITIONS
+ST definitions for MLST scheme (required if mlst_db
+supplied and you want to calculate STs)
+.TP
+\fB\-\-mlst_max_mismatch\fR MLST_MAX_MISMATCH
+Maximum number of mismatches per read for MLST allele
+calling (default 10)
+.TP
+\fB\-\-gene_db\fR GENE_DB [GENE_DB ...]
+Fasta file/s for gene databases (optional)
+.TP
+\fB\-\-no_gene_details\fR
+Switch OFF verbose reporting of gene typing
+.TP
+\fB\-\-gene_max_mismatch\fR GENE_MAX_MISMATCH
+Maximum number of mismatches per read for gene
+detection and allele calling (default 10)
+.TP
+\fB\-\-min_coverage\fR MIN_COVERAGE
+Minimum %coverage cutoff for gene reporting (default
+90)
+.TP
+\fB\-\-max_divergence\fR MAX_DIVERGENCE
+Maximum %divergence cutoff for gene reporting (default
+10)
+.TP
+\fB\-\-min_depth\fR MIN_DEPTH
+Minimum mean depth to flag as dubious allele call
+(default 5)
+.TP
+\fB\-\-min_edge_depth\fR MIN_EDGE_DEPTH
+Minimum edge depth to flag as dubious allele call
+(default 2)
+.TP
+\fB\-\-prob_err\fR PROB_ERR
+Probability of sequencing error (default 0.01)
+.TP
+\fB\-\-stop_after\fR STOP_AFTER
+Stop mapping after this number of reads have been
+mapped (otherwise map all)
+.TP
+\fB\-\-other\fR OTHER
+Other arguments to pass to bowtie2 (must be escaped,
+e.g. "\e\-\-no\-mixed".
+.TP
+\fB\-\-mapq\fR MAPQ
+Samtools \fB\-q\fR parameter (default 1)
+.TP
+\fB\-\-baseq\fR BASEQ
+Samtools \fB\-Q\fR parameter (default 20)
+.TP
+\fB\-\-samtools_args\fR SAMTOOLS_ARGS
+Other arguments to pass to samtools mpileup (must be
+escaped, e.g. "\e\-A").
+.TP
+\fB\-\-output\fR OUTPUT
+Prefix for srst2 output files
+.TP
+\fB\-\-log\fR
+Switch ON logging to file (otherwise log to stdout)
+.TP
+\fB\-\-save_scores\fR
+Switch ON verbose reporting of all scores
+.TP
+\fB\-\-report_new_consensus\fR
+If a matching alleles is not found, report the
+consensus allele. Note, only SNP differences are
+considered, not indels.
+.TP
+\fB\-\-report_all_consensus\fR
+Report the consensus allele for the most likely
+allele. Note, only SNP differences are considered, not
+indels.
+.TP
+\fB\-\-use_existing_pileup\fR
+Use existing pileups if available, otherwise they will
+be generated
+.TP
+\fB\-\-use_existing_scores\fR
+Use existing scores files if available, otherwise they
+will be generated
+.TP
+\fB\-\-keep_interim_alignment\fR
+Keep interim files (sam & unsorted bam), otherwise
+they will be deleted after sorted bam is created
+.TP
+\fB\-\-prev_output\fR PREV_OUTPUT [PREV_OUTPUT ...]
+SRST2 results files to compile (any new results from
+this run will also be incorporated)
+.SH AUTHOR
+Michael Inouye (minouye at unimelb.edu.au), Harriet Dashnow (h.dashnow at gmail.com),
+Kathryn Holt (kholt at unimelb.edu.au), Bernie Pope (bjpope at unimelb.edu.au)
+.P
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
Added: trunk/packages/srst2/trunk/debian/rules
===================================================================
--- trunk/packages/srst2/trunk/debian/rules (rev 0)
+++ trunk/packages/srst2/trunk/debian/rules 2015-12-08 08:04:25 UTC (rev 20671)
@@ -0,0 +1,29 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+
+%:
+ dh $@ --with python2
+
+override_dh_auto_build:
+ dh_auto_build
+ markdown_py -f README.html README.md
+
+override_dh_install:
+ dh_install
+ mkdir -p debian/$(DEBPKGNAME)/usr/share
+ mv debian/$(DEBPKGNAME)/usr/lib/*/dist-packages/$(DEBPKGNAME) debian/$(DEBPKGNAME)/usr/share
+ rm -rf debian/*/usr/bin/*.py debian/$(DEBPKGNAME)/usr/lib/*/dist-packages/
+
+override_dh_fixperms:
+ dh_fixperms
+ chmod +x debian/$(DEBPKGNAME)/usr/share/$(DEBPKGNAME)/getmlst.py
+ chmod +x debian/$(DEBPKGNAME)/usr/share/$(DEBPKGNAME)/scores_vs_expected.py
+ chmod +x debian/$(DEBPKGNAME)/usr/share/$(DEBPKGNAME)/slurm_srst2.py
+ chmod +x debian/$(DEBPKGNAME)/usr/share/$(DEBPKGNAME)/srst2.py
+
+# README.html contains a really maintained changelog
+#override_dh_installchangelogs:
+# dh_installchangelogs CHANGES.txt
Property changes on: trunk/packages/srst2/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/srst2/trunk/debian/source/format
===================================================================
--- trunk/packages/srst2/trunk/debian/source/format (rev 0)
+++ trunk/packages/srst2/trunk/debian/source/format 2015-12-08 08:04:25 UTC (rev 20671)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/srst2/trunk/debian/upstream/metadata
===================================================================
--- trunk/packages/srst2/trunk/debian/upstream/metadata (rev 0)
+++ trunk/packages/srst2/trunk/debian/upstream/metadata 2015-12-08 08:04:25 UTC (rev 20671)
@@ -0,0 +1,12 @@
+Reference:
+ Author: Michael Inouye and Harriet Dashnow and Lesley-Ann Raven and Mark B Schultz and Bernard J Pope and Takehiro Tomita and Justin Zobel and Kathryn E Holt3
+ Title: "SRST2: Rapid genomic surveillance for public health and hospital microbiology labs"
+ Journal: Genome Medicine
+ Year: 2014
+ Volume: 6
+ Number: 11
+ Pages: 90
+ DOI: 10.1186/s13073-014-0090-6
+ PMID: 25422674
+ URL: http://www.genomemedicine.com/content/6/11/90
+ eprint: http://www.genomemedicine.com/content/pdf/s13073-014-0090-6.pdf
Added: trunk/packages/srst2/trunk/debian/watch
===================================================================
--- trunk/packages/srst2/trunk/debian/watch (rev 0)
+++ trunk/packages/srst2/trunk/debian/watch 2015-12-08 08:04:25 UTC (rev 20671)
@@ -0,0 +1,3 @@
+version=3
+
+https://github.com/katholt/srst2/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
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