New Upstream Snapshot - virulencefinder
Ready changes
Summary
Merged new upstream version: 2.0.4+git20200704.1.5cf8f0c (was: 2.0.4).
Resulting package
Built on 2022-12-19T10:22 (took 11m47s)
The resulting binary packages can be installed (if you have the apt repository enabled) by running one of:
apt install -t fresh-snapshots virulencefinder-examplesapt install -t fresh-snapshots virulencefinder
Lintian Result
- virulencefinder-examples_2.0.4+git20200704.1.5cf8f0c-1~jan+nus2_all.deb
- virulencefinder_2.0.4+git20200704.1.5cf8f0c-1~jan+nus2.dsc
- virulencefinder_2.0.4+git20200704.1.5cf8f0c-1~jan+nus2_all.deb
- virulencefinder_2.0.4+git20200704.1.5cf8f0c-1~jan+nus2_amd64.buildinfo
- virulencefinder_2.0.4+git20200704.1.5cf8f0c-1~jan+nus2_amd64.changes
Diff
diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index af7957c..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,5 +0,0 @@
-.DS_Store
-blast-2.2.26
-Output
-*.gz
-*~
diff --git a/README.md b/README.md
index 5038967..adb9846 100644
--- a/README.md
+++ b/README.md
@@ -56,6 +56,28 @@ python3 INSTALL.py kma_index
If kma_index has no bin install please install kma_index from the kma repository:
https://bitbucket.org/genomicepidemiology/kma
+## Dependencies
+In order to run the program without using docker, Python 3.5 (or newer) should be installed along with the following versions of the modules (or newer).
+
+#### Modules
+- cgecore 1.5.5
+- tabulate 0.7.7
+
+Modules can be installed using the following command. Here, the installation of the module cgecore is used as an example:
+```bash
+pip3 install cgecore
+```
+#### KMA and BLAST
+Additionally KMA and BLAST version 2.8.1 or newer should be installed.
+The newest versions of KMA and BLAST can be installed from here:
+```url
+https://bitbucket.org/genomicepidemiology/kma
+```
+
+```url
+ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
+```
+
## Usage
The program can be invoked with the -h option to get help and more information of the service.
@@ -113,6 +135,11 @@ Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, Aarestrup FM.
J. Clin. Micobiol. 2014. 52(5): 1501-1510.
[Epub ahead of print]
+References
+=======
+
+1. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics 2009; 10:421.
+2. Clausen PTLC, Aarestrup FM, Lund O. Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinformatics 2018; 19:307.
License
=======
diff --git a/debian/changelog b/debian/changelog
index 0615d59..b25f017 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+virulencefinder (2.0.4+git20200704.1.5cf8f0c-1) UNRELEASED; urgency=low
+
+ * New upstream snapshot.
+
+ -- Debian Janitor <janitor@jelmer.uk> Mon, 19 Dec 2022 10:14:04 -0000
+
virulencefinder (2.0.4-3) unstable; urgency=medium
* d/control: add myself to uploaders.
diff --git a/debian/patches/reproducible_build.patch b/debian/patches/reproducible_build.patch
index 5d3586d..c61807c 100644
--- a/debian/patches/reproducible_build.patch
+++ b/debian/patches/reproducible_build.patch
@@ -3,9 +3,11 @@ Author: Chris Lamb <lamby@debian.org>
Last-Update: 2019-08-03
Bug-Debian: https://bugs.debian.org/933783
---- virulencefinder-0.0+git20190402.4812325.orig/virulencefinder.py
-+++ virulencefinder-0.0+git20190402.4812325/virulencefinder.py
-@@ -473,8 +473,8 @@ for db in results:
+Index: virulencefinder.git/virulencefinder.py
+===================================================================
+--- virulencefinder.git.orig/virulencefinder.py
++++ virulencefinder.git/virulencefinder.py
+@@ -476,8 +476,8 @@ for db in results:
# Get run info for JSON file
service = os.path.basename(__file__).replace(".py", "")
Debdiff
File lists identical (after any substitutions)
No differences were encountered between the control files of package virulencefinder
No differences were encountered between the control files of package virulencefinder-examples