[med-svn] r22057 - in trunk/packages/srst2/trunk/debian: . mans
Andreas Tille
tille at moszumanska.debian.org
Tue May 31 20:27:42 UTC 2016
Author: tille
Date: 2016-05-31 20:27:41 +0000 (Tue, 31 May 2016)
New Revision: 22057
Modified:
trunk/packages/srst2/trunk/debian/changelog
trunk/packages/srst2/trunk/debian/control
trunk/packages/srst2/trunk/debian/docs
trunk/packages/srst2/trunk/debian/links
trunk/packages/srst2/trunk/debian/mans/getmlst.1
trunk/packages/srst2/trunk/debian/mans/srst2.1
trunk/packages/srst2/trunk/debian/rules
Log:
Commit current packaging state
Modified: trunk/packages/srst2/trunk/debian/changelog
===================================================================
--- trunk/packages/srst2/trunk/debian/changelog 2016-05-31 20:24:40 UTC (rev 22056)
+++ trunk/packages/srst2/trunk/debian/changelog 2016-05-31 20:27:41 UTC (rev 22057)
@@ -1,5 +1,5 @@
-srst2 (0.1.6-1) UNRELEASED; urgency=low
+srst2 (0.1.8-1) UNRELEASED; urgency=low
* Initial release (Closes: #<bug>)
- -- Andreas Tille <tille at debian.org> Mon, 07 Dec 2015 14:37:55 +0100
+ -- Andreas Tille <tille at debian.org> Tue, 31 May 2016 15:02:45 +0200
Modified: trunk/packages/srst2/trunk/debian/control
===================================================================
--- trunk/packages/srst2/trunk/debian/control 2016-05-31 20:24:40 UTC (rev 22056)
+++ trunk/packages/srst2/trunk/debian/control 2016-05-31 20:27:41 UTC (rev 22057)
@@ -8,8 +8,8 @@
python-all,
python-setuptools,
python-markdown
-Standards-Version: 3.9.6
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/srst2/trunk/
+Standards-Version: 3.9.8
+Vcs-Browser: https://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/
@@ -18,8 +18,10 @@
Depends: ${python:Depends},
${misc:Depends},
bowtie2,
+ cd-hit,
samtools,
- python-scipy
+ python-scipy,
+ python-biopython
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
Modified: trunk/packages/srst2/trunk/debian/docs
===================================================================
--- trunk/packages/srst2/trunk/debian/docs 2016-05-31 20:24:40 UTC (rev 22056)
+++ trunk/packages/srst2/trunk/debian/docs 2016-05-31 20:27:41 UTC (rev 22057)
@@ -1,2 +1,2 @@
-README.html
+README*.html
example.txt
Modified: trunk/packages/srst2/trunk/debian/links
===================================================================
--- trunk/packages/srst2/trunk/debian/links 2016-05-31 20:24:40 UTC (rev 22056)
+++ trunk/packages/srst2/trunk/debian/links 2016-05-31 20:27:41 UTC (rev 22057)
@@ -1,4 +1,9 @@
-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
+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
+usr/share/srst2/database_clustering/get_all_vfdb.sh usr/bin/get_all_vfdb
+usr/share/srst2/database_clustering/get_genus_vfdb.sh usr/bin/get_genus_vfdb
+usr/share/srst2/database_clustering/csv_to_gene_db.py usr/bin/csv_to_gene_db
+usr/share/srst2/database_clustering/VFDBgenus.py usr/bin/VFDBgenus
+usr/share/srst2/database_clustering/VFDB_cdhit_to_csv.py usr/bin/VFDB_cdhit_to_csv
Modified: trunk/packages/srst2/trunk/debian/mans/getmlst.1
===================================================================
--- trunk/packages/srst2/trunk/debian/mans/getmlst.1 2016-05-31 20:24:40 UTC (rev 22056)
+++ trunk/packages/srst2/trunk/debian/mans/getmlst.1 2016-05-31 20:27:41 UTC (rev 22057)
@@ -39,5 +39,7 @@
\fB\-\-force_scheme_name\fR
Flage to force downloading of specific scheme name
(e.g. "Clostridium difficile")
+.SH EXAMPLE
+getmlst --species "Escherichia coli#1"
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
Modified: trunk/packages/srst2/trunk/debian/mans/srst2.1
===================================================================
--- trunk/packages/srst2/trunk/debian/mans/srst2.1 2016-05-31 20:24:40 UTC (rev 22056)
+++ trunk/packages/srst2/trunk/debian/mans/srst2.1 2016-05-31 20:27:41 UTC (rev 22057)
@@ -152,6 +152,25 @@
\fB\-\-prev_output\fR PREV_OUTPUT [PREV_OUTPUT ...]
SRST2 results files to compile (any new results from
this run will also be incorporated)
+.SH EXAMPLE
+Assume you have a database downloaded by getmlst(1) by using
+.IP
+getmlst --species "Escherichia coli#1"
+.P
+For SRST2, remember to check what separator is being used in this allele database
+.P
+Looks like --mlst_delimiter '-'
+.IP
+ >adk-1 --> --> ('adk', '-', '1')
+.P
+Suggested srst2 command for use with this MLST database:
+.IP
+srst2 --output test --input_pe *.fastq.gz --mlst_db Escherichia_coli#1.fasta --mlst_definitions ecoli.txt --mlst_delimiter '-'
+.P
+Note, this is correctly guessing that we should use the default --mlst_delimiter '-' with
+this database. The log file will tell you exactly what files were downloaded.
+.P
+More verbose example usage is described in /usr/share/doc/srst2/example.txt.gz
.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)
Modified: trunk/packages/srst2/trunk/debian/rules
===================================================================
--- trunk/packages/srst2/trunk/debian/rules 2016-05-31 20:24:40 UTC (rev 22056)
+++ trunk/packages/srst2/trunk/debian/rules 2016-05-31 20:27:41 UTC (rev 22057)
@@ -10,11 +10,11 @@
override_dh_auto_build:
dh_auto_build
markdown_py -f README.html README.md
+ markdown_py -f README_database_clustering.html database_clustering/README.md
override_dh_install:
dh_install
- mkdir -p debian/$(DEBPKGNAME)/usr/share
- mv debian/$(DEBPKGNAME)/usr/lib/*/dist-packages/$(DEBPKGNAME) debian/$(DEBPKGNAME)/usr/share
+ mv debian/$(DEBPKGNAME)/usr/lib/*/dist-packages/$(DEBPKGNAME)/* debian/$(DEBPKGNAME)/usr/share/$(DEBPKGNAME)
rm -rf debian/*/usr/bin/*.py debian/$(DEBPKGNAME)/usr/lib/*/dist-packages/
override_dh_fixperms:
@@ -23,6 +23,10 @@
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
+ chmod -x debian/$(DEBPKGNAME)/usr/share/$(DEBPKGNAME)/database_clustering/align_plot_tree_min3.py
+ chmod +x debian/$(DEBPKGNAME)/usr/share/$(DEBPKGNAME)/database_clustering/VFDB*.py
+ chmod +x debian/$(DEBPKGNAME)/usr/share/$(DEBPKGNAME)/database_clustering/csv_to_gene_db.py
+ chmod +x debian/$(DEBPKGNAME)/usr/share/$(DEBPKGNAME)/database_clustering/*.sh
# README.html contains a really maintained changelog
#override_dh_installchangelogs:
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