[med-svn] r22718 - in trunk/packages/srst2/trunk/debian: . mans
Andreas Tille
tille at moszumanska.debian.org
Thu Aug 25 09:24:31 UTC 2016
Author: tille
Date: 2016-08-25 09:24:30 +0000 (Thu, 25 Aug 2016)
New Revision: 22718
Removed:
trunk/packages/srst2/trunk/debian/mans/scores_vs_expected.1
Modified:
trunk/packages/srst2/trunk/debian/changelog
trunk/packages/srst2/trunk/debian/control
trunk/packages/srst2/trunk/debian/links
trunk/packages/srst2/trunk/debian/rules
Log:
Adapt to new upstream version and upload
Modified: trunk/packages/srst2/trunk/debian/changelog
===================================================================
--- trunk/packages/srst2/trunk/debian/changelog 2016-08-25 09:23:48 UTC (rev 22717)
+++ trunk/packages/srst2/trunk/debian/changelog 2016-08-25 09:24:30 UTC (rev 22718)
@@ -1,6 +1,7 @@
-srst2 (0.2.0-1) UNRELEASED; urgency=medium
+srst2 (0.2.0-1) unstable; urgency=medium
* New upstream version
+ * Recommends: python-rpy2
-- Andreas Tille <tille at debian.org> Tue, 09 Aug 2016 16:57:15 +0200
Modified: trunk/packages/srst2/trunk/debian/control
===================================================================
--- trunk/packages/srst2/trunk/debian/control 2016-08-25 09:23:48 UTC (rev 22717)
+++ trunk/packages/srst2/trunk/debian/control 2016-08-25 09:24:30 UTC (rev 22718)
@@ -27,6 +27,7 @@
samtools,
python-scipy,
python-biopython
+Recommends: python-rpy2
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/links
===================================================================
--- trunk/packages/srst2/trunk/debian/links 2016-08-25 09:23:48 UTC (rev 22717)
+++ trunk/packages/srst2/trunk/debian/links 2016-08-25 09:24:30 UTC (rev 22718)
@@ -1,5 +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
usr/share/srst2/database_clustering/get_all_vfdb.sh usr/bin/get_all_vfdb
Deleted: trunk/packages/srst2/trunk/debian/mans/scores_vs_expected.1
===================================================================
--- trunk/packages/srst2/trunk/debian/mans/scores_vs_expected.1 2016-08-25 09:23:48 UTC (rev 22717)
+++ trunk/packages/srst2/trunk/debian/mans/scores_vs_expected.1 2016-08-25 09:24:30 UTC (rev 22718)
@@ -1,67 +0,0 @@
-.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.
Modified: trunk/packages/srst2/trunk/debian/rules
===================================================================
--- trunk/packages/srst2/trunk/debian/rules 2016-08-25 09:23:48 UTC (rev 22717)
+++ trunk/packages/srst2/trunk/debian/rules 2016-08-25 09:24:30 UTC (rev 22718)
@@ -18,17 +18,13 @@
rm -rf debian/*/usr/bin/*.py debian/$(DEBPKGNAME)/usr/lib/*/dist-packages/
# fix line endings to make sure Python interpreter will be found
find debian/*/usr/share -name "VFDB*" -exec dos2unix \{\} \;
+ sed -i '1s:^#!/usr/local.*python[.0-9]*$$:/usr/bin/python:' debian/$(DEBPKGNAME)/usr/share/$(DEBPKGNAME)/qsub_srst2.py
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
- 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
+ chmod +x debian/$(DEBPKGNAME)/usr/share/srst2/database_clustering/get_genus_vfdb.sh
+ chmod +x debian/$(DEBPKGNAME)/usr/share/srst2/database_clustering/get_all_vfdb.sh
+ chmod -x debian/$(DEBPKGNAME)/usr/share/srst2/database_clustering/align_plot_tree_min3.py
override_dh_auto_test:
cd tests && python test_slurm_srst2.py && python test_srst2.py
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