[med-svn] [roary] 01/03: New upstream version 3.8.0+dfsg
Sascha Steinbiss
satta at debian.org
Wed Jan 25 15:51:28 UTC 2017
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository roary.
commit 1a1a97a6cf09455595ebb8ce45725d56eb2fb754
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Wed Jan 25 16:42:30 2017 +0100
New upstream version 3.8.0+dfsg
---
README.md | 11 +++++------
dist.ini | 2 +-
lib/Bio/Roary/CommandLine/IterativeCdhit.pm | 6 ++++--
lib/Bio/Roary/CommandLine/Roary.pm | 2 +-
lib/Bio/Roary/External/Makeblastdb.pm | 1 -
t/Bio/Roary/External/Makeblastdb.t | 2 +-
t/bin/dummy_makeblastdb | 1 -
t/bin/dummy_segmasker | 1 -
8 files changed, 12 insertions(+), 14 deletions(-)
diff --git a/README.md b/README.md
index 7e9e0bf..5a4f94f 100644
--- a/README.md
+++ b/README.md
@@ -18,20 +18,19 @@ Theres are a number of dependancies required for Roary, with instructions specif
* Homebrew/Linuxbrew - OSX/Linux
* Guix - Linux
* Virtual Machine - OSX/Linux/Windows
-* Docker
+* Docker - OSX/Linux/Windows/Cloud
* Installing from source - OSX/Linux
If the installation fails please contact your system administrator. If you encounter a bug please let us know by emailing roary at sanger.ac.uk .
##Ubuntu/Debian
-### Ubuntu 16.04
-
+###Debian Testing
```
sudo apt-get install roary
```
-###Ubuntu 14.04
-All the dependancies can be installed using apt and cpanm. Root permissions are required.
+###Ubuntu 14.04/16.04
+All the dependancies can be installed using apt and cpanm. Root permissions are required. Ubuntu 16.04 contains a package for Roary but it is frozen at v3.6.0.
```
sudo apt-get install bedtools cd-hit ncbi-blast+ mcl parallel cpanminus prank mafft fasttree
@@ -67,7 +66,7 @@ ftp://ftp.sanger.ac.uk/pub/pathogens/pathogens-vm/pathogens-vm.latest.ova
More importantly though, if your trying to do bioinformatics on Windows, your not going to get very far and you should seriously consider upgrading to Linux.
-##Docker
+##Docker - OSX/Linux/Windows/Cloud
We have a docker container which gets automatically built from the latest version of Roary in Debian Med. To install it:
```
diff --git a/dist.ini b/dist.ini
index 37708e3..bfcd266 100644
--- a/dist.ini
+++ b/dist.ini
@@ -1,5 +1,5 @@
name = Bio-Roary
-version = 3.7.0
+version = 3.8.0
author = Andrew J. Page <ap13 at sanger.ac.uk>
license = GPL_3
copyright_holder = Wellcome Trust Sanger Institute
diff --git a/lib/Bio/Roary/CommandLine/IterativeCdhit.pm b/lib/Bio/Roary/CommandLine/IterativeCdhit.pm
index eef7966..b153a2d 100644
--- a/lib/Bio/Roary/CommandLine/IterativeCdhit.pm
+++ b/lib/Bio/Roary/CommandLine/IterativeCdhit.pm
@@ -97,10 +97,12 @@ sub usage_text {
return <<USAGE;
Usage: iterative_cdhit [options]
-Iteratively cluster a set of proteins with CD-hit, lower the threshold each time and extracting core genes (1 per isolate) to another file, and remove them from the input proteins file.
+Iteratively cluster a FASTA file of proteins with CD-hit, lower the threshold each time and extracting core genes (1 per isolate) to another file, and remove them from the input proteins file.
+
+Required arguments:
+ -m STR input FASTA file of protein sequences [_combined_files]
Options: -p INT number of threads [1]
- -m STR output filename for combined proteins [_combined_files]
-n INT number of isolates [1]
-c STR cd-hit output filename [_clustered]
-f STR output filename for filtered sequences [_clustered_filtered.fa]
diff --git a/lib/Bio/Roary/CommandLine/Roary.pm b/lib/Bio/Roary/CommandLine/Roary.pm
index 103c0b9..f1a8ff1 100644
--- a/lib/Bio/Roary/CommandLine/Roary.pm
+++ b/lib/Bio/Roary/CommandLine/Roary.pm
@@ -50,7 +50,7 @@ has 'mafft' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'group_limit' => ( is => 'rw', isa => 'Num', default => 50000 );
has 'core_definition' => ( is => 'rw', isa => 'Num', default => 0.99 );
has 'verbose' => ( is => 'rw', isa => 'Bool', default => 0 );
-has 'kraken_db' => ( is => 'rw', isa => 'Str', default => '/lustre/scratch108/pathogen/pathpipe/kraken/minikraken_20140330/' );
+has 'kraken_db' => ( is => 'rw', isa => 'Str', default => '/lustre/scratch118/infgen/pathogen/pathpipe/kraken/minikraken_20140330/' );
has 'run_qc' => ( is => 'rw', isa => 'Bool', default => 0 );
has '_working_directory' => ( is => 'rw', isa => 'File::Temp::Dir', lazy => 1, builder => '_build__working_directory' );
diff --git a/lib/Bio/Roary/External/Makeblastdb.pm b/lib/Bio/Roary/External/Makeblastdb.pm
index e1b75e3..1659e50 100644
--- a/lib/Bio/Roary/External/Makeblastdb.pm
+++ b/lib/Bio/Roary/External/Makeblastdb.pm
@@ -49,7 +49,6 @@ sub _command_to_run {
$self->exec,
'-in', $self->fasta_file,
'-dbtype', $self->_dbtype,
- '-parse_seqids',
'-out', $self->output_database,
'-logfile', $self->_logfile
)
diff --git a/t/Bio/Roary/External/Makeblastdb.t b/t/Bio/Roary/External/Makeblastdb.t
old mode 100644
new mode 100755
index 02dab30..f76d740
--- a/t/Bio/Roary/External/Makeblastdb.t
+++ b/t/Bio/Roary/External/Makeblastdb.t
@@ -20,7 +20,7 @@ ok($obj = Bio::Roary::External::Makeblastdb->new(
mask_data => 'masking_data_file'
),'initialise object');
-is($obj->_command_to_run, $cwd.'/t/bin/dummy_makeblastdb -in t/data/some_fasta_file.fa -dbtype prot -parse_seqids -out '.$obj->_working_directory->dirname().'/output_contigs -logfile /dev/null', 'Command constructed as expected');
+is($obj->_command_to_run, $cwd.'/t/bin/dummy_makeblastdb -in t/data/some_fasta_file.fa -dbtype prot -out '.$obj->_working_directory->dirname().'/output_contigs -logfile /dev/null', 'Command constructed as expected');
ok($obj->run(), 'run dummy command');
unlink("output_contigs.phr");
diff --git a/t/bin/dummy_makeblastdb b/t/bin/dummy_makeblastdb
index 885b6e4..0e293f2 100755
--- a/t/bin/dummy_makeblastdb
+++ b/t/bin/dummy_makeblastdb
@@ -7,7 +7,6 @@ GetOptions(
'd|dbtype=s' => \$dbtype,
'l|logfile=s' => \$logfile,
'i|in=s' => \$in,
- 'parse_seqids' => \$parse_seqids,
'mask_data=s' => \$mask_data,
);
diff --git a/t/bin/dummy_segmasker b/t/bin/dummy_segmasker
index 1069b82..06b221d 100755
--- a/t/bin/dummy_segmasker
+++ b/t/bin/dummy_segmasker
@@ -7,7 +7,6 @@ GetOptions(
'i|in=s' => \$in,
'infmt=s' => \$infmt,
'outfmt=s' => \$outfmt,
- 'parse_seqids' => \$parse_seqids,
'mask_data=s' => \$mask_data,
);
--
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